From b18868903a17152120a3c7fedea60559d7f83b8d Mon Sep 17 00:00:00 2001 From: Akash Date: Fri, 11 Oct 2024 16:39:39 -0400 Subject: [PATCH 1/2] This commit fixes the duplicate variant issue in the find_subject_dx_implication and find_subject_tx_implication functions. This method of creating a variant list and checcking variant IDs against is okay for now but might have scalability issues. Future implementations should try to limit the variant responses from MongoDB to unique responses. --- .vscode/launch.json | 29 + app/endpoints.py | 65 +- .../find_subject_dx_implications/3.json | 9324 +-- .../find_subject_dx_implications/4.json | 3906 +- .../find_subject_dx_implications/5.json | 49402 ++-------------- .../find_subject_tx_implications/1.json | 322 - .../find_subject_tx_implications/3.json | 6846 +-- .../find_subject_tx_implications/5.json | 322 - .../find_subject_tx_implications/6.json | 15481 +---- tests/utilities.py | 2 +- 10 files changed, 11912 insertions(+), 73787 deletions(-) create mode 100644 .vscode/launch.json diff --git a/.vscode/launch.json b/.vscode/launch.json new file mode 100644 index 000000000..40dcf3842 --- /dev/null +++ b/.vscode/launch.json @@ -0,0 +1,29 @@ +{ + // Use IntelliSense to learn about possible attributes. + // Hover to view descriptions of existing attributes. + // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387 + "version": "0.2.0", + "configurations": [ + { + "name": "Debug app", + "type": "debugpy", + "request": "launch", + "program": "${workspaceFolder}/run.py", + "console": "integratedTerminal", + "justMyCode": false + }, + { + "name": "Debug Unit Test", + "type": "debugpy", + "request": "launch", + "justMyCode": false, + }, + { + "name": "Debug File", + "type": "debugpy", + "request": "launch", + "program": "${file}", + "console": "integratedTerminal" + } + ] +} diff --git a/app/endpoints.py b/app/endpoints.py index 8386c70ab..a16767141 100644 --- a/app/endpoints.py +++ b/app/endpoints.py @@ -847,6 +847,7 @@ def find_subject_tx_implications( result = OrderedDict() result["resourceType"] = "Parameters" result["parameter"] = [] + list_variants = [] if normalized_variants: if not ranges: @@ -880,11 +881,13 @@ def find_subject_tx_implications( resource = common.create_fhir_variant_resource( res, ref_seq, subject) - variant_param = { - "name": "variant", - "resource": resource - } - result["parameter"].append(variant_param) + if resource['id'] not in list_variants: + list_variants.append(resource['id']) + variant_param = { + "name": "variant", + "resource": resource + } + result["parameter"].append(variant_param) if not result["parameter"]: result.pop("parameter") @@ -1000,11 +1003,13 @@ def find_subject_tx_implications( variant_fhir_profiles = sorted(variant_fhir_profiles, key=lambda d: d['id']) for resource in variant_fhir_profiles: - variant_param = { - "name": "variant", - "resource": resource - } - result["parameter"].append(variant_param) + if resource['id'] not in list_variants: + list_variants.append(resource['id']) + variant_param = { + "name": "variant", + "resource": resource + } + result["parameter"].append(variant_param) if not result["parameter"]: result.pop("parameter") @@ -1038,11 +1043,13 @@ def find_subject_tx_implications( variant_fhir_profiles = sorted(variant_fhir_profiles, key=lambda d: d['id']) for resource in variant_fhir_profiles: - variant_param = { - "name": "variant", - "resource": resource - } - result["parameter"].append(variant_param) + if resource['id'] not in list_variants: + list_variants.append(resource['id']) + variant_param = { + "name": "variant", + "resource": resource + } + result["parameter"].append(variant_param) if not result["parameter"]: result.pop("parameter") @@ -1113,7 +1120,7 @@ def find_subject_dx_implications( result = OrderedDict() result["resourceType"] = "Parameters" result["parameter"] = [] - + list_variants = [] if normalized_variants: if not ranges: genomics_build_presence = common.get_genomics_build_presence(query) @@ -1146,11 +1153,14 @@ def find_subject_dx_implications( resource = common.create_fhir_variant_resource( res, ref_seq, subject) - variant_param = { - "name": "variant", - "resource": resource - } - result["parameter"].append(variant_param) + + if resource['id'] not in list_variants: + list_variants.append(resource['id']) + variant_param = { + "name": "variant", + "resource": resource + } + result["parameter"].append(variant_param) if not result["parameter"]: result.pop("parameter") @@ -1180,11 +1190,14 @@ def find_subject_dx_implications( ref_seq = common.get_ref_seq_by_chrom_and_build(varItem['genomicBuild'], varItem['CHROM']) resource = common.create_fhir_variant_resource(varItem, ref_seq, subject) - variant_param = { - "name": "variant", - "resource": resource - } - result["parameter"].append(variant_param) + if resource['id'] not in list_variants: + list_variants.append(resource['id']) + + variant_param = { + "name": "variant", + "resource": resource + } + result["parameter"].append(variant_param) if not result["parameter"]: result.pop("parameter") diff --git a/tests/expected_outputs/find_subject_dx_implications/3.json b/tests/expected_outputs/find_subject_dx_implications/3.json index 5bdd97bb2..15ee12c4b 100644 --- a/tests/expected_outputs/find_subject_dx_implications/3.json +++ b/tests/expected_outputs/find_subject_dx_implications/3.json @@ -5,7 +5,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab66e5932091e78c17733", + "id": "dv-62fab6ab5932091e78c3cfb0", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -35,7 +35,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-b96b0bdcbc3a4a68913378136736b773" + "reference": "Observation/dv-dd6a5ae0dbc24360aea5a7c161101a68" } ], "component": [ @@ -53,8 +53,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA26333-7", + "display": "Uncertain significance" } ] } @@ -73,8 +73,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0020445", - "display": "Familial hypercholesterolemia" + "code": "C4552100", + "display": "Lynch syndrome" } ] } @@ -97,11 +97,11 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "128425" + "value": "336427" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000902523.1" + "value": "SCV000430916.2" } ] } @@ -110,7 +110,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-b96b0bdcbc3a4a68913378136736b773", + "id": "dv-dd6a5ae0dbc24360aea5a7c161101a68", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -222,8 +222,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:21009322:G:A", - "display": "NC_000002.12:21009322:G:A" + "code": "NC_000002.12:47414420:AAAAAAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAAAAAA", + "display": "NC_000002.12:47414420:AAAAAAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAAAAAA" } ] } @@ -239,7 +239,7 @@ ] }, "valueQuantity": { - "value": 0.5, + "value": 0, "unit": "relative frequency of a particular allele in the specimen", "system": "http://unitsofmeasure.org", "code": "1" @@ -255,7 +255,7 @@ } ] }, - "valueString": "G" + "valueString": "TAA" }, { "code": { @@ -267,7 +267,7 @@ } ] }, - "valueString": "A" + "valueString": "T" }, { "code": { @@ -301,25 +301,9 @@ }, "valueRange": { "low": { - "value": 21009322 + "value": 47414419 } } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.388555, - "system": "http://unitsofmeasure.org", - "code": "1" - } } ] } @@ -328,7 +312,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6a85932091e78c3bb46", + "id": "dv-62fab6665932091e78c11fa3", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -358,7 +342,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-6f1550b878b740c29dae310d745dbc76" + "reference": "Observation/dv-e1932783d03241559c7627fcde3fbec2" } ], "component": [ @@ -396,8 +380,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0020445", - "display": "Familial hypercholesterolemia" + "code": "C4552100", + "display": "Lynch syndrome" } ] } @@ -413,18 +397,18 @@ ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "reviewed by expert panel" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "328058" + "value": "90368" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001717063.2" + "value": "SCV000106876.2" } ] } @@ -433,7 +417,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-6f1550b878b740c29dae310d745dbc76", + "id": "dv-e1932783d03241559c7627fcde3fbec2", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -506,7 +490,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.10" + "code": "NC_000003.12" } ] } @@ -545,8 +529,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.10:11131630:G:C", - "display": "NC_000019.10:11131630:G:C" + "code": "NC_000003.12:37016099:C:T", + "display": "NC_000003.12:37016099:C:T" } ] } @@ -578,7 +562,7 @@ } ] }, - "valueString": "G" + "valueString": "C" }, { "code": { @@ -590,7 +574,7 @@ } ] }, - "valueString": "C" + "valueString": "T" }, { "code": { @@ -624,25 +608,9 @@ }, "valueRange": { "low": { - "value": 11131630 + "value": 37016099 } } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.818994, - "system": "http://unitsofmeasure.org", - "code": "1" - } } ] } @@ -651,7 +619,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab69e5932091e78c3549c", + "id": "dv-62fab6665932091e78c126e8", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -681,7 +649,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-37304b7e844c41258d4a25a6dffada5b" + "reference": "Observation/dv-4bde3f4b60a843a88d84e9974aa86fa7" } ], "component": [ @@ -719,8 +687,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0020445", - "display": "Familial hypercholesterolemia" + "code": "C4552100", + "display": "Lynch syndrome" } ] } @@ -736,18 +704,18 @@ ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "reviewed by expert panel" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "252262" + "value": "90924" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001461329.1" + "value": "SCV000107454.2" } ] } @@ -756,7 +724,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-37304b7e844c41258d4a25a6dffada5b", + "id": "dv-4bde3f4b60a843a88d84e9974aa86fa7", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -829,7 +797,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.10" + "code": "NC_000002.12" } ] } @@ -848,8 +816,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "LA6706-1", + "display": "heterozygous" } ] } @@ -868,8 +836,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.10:11123264:A:G", - "display": "NC_000019.10:11123264:A:G" + "code": "NC_000002.12:47476887:G:C", + "display": "NC_000002.12:47476887:G:C" } ] } @@ -885,7 +853,7 @@ ] }, "valueQuantity": { - "value": 1.0, + "value": 0.5, "unit": "relative frequency of a particular allele in the specimen", "system": "http://unitsofmeasure.org", "code": "1" @@ -901,7 +869,7 @@ } ] }, - "valueString": "A" + "valueString": "G" }, { "code": { @@ -913,7 +881,7 @@ } ] }, - "valueString": "G" + "valueString": "C" }, { "code": { @@ -947,8 +915,69 @@ }, "valueRange": { "low": { - "value": 11123264 + "value": 47476887 + } + } + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab6ab5932091e78c3cfb3", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/NB6TK329" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-dd6a5ae0dbc24360aea5a7c161101a68" + } + ], + "component": [ + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "53037-8", + "display": "Genetic variation clinical significance" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA26333-7", + "display": "Uncertain significance" + } + ] } }, { @@ -956,17 +985,45 @@ "coding": [ { "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueQuantity": { - "value": 0.781146, - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C4552100", + "display": "Lynch syndrome" + } + ] + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "93044-6", + "display": "Level of evidence" + } + ] + }, + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "336427" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000430917.2" + } ] } }, @@ -974,7 +1031,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6655932091e78c11c6a", + "id": "dv-62fab63a5932091e78bf71d5", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -1004,7 +1061,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-fcf9e127dc524dbab17c34123fd5aaf0" + "reference": "Observation/dv-38f8d84905ff4a5e9547b1e339f3ce02" } ], "component": [ @@ -1059,18 +1116,18 @@ ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "text": "no assertion criteria provided" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "90227" + "value": "36685" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000106721.2" + "value": "SCV000053031.2" } ] } @@ -1079,7 +1136,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-fcf9e127dc524dbab17c34123fd5aaf0", + "id": "dv-38f8d84905ff4a5e9547b1e339f3ce02", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -1152,7 +1209,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000003.12" + "code": "NC_000007.14" } ] } @@ -1191,8 +1248,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000003.12:37007141:A:G", - "display": "NC_000003.12:37007141:A:G" + "code": "NC_000007.14:5987356:G:A", + "display": "NC_000007.14:5987356:G:A" } ] } @@ -1224,7 +1281,7 @@ } ] }, - "valueString": "A" + "valueString": "G" }, { "code": { @@ -1236,7 +1293,7 @@ } ] }, - "valueString": "G" + "valueString": "A" }, { "code": { @@ -1270,18 +1327,34 @@ }, "valueRange": { "low": { - "value": 37007141 + "value": 5987356 } } - } - ] - } - }, - { - "name": "implication", - "resource": { + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "92821-8", + "display": "Population allele frequency" + } + ] + }, + "valueQuantity": { + "value": 0.387786, + "system": "http://unitsofmeasure.org", + "code": "1" + } + } + ] + } + }, + { + "name": "implication", + "resource": { "resourceType": "Observation", - "id": "dv-62fab6395932091e78bf6bfe", + "id": "dv-62fab63a5932091e78bf7251", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -1311,7 +1384,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-210349083123421e9899d9f21af3ef71" + "reference": "Observation/dv-4435221b91444669b3f6237f6b6fa954" } ], "component": [ @@ -1366,18 +1439,18 @@ ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "reviewed by expert panel" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "36564" + "value": "36692" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000052904.2" + "value": "SCV000108377.2" } ] } @@ -1386,7 +1459,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-210349083123421e9899d9f21af3ef71", + "id": "dv-4435221b91444669b3f6237f6b6fa954", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -1459,7 +1532,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "NC_000007.14" } ] } @@ -1478,8 +1551,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "code": "LA6705-3", + "display": "homozygous" } ] } @@ -1498,8 +1571,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47429661:G:A", - "display": "NC_000002.12:47429661:G:A" + "code": "NC_000007.14:5999090:T:C", + "display": "NC_000007.14:5999090:T:C" } ] } @@ -1515,7 +1588,7 @@ ] }, "valueQuantity": { - "value": 0.5, + "value": 1.0, "unit": "relative frequency of a particular allele in the specimen", "system": "http://unitsofmeasure.org", "code": "1" @@ -1531,7 +1604,7 @@ } ] }, - "valueString": "G" + "valueString": "T" }, { "code": { @@ -1543,7 +1616,7 @@ } ] }, - "valueString": "A" + "valueString": "C" }, { "code": { @@ -1577,9 +1650,25 @@ }, "valueRange": { "low": { - "value": 47429661 + "value": 5999090 } } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "92821-8", + "display": "Population allele frequency" + } + ] + }, + "valueQuantity": { + "value": 0.368213, + "system": "http://unitsofmeasure.org", + "code": "1" + } } ] } @@ -1588,7 +1677,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab63a5932091e78bf71dc", + "id": "dv-62fab63a5932091e78bf6fcc", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -1618,7 +1707,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-38f8d84905ff4a5e9547b1e339f3ce02" + "reference": "Observation/dv-b8cc4e2fbe604134979c80e1aa8c4cee" } ], "component": [ @@ -1680,11 +1769,11 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "36685" + "value": "36594" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000108294.2" + "value": "SCV000108147.2" } ] } @@ -1693,7 +1782,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-38f8d84905ff4a5e9547b1e339f3ce02", + "id": "dv-b8cc4e2fbe604134979c80e1aa8c4cee", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -1766,7 +1855,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "code": "NC_000002.12" } ] } @@ -1805,8 +1894,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:5987356:G:A", - "display": "NC_000007.14:5987356:G:A" + "code": "NC_000002.12:47806411:C:G", + "display": "NC_000002.12:47806411:C:G" } ] } @@ -1838,7 +1927,7 @@ } ] }, - "valueString": "G" + "valueString": "C" }, { "code": { @@ -1850,7 +1939,7 @@ } ] }, - "valueString": "A" + "valueString": "G" }, { "code": { @@ -1884,7 +1973,7 @@ }, "valueRange": { "low": { - "value": 5987356 + "value": 47806411 } } }, @@ -1899,7 +1988,7 @@ ] }, "valueQuantity": { - "value": 0.387786, + "value": 0.733985, "system": "http://unitsofmeasure.org", "code": "1" } @@ -1911,7 +2000,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab68a5932091e78c28ebb", + "id": "dv-62fab66e5932091e78c17715", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -1941,7 +2030,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-f2d0de4c461c487fa0d7b2b0a9034361" + "reference": "Observation/dv-1692d4f52d4944a391a1e1e57347d8eb" } ], "component": [ @@ -1996,18 +2085,18 @@ ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "200916" + "value": "128422" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001460277.1" + "value": "SCV002524050.1" } ] } @@ -2016,7 +2105,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-f2d0de4c461c487fa0d7b2b0a9034361", + "id": "dv-1692d4f52d4944a391a1e1e57347d8eb", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -2089,7 +2178,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.10" + "code": "NC_000002.12" } ] } @@ -2128,8 +2217,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.10:11113588:A:G", - "display": "NC_000019.10:11113588:A:G" + "code": "NC_000002.12:21041027:G:A", + "display": "NC_000002.12:21041027:G:A" } ] } @@ -2161,7 +2250,7 @@ } ] }, - "valueString": "A" + "valueString": "G" }, { "code": { @@ -2173,7 +2262,7 @@ } ] }, - "valueString": "G" + "valueString": "A" }, { "code": { @@ -2207,7 +2296,7 @@ }, "valueRange": { "low": { - "value": 11113588 + "value": 21041027 } } }, @@ -2222,7 +2311,7 @@ ] }, "valueQuantity": { - "value": 0.632026, + "value": 0.25802, "system": "http://unitsofmeasure.org", "code": "1" } @@ -2234,7 +2323,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6395932091e78bf6afa", + "id": "dv-62fab6645932091e78c11178", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -2264,7 +2353,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-437c728d910a46189036896c9a3fe97f" + "reference": "Observation/dv-234ee4ca3da04ab39f5ebfed027792dd" } ], "component": [ @@ -2326,11 +2415,11 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "36542" + "value": "89525" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000106295.2" + "value": "SCV000108211.2" } ] } @@ -2339,7 +2428,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-437c728d910a46189036896c9a3fe97f", + "id": "dv-234ee4ca3da04ab39f5ebfed027792dd", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -2412,7 +2501,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000003.12" + "code": "NC_000002.12" } ] } @@ -2431,8 +2520,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "LA6706-1", + "display": "heterozygous" } ] } @@ -2451,8 +2540,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000003.12:37042248:A:G", - "display": "NC_000003.12:37042248:A:G" + "code": "NC_000002.12:47791516:T:C", + "display": "NC_000002.12:47791516:T:C" } ] } @@ -2468,7 +2557,7 @@ ] }, "valueQuantity": { - "value": 1.0, + "value": 0.5, "unit": "relative frequency of a particular allele in the specimen", "system": "http://unitsofmeasure.org", "code": "1" @@ -2484,7 +2573,7 @@ } ] }, - "valueString": "A" + "valueString": "T" }, { "code": { @@ -2496,7 +2585,7 @@ } ] }, - "valueString": "G" + "valueString": "C" }, { "code": { @@ -2530,25 +2619,9 @@ }, "valueRange": { "low": { - "value": 37042248 + "value": 47791516 } } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.370828, - "system": "http://unitsofmeasure.org", - "code": "1" - } } ] } @@ -2557,7 +2630,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab66e5932091e78c176c8", + "id": "dv-62fab6645932091e78c11177", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -2587,7 +2660,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-d675ed9e0e514a478542b503a5250ab3" + "reference": "Observation/dv-1aa0fdfa74344f23b55e811414e4dcdf" } ], "component": [ @@ -2625,8 +2698,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0020445", - "display": "Familial hypercholesterolemia" + "code": "C4552100", + "display": "Lynch syndrome" } ] } @@ -2642,18 +2715,18 @@ ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "reviewed by expert panel" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "128418" + "value": "89521" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000902521.1" + "value": "SCV000108207.2" } ] } @@ -2662,7 +2735,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-d675ed9e0e514a478542b503a5250ab3", + "id": "dv-1aa0fdfa74344f23b55e811414e4dcdf", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -2754,8 +2827,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "LA6706-1", + "display": "heterozygous" } ] } @@ -2774,8 +2847,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:21002408:C:T", - "display": "NC_000002.12:21002408:C:T" + "code": "NC_000002.12:47792345:T:C", + "display": "NC_000002.12:47792345:T:C" } ] } @@ -2791,7 +2864,7 @@ ] }, "valueQuantity": { - "value": 1.0, + "value": 0.5, "unit": "relative frequency of a particular allele in the specimen", "system": "http://unitsofmeasure.org", "code": "1" @@ -2807,7 +2880,7 @@ } ] }, - "valueString": "C" + "valueString": "T" }, { "code": { @@ -2819,7 +2892,7 @@ } ] }, - "valueString": "T" + "valueString": "C" }, { "code": { @@ -2853,25 +2926,9 @@ }, "valueRange": { "low": { - "value": 21002408 + "value": 47792345 } } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.704884, - "system": "http://unitsofmeasure.org", - "code": "1" - } } ] } @@ -2880,7 +2937,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6655932091e78c1146d", + "id": "dv-62fab66c5932091e78c15c00", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -2910,7 +2967,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-89eb7b13687a4828baa470fb82be0c0d" + "reference": "Observation/dv-edfe8714ceaf4687910f600e46f6806e" } ], "component": [ @@ -2948,8 +3005,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome" } ] } @@ -2965,18 +3022,18 @@ ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "text": "criteria provided, single submitter" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "89615" + "value": "126022" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000106073.2" + "value": "SCV000494320.1" } ] } @@ -2985,7 +3042,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-89eb7b13687a4828baa470fb82be0c0d", + "id": "dv-edfe8714ceaf4687910f600e46f6806e", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -3058,7 +3115,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000003.12" + "code": "NC_000013.11" } ] } @@ -3097,8 +3154,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000003.12:37020548:T:C", - "display": "NC_000003.12:37020548:T:C" + "code": "NC_000013.11:32338161:T:C", + "display": "NC_000013.11:32338161:T:C" } ] } @@ -3176,9 +3233,25 @@ }, "valueRange": { "low": { - "value": 37020548 + "value": 32338161 } } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "92821-8", + "display": "Population allele frequency" + } + ] + }, + "valueQuantity": { + "value": 0.174603, + "system": "http://unitsofmeasure.org", + "code": "1" + } } ] } @@ -3187,7 +3260,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6655932091e78c11615", + "id": "dv-62fab6395932091e78bf6bfd", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -3217,7 +3290,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-e8e157f976b34a78ab1210328a2acd53" + "reference": "Observation/dv-210349083123421e9899d9f21af3ef71" } ], "component": [ @@ -3279,11 +3352,11 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "89773" + "value": "36564" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000106243.2" + "value": "SCV000107047.2" } ] } @@ -3292,7 +3365,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-e8e157f976b34a78ab1210328a2acd53", + "id": "dv-210349083123421e9899d9f21af3ef71", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -3365,7 +3438,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000003.12" + "code": "NC_000002.12" } ] } @@ -3384,8 +3457,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "LA6706-1", + "display": "heterozygous" } ] } @@ -3404,8 +3477,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000003.12:37031135:A:C", - "display": "NC_000003.12:37031135:A:C" + "code": "NC_000002.12:47429661:G:A", + "display": "NC_000002.12:47429661:G:A" } ] } @@ -3421,7 +3494,7 @@ ] }, "valueQuantity": { - "value": 1.0, + "value": 0.5, "unit": "relative frequency of a particular allele in the specimen", "system": "http://unitsofmeasure.org", "code": "1" @@ -3437,7 +3510,7 @@ } ] }, - "valueString": "A" + "valueString": "G" }, { "code": { @@ -3449,7 +3522,7 @@ } ] }, - "valueString": "C" + "valueString": "A" }, { "code": { @@ -3483,7 +3556,7 @@ }, "valueRange": { "low": { - "value": 37031135 + "value": 47429661 } } } @@ -3494,7 +3567,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cbd", + "id": "dv-62fab68e5932091e78c2b13d", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -3524,7 +3597,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-c7c0803976fd4ab881f1588c713419ff" + "reference": "Observation/dv-87f77277c4c84151bb54754435b23d8c" } ], "component": [ @@ -3586,11 +3659,11 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" + "value": "209600" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000635377.5" + "value": "SCV001000937.4" } ] } @@ -3599,7 +3672,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-c7c0803976fd4ab881f1588c713419ff", + "id": "dv-87f77277c4c84151bb54754435b23d8c", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -3711,8 +3784,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.11:32338917:A:G", - "display": "NC_000013.11:32338917:A:G" + "code": "NC_000013.11:32315654:A:G", + "display": "NC_000013.11:32315654:A:G" } ] } @@ -3790,25 +3863,9 @@ }, "valueRange": { "low": { - "value": 32338917 + "value": 32315654 } } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994359, - "system": "http://unitsofmeasure.org", - "code": "1" - } } ] } @@ -3817,7 +3874,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6435932091e78bfc9ac", + "id": "dv-62fab6905932091e78c2c798", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -3847,7 +3904,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-5071403516aa4a17871949bf246b8b5d" + "reference": "Observation/dv-e28737e34fd843fbbe1717b56b96d1f8" } ], "component": [ @@ -3902,18 +3959,18 @@ ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "text": "criteria provided, single submitter" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "42471" + "value": "218461" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000108065.2" + "value": "SCV000257705.2" } ] } @@ -3922,7 +3979,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-5071403516aa4a17871949bf246b8b5d", + "id": "dv-e28737e34fd843fbbe1717b56b96d1f8", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -3995,7 +4052,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "NC_000007.14" } ] } @@ -4034,8 +4091,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47803698:A:T", - "display": "NC_000002.12:47803698:A:T" + "code": "NC_000007.14:5997426:AAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAA", + "display": "NC_000007.14:5997426:AAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAA" } ] } @@ -4067,7 +4124,7 @@ } ] }, - "valueString": "A" + "valueString": "GA" }, { "code": { @@ -4079,7 +4136,7 @@ } ] }, - "valueString": "T" + "valueString": "G" }, { "code": { @@ -4113,7 +4170,7 @@ }, "valueRange": { "low": { - "value": 47803698 + "value": 5997425 } } }, @@ -4128,7 +4185,7 @@ ] }, "valueQuantity": { - "value": 0.411752, + "value": 0.430816, "system": "http://unitsofmeasure.org", "code": "1" } @@ -4140,7 +4197,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab63a5932091e78bf6f9a", + "id": "dv-62fab63a5932091e78bf6f98", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -4225,7 +4282,7 @@ ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "text": "criteria provided, single submitter" } } ], @@ -4236,7 +4293,7 @@ }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000107992.2" + "value": "SCV000052932.2" } ] } @@ -4463,7 +4520,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6655932091e78c11a58", + "id": "dv-62fab63a5932091e78bf7252", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -4493,7 +4550,112 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-396515d9058748f2a3ce8d4e5149620b" + "reference": "Observation/dv-4435221b91444669b3f6237f6b6fa954" + } + ], + "component": [ + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "53037-8", + "display": "Genetic variation clinical significance" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA6675-8", + "display": "Benign" + } + ] + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "81259-4", + "display": "predicted phenotype" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C4552100", + "display": "Lynch syndrome" + } + ] + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "93044-6", + "display": "Level of evidence" + } + ] + }, + "valueCodeableConcept": { + "text": "criteria provided, single submitter" + } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "36692" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000053038.2" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab6645932091e78c11181", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/NB6TK329" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-49c6c5a200fb42fba2c02268d74d00a3" } ], "component": [ @@ -4555,11 +4717,11 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "90024" + "value": "89526" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000106504.2" + "value": "SCV000108213.2" } ] } @@ -4568,7 +4730,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-396515d9058748f2a3ce8d4e5149620b", + "id": "dv-49c6c5a200fb42fba2c02268d74d00a3", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -4641,7 +4803,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000003.12" + "code": "NC_000002.12" } ] } @@ -4660,8 +4822,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "LA6706-1", + "display": "heterozygous" } ] } @@ -4680,8 +4842,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000003.12:36997279:C:T", - "display": "NC_000003.12:36997279:C:T" + "code": "NC_000002.12:47791174:T:A", + "display": "NC_000002.12:47791174:T:A" } ] } @@ -4697,7 +4859,7 @@ ] }, "valueQuantity": { - "value": 1.0, + "value": 0.5, "unit": "relative frequency of a particular allele in the specimen", "system": "http://unitsofmeasure.org", "code": "1" @@ -4713,7 +4875,7 @@ } ] }, - "valueString": "C" + "valueString": "T" }, { "code": { @@ -4725,7 +4887,7 @@ } ] }, - "valueString": "T" + "valueString": "A" }, { "code": { @@ -4759,7 +4921,7 @@ }, "valueRange": { "low": { - "value": 36997279 + "value": 47791174 } } } @@ -4770,7 +4932,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6655932091e78c11355", + "id": "dv-62fab6655932091e78c1145b", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -4800,7 +4962,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-8154922662b44a9aa5260207fea8d5b6" + "reference": "Observation/dv-0c3e9547181e4b789c13b04121a9ced8" } ], "component": [ @@ -4862,11 +5024,11 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "89544" + "value": "89611" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000108233.2" + "value": "SCV000106069.2" } ] } @@ -4875,7 +5037,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-8154922662b44a9aa5260207fea8d5b6", + "id": "dv-0c3e9547181e4b789c13b04121a9ced8", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -4948,7 +5110,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "NC_000003.12" } ] } @@ -4987,8 +5149,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47797736:C:T", - "display": "NC_000002.12:47797736:C:T" + "code": "NC_000003.12:37021467:G:T", + "display": "NC_000003.12:37021467:G:T" } ] } @@ -5020,7 +5182,7 @@ } ] }, - "valueString": "C" + "valueString": "G" }, { "code": { @@ -5066,7 +5228,7 @@ }, "valueRange": { "low": { - "value": 47797736 + "value": 37021467 } } } @@ -5077,7 +5239,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17ce1", + "id": "dv-62fab6645932091e78c10b9e", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -5107,7 +5269,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-d47c74da1d8340e3976b600eedc794ac" + "reference": "Observation/dv-525568db5bbb42e79c7b9c4b5d27fd28" } ], "component": [ @@ -5145,8 +5307,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" + "code": "C4552100", + "display": "Lynch syndrome" } ] } @@ -5162,18 +5324,18 @@ ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "reviewed by expert panel" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" + "value": "89301" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000494339.1" + "value": "SCV000107977.2" } ] } @@ -5182,7 +5344,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-d47c74da1d8340e3976b600eedc794ac", + "id": "dv-525568db5bbb42e79c7b9c4b5d27fd28", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -5255,7 +5417,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.11" + "code": "NC_000002.12" } ] } @@ -5274,8 +5436,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "LA6706-1", + "display": "heterozygous" } ] } @@ -5294,8 +5456,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.11:32340867:G:C", - "display": "NC_000013.11:32340867:G:C" + "code": "NC_000002.12:47790890:A:G", + "display": "NC_000002.12:47790890:A:G" } ] } @@ -5311,7 +5473,7 @@ ] }, "valueQuantity": { - "value": 1.0, + "value": 0.5, "unit": "relative frequency of a particular allele in the specimen", "system": "http://unitsofmeasure.org", "code": "1" @@ -5327,7 +5489,7 @@ } ] }, - "valueString": "G" + "valueString": "A" }, { "code": { @@ -5339,7 +5501,7 @@ } ] }, - "valueString": "C" + "valueString": "G" }, { "code": { @@ -5373,7 +5535,7 @@ }, "valueRange": { "low": { - "value": 32340867 + "value": 47790890 } } }, @@ -5388,7 +5550,7 @@ ] }, "valueQuantity": { - "value": 0.994199, + "value": 0.0372618, "system": "http://unitsofmeasure.org", "code": "1" } @@ -5400,7 +5562,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cd7", + "id": "dv-62fab6665932091e78c1245b", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -5430,7 +5592,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-d47c74da1d8340e3976b600eedc794ac" + "reference": "Observation/dv-ddbfcfdb118b4385a9dad7e38d9b6da5" } ], "component": [ @@ -5468,8 +5630,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" + "code": "C4552100", + "display": "Lynch syndrome" } ] } @@ -5485,18 +5647,18 @@ ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "reviewed by expert panel" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" + "value": "90687" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000635514.5" + "value": "SCV000107200.2" } ] } @@ -5505,7 +5667,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-d47c74da1d8340e3976b600eedc794ac", + "id": "dv-ddbfcfdb118b4385a9dad7e38d9b6da5", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -5578,7 +5740,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.11" + "code": "NC_000002.12" } ] } @@ -5597,8 +5759,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "LA6706-1", + "display": "heterozygous" } ] } @@ -5617,8 +5779,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.11:32340867:G:C", - "display": "NC_000013.11:32340867:G:C" + "code": "NC_000002.12:47465141:C:T", + "display": "NC_000002.12:47465141:C:T" } ] } @@ -5634,7 +5796,7 @@ ] }, "valueQuantity": { - "value": 1.0, + "value": 0.5, "unit": "relative frequency of a particular allele in the specimen", "system": "http://unitsofmeasure.org", "code": "1" @@ -5650,7 +5812,7 @@ } ] }, - "valueString": "G" + "valueString": "C" }, { "code": { @@ -5662,7 +5824,7 @@ } ] }, - "valueString": "C" + "valueString": "T" }, { "code": { @@ -5696,25 +5858,9 @@ }, "valueRange": { "low": { - "value": 32340867 + "value": 47465141 } } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994199, - "system": "http://unitsofmeasure.org", - "code": "1" - } } ] } @@ -5723,7 +5869,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab63a5932091e78bf7251", + "id": "dv-62fab68a5932091e78c28ebb", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -5753,7 +5899,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-4435221b91444669b3f6237f6b6fa954" + "reference": "Observation/dv-f2d0de4c461c487fa0d7b2b0a9034361" } ], "component": [ @@ -5791,8 +5937,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" + "code": "C0020445", + "display": "Familial hypercholesterolemia" } ] } @@ -5808,18 +5954,18 @@ ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "text": "no assertion criteria provided" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "36692" + "value": "200916" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000108377.2" + "value": "SCV001460277.1" } ] } @@ -5828,7 +5974,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-4435221b91444669b3f6237f6b6fa954", + "id": "dv-f2d0de4c461c487fa0d7b2b0a9034361", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -5901,7 +6047,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "code": "NC_000019.10" } ] } @@ -5920,8 +6066,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "LA6706-1", + "display": "heterozygous" } ] } @@ -5940,8 +6086,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:5999090:T:C", - "display": "NC_000007.14:5999090:T:C" + "code": "NC_000019.10:11113588:A:G", + "display": "NC_000019.10:11113588:A:G" } ] } @@ -5957,7 +6103,7 @@ ] }, "valueQuantity": { - "value": 1.0, + "value": 0.5, "unit": "relative frequency of a particular allele in the specimen", "system": "http://unitsofmeasure.org", "code": "1" @@ -5973,7 +6119,7 @@ } ] }, - "valueString": "T" + "valueString": "A" }, { "code": { @@ -5985,7 +6131,7 @@ } ] }, - "valueString": "C" + "valueString": "G" }, { "code": { @@ -6019,7 +6165,7 @@ }, "valueRange": { "low": { - "value": 5999090 + "value": 11113588 } } }, @@ -6034,7 +6180,7 @@ ] }, "valueQuantity": { - "value": 0.368213, + "value": 0.632026, "system": "http://unitsofmeasure.org", "code": "1" } @@ -6046,7 +6192,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6395932091e78bf6b0a", + "id": "dv-62fab6645932091e78c10b9a", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -6076,7 +6222,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-437c728d910a46189036896c9a3fe97f" + "reference": "Observation/dv-d83d284e564e4106a409fcd7bb222eb9" } ], "component": [ @@ -6131,18 +6277,18 @@ ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "reviewed by expert panel" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "36542" + "value": "89296" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000052882.2" + "value": "SCV000107958.2" } ] } @@ -6151,7 +6297,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-437c728d910a46189036896c9a3fe97f", + "id": "dv-d83d284e564e4106a409fcd7bb222eb9", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -6224,7 +6370,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000003.12" + "code": "NC_000002.12" } ] } @@ -6243,8 +6389,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "LA6706-1", + "display": "heterozygous" } ] } @@ -6263,8 +6409,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000003.12:37042248:A:G", - "display": "NC_000003.12:37042248:A:G" + "code": "NC_000002.12:47785959:A:G", + "display": "NC_000002.12:47785959:A:G" } ] } @@ -6280,7 +6426,7 @@ ] }, "valueQuantity": { - "value": 1.0, + "value": 0.5, "unit": "relative frequency of a particular allele in the specimen", "system": "http://unitsofmeasure.org", "code": "1" @@ -6342,25 +6488,9 @@ }, "valueRange": { "low": { - "value": 37042248 + "value": 47785959 } } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.370828, - "system": "http://unitsofmeasure.org", - "code": "1" - } } ] } @@ -6369,7 +6499,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6665932091e78c126e8", + "id": "dv-62fab6645932091e78c111bb", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -6399,7 +6529,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-4bde3f4b60a843a88d84e9974aa86fa7" + "reference": "Observation/dv-37cd8d0c069d43cca4761374a718b6e8" } ], "component": [ @@ -6461,11 +6591,11 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "90924" + "value": "89543" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000107454.2" + "value": "SCV000108232.2" } ] } @@ -6474,7 +6604,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-4bde3f4b60a843a88d84e9974aa86fa7", + "id": "dv-37cd8d0c069d43cca4761374a718b6e8", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -6586,8 +6716,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47476887:G:C", - "display": "NC_000002.12:47476887:G:C" + "code": "NC_000002.12:47798554:C:T", + "display": "NC_000002.12:47798554:C:T" } ] } @@ -6619,7 +6749,7 @@ } ] }, - "valueString": "G" + "valueString": "C" }, { "code": { @@ -6631,7 +6761,7 @@ } ] }, - "valueString": "C" + "valueString": "T" }, { "code": { @@ -6665,7 +6795,7 @@ }, "valueRange": { "low": { - "value": 47476887 + "value": 47798554 } } } @@ -6676,7 +6806,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab63a5932091e78bf6fcc", + "id": "dv-62fab66e5932091e78c176c8", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -6706,7 +6836,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-b8cc4e2fbe604134979c80e1aa8c4cee" + "reference": "Observation/dv-d675ed9e0e514a478542b503a5250ab3" } ], "component": [ @@ -6744,8 +6874,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" + "code": "C0020445", + "display": "Familial hypercholesterolemia" } ] } @@ -6761,18 +6891,18 @@ ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "text": "criteria provided, single submitter" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "36594" + "value": "128418" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000108147.2" + "value": "SCV000902521.1" } ] } @@ -6781,7 +6911,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-b8cc4e2fbe604134979c80e1aa8c4cee", + "id": "dv-d675ed9e0e514a478542b503a5250ab3", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -6893,8 +7023,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47806411:C:G", - "display": "NC_000002.12:47806411:C:G" + "code": "NC_000002.12:21002408:C:T", + "display": "NC_000002.12:21002408:C:T" } ] } @@ -6938,7 +7068,7 @@ } ] }, - "valueString": "G" + "valueString": "T" }, { "code": { @@ -6972,7 +7102,7 @@ }, "valueRange": { "low": { - "value": 47806411 + "value": 21002408 } } }, @@ -6987,7 +7117,7 @@ ] }, "valueQuantity": { - "value": 0.733985, + "value": 0.704884, "system": "http://unitsofmeasure.org", "code": "1" } @@ -6999,7 +7129,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6665932091e78c11fa3", + "id": "dv-62fab69e5932091e78c3549d", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -7029,7 +7159,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-e1932783d03241559c7627fcde3fbec2" + "reference": "Observation/dv-37304b7e844c41258d4a25a6dffada5b" } ], "component": [ @@ -7067,8 +7197,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" + "code": "C0020445", + "display": "Familial hypercholesterolemia" } ] } @@ -7084,18 +7214,18 @@ ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "text": "criteria provided, single submitter" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "90368" + "value": "252262" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000106876.2" + "value": "SCV001717062.2" } ] } @@ -7104,7 +7234,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-e1932783d03241559c7627fcde3fbec2", + "id": "dv-37304b7e844c41258d4a25a6dffada5b", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -7177,7 +7307,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000003.12" + "code": "NC_000019.10" } ] } @@ -7216,8 +7346,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000003.12:37016099:C:T", - "display": "NC_000003.12:37016099:C:T" + "code": "NC_000019.10:11123264:A:G", + "display": "NC_000019.10:11123264:A:G" } ] } @@ -7249,7 +7379,7 @@ } ] }, - "valueString": "C" + "valueString": "A" }, { "code": { @@ -7261,7 +7391,7 @@ } ] }, - "valueString": "T" + "valueString": "G" }, { "code": { @@ -7295,9 +7425,25 @@ }, "valueRange": { "low": { - "value": 37016099 + "value": 11123264 } } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "92821-8", + "display": "Population allele frequency" + } + ] + }, + "valueQuantity": { + "value": 0.781146, + "system": "http://unitsofmeasure.org", + "code": "1" + } } ] } @@ -7306,7 +7452,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab66e5932091e78c176b0", + "id": "dv-62fab63a5932091e78bf71dc", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -7336,7 +7482,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-719286980a454cc792902098a0122614" + "reference": "Observation/dv-38f8d84905ff4a5e9547b1e339f3ce02" } ], "component": [ @@ -7374,8 +7520,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0020445", - "display": "Familial hypercholesterolemia" + "code": "C4552100", + "display": "Lynch syndrome" } ] } @@ -7391,27 +7537,132 @@ ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "reviewed by expert panel" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "128416" + "value": "36685" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000902556.1" + "value": "SCV000108294.2" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-719286980a454cc792902098a0122614", + "id": "dv-62fab6645932091e78c10b9c", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/NB6TK329" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-6b10bc016d794b2d891a2da2b7b49512" + } + ], + "component": [ + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "53037-8", + "display": "Genetic variation clinical significance" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA6675-8", + "display": "Benign" + } + ] + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "81259-4", + "display": "predicted phenotype" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C4552100", + "display": "Lynch syndrome" + } + ] + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "93044-6", + "display": "Level of evidence" + } + ] + }, + "valueCodeableConcept": { + "text": "reviewed by expert panel" + } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "89300" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000107976.2" + } + ] + } + }, + { + "name": "variant", + "resource": { + "resourceType": "Observation", + "id": "dv-6b10bc016d794b2d891a2da2b7b49512", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -7523,8 +7774,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:21005954:C:T", - "display": "NC_000002.12:21005954:C:T" + "code": "NC_000002.12:47789756:G:T", + "display": "NC_000002.12:47789756:G:T" } ] } @@ -7556,7 +7807,7 @@ } ] }, - "valueString": "C" + "valueString": "G" }, { "code": { @@ -7602,25 +7853,9 @@ }, "valueRange": { "low": { - "value": 21005954 + "value": 47789756 } } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.0700284, - "system": "http://unitsofmeasure.org", - "code": "1" - } } ] } @@ -7629,7 +7864,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6ab5932091e78c3cfb0", + "id": "dv-62fab6a85932091e78c3bb46", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -7659,7 +7894,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-dd6a5ae0dbc24360aea5a7c161101a68" + "reference": "Observation/dv-6f1550b878b740c29dae310d745dbc76" } ], "component": [ @@ -7677,8 +7912,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA26333-7", - "display": "Uncertain significance" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -7697,8 +7932,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" + "code": "C0020445", + "display": "Familial hypercholesterolemia" } ] } @@ -7721,11 +7956,11 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "336427" + "value": "328058" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000430916.2" + "value": "SCV001717063.2" } ] } @@ -7734,7 +7969,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-dd6a5ae0dbc24360aea5a7c161101a68", + "id": "dv-6f1550b878b740c29dae310d745dbc76", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -7807,7 +8042,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "NC_000019.10" } ] } @@ -7826,8 +8061,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "code": "LA6705-3", + "display": "homozygous" } ] } @@ -7846,8 +8081,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47414420:AAAAAAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAAAAAA", - "display": "NC_000002.12:47414420:AAAAAAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAAAAAA" + "code": "NC_000019.10:11131630:G:C", + "display": "NC_000019.10:11131630:G:C" } ] } @@ -7863,7 +8098,7 @@ ] }, "valueQuantity": { - "value": 0, + "value": 1.0, "unit": "relative frequency of a particular allele in the specimen", "system": "http://unitsofmeasure.org", "code": "1" @@ -7879,7 +8114,7 @@ } ] }, - "valueString": "TAA" + "valueString": "G" }, { "code": { @@ -7891,7 +8126,7 @@ } ] }, - "valueString": "T" + "valueString": "C" }, { "code": { @@ -7925,9 +8160,25 @@ }, "valueRange": { "low": { - "value": 47414419 + "value": 11131630 } } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "92821-8", + "display": "Population allele frequency" + } + ] + }, + "valueQuantity": { + "value": 0.818994, + "system": "http://unitsofmeasure.org", + "code": "1" + } } ] } @@ -7936,7 +8187,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab63a5932091e78bf71d5", + "id": "dv-62fab66c5932091e78c15b7b", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -7966,7 +8217,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-38f8d84905ff4a5e9547b1e339f3ce02" + "reference": "Observation/dv-99d2b1819c554636b70c366c3f79f914" } ], "component": [ @@ -8004,8 +8255,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome" } ] } @@ -8021,18 +8272,18 @@ ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "36685" + "value": "125991" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000053031.2" + "value": "SCV001719551.2" } ] } @@ -8041,7 +8292,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-38f8d84905ff4a5e9547b1e339f3ce02", + "id": "dv-99d2b1819c554636b70c366c3f79f914", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -8114,7 +8365,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "code": "NC_000013.11" } ] } @@ -8133,8 +8384,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "LA6706-1", + "display": "heterozygous" } ] } @@ -8153,8 +8404,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:5987356:G:A", - "display": "NC_000007.14:5987356:G:A" + "code": "NC_000013.11:32316588:T:G", + "display": "NC_000013.11:32316588:T:G" } ] } @@ -8170,7 +8421,7 @@ ] }, "valueQuantity": { - "value": 1.0, + "value": 0.5, "unit": "relative frequency of a particular allele in the specimen", "system": "http://unitsofmeasure.org", "code": "1" @@ -8186,7 +8437,7 @@ } ] }, - "valueString": "G" + "valueString": "T" }, { "code": { @@ -8198,7 +8449,7 @@ } ] }, - "valueString": "A" + "valueString": "G" }, { "code": { @@ -8232,25 +8483,9 @@ }, "valueRange": { "low": { - "value": 5987356 + "value": 32316588 } } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.387786, - "system": "http://unitsofmeasure.org", - "code": "1" - } } ] } @@ -8259,7 +8494,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15c00", + "id": "dv-62fab66f5932091e78c17cb2", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -8289,7 +8524,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-edfe8714ceaf4687910f600e46f6806e" + "reference": "Observation/dv-c7c0803976fd4ab881f1588c713419ff" } ], "component": [ @@ -8351,11 +8586,11 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "132779" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000494320.1" + "value": "SCV002026104.2" } ] } @@ -8364,7 +8599,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-edfe8714ceaf4687910f600e46f6806e", + "id": "dv-c7c0803976fd4ab881f1588c713419ff", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -8476,8 +8711,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.11:32338161:T:C", - "display": "NC_000013.11:32338161:T:C" + "code": "NC_000013.11:32338917:A:G", + "display": "NC_000013.11:32338917:A:G" } ] } @@ -8509,7 +8744,7 @@ } ] }, - "valueString": "T" + "valueString": "A" }, { "code": { @@ -8521,7 +8756,7 @@ } ] }, - "valueString": "C" + "valueString": "G" }, { "code": { @@ -8555,7 +8790,7 @@ }, "valueRange": { "low": { - "value": 32338161 + "value": 32338917 } } }, @@ -8570,7 +8805,7 @@ ] }, "valueQuantity": { - "value": 0.174603, + "value": 0.994359, "system": "http://unitsofmeasure.org", "code": "1" } @@ -8582,7 +8817,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6ab5932091e78c3cfb3", + "id": "dv-62fab6655932091e78c11631", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -8612,7 +8847,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-dd6a5ae0dbc24360aea5a7c161101a68" + "reference": "Observation/dv-e7a8dac6a6aa45c5b219fea9973e34ab" } ], "component": [ @@ -8630,8 +8865,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA26333-7", - "display": "Uncertain significance" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -8667,18 +8902,18 @@ ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "reviewed by expert panel" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "336427" + "value": "89785" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000430917.2" + "value": "SCV000106257.2" } ] } @@ -8687,7 +8922,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-dd6a5ae0dbc24360aea5a7c161101a68", + "id": "dv-e7a8dac6a6aa45c5b219fea9973e34ab", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -8760,7 +8995,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "NC_000003.12" } ] } @@ -8779,8 +9014,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "code": "LA6705-3", + "display": "homozygous" } ] } @@ -8799,8 +9034,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47414420:AAAAAAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAAAAAA", - "display": "NC_000002.12:47414420:AAAAAAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAAAAAA" + "code": "NC_000003.12:37037014:A:G", + "display": "NC_000003.12:37037014:A:G" } ] } @@ -8816,7 +9051,7 @@ ] }, "valueQuantity": { - "value": 0, + "value": 1.0, "unit": "relative frequency of a particular allele in the specimen", "system": "http://unitsofmeasure.org", "code": "1" @@ -8832,7 +9067,7 @@ } ] }, - "valueString": "TAA" + "valueString": "A" }, { "code": { @@ -8844,7 +9079,7 @@ } ] }, - "valueString": "T" + "valueString": "G" }, { "code": { @@ -8878,7 +9113,7 @@ }, "valueRange": { "low": { - "value": 47414419 + "value": 37037014 } } } @@ -8889,7 +9124,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab68e5932091e78c2b13d", + "id": "dv-62fab63a5932091e78bf6f9a", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -8919,7 +9154,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-87f77277c4c84151bb54754435b23d8c" + "reference": "Observation/dv-70b3a31ae2224e559d8be65a11a9eddb" } ], "component": [ @@ -8957,8 +9192,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" + "code": "C4552100", + "display": "Lynch syndrome" } ] } @@ -8974,18 +9209,123 @@ ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "reviewed by expert panel" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "209600" + "value": "36587" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001000937.4" + "value": "SCV000107992.2" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab6655932091e78c119bb", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/NB6TK329" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-983532b4ef8b4928978bfaeba42af3db" + } + ], + "component": [ + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "53037-8", + "display": "Genetic variation clinical significance" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA6675-8", + "display": "Benign" + } + ] + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "81259-4", + "display": "predicted phenotype" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C4552100", + "display": "Lynch syndrome" + } + ] + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "93044-6", + "display": "Level of evidence" + } + ] + }, + "valueCodeableConcept": { + "text": "reviewed by expert panel" + } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "89983" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000106463.2" } ] } @@ -8994,7 +9334,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-87f77277c4c84151bb54754435b23d8c", + "id": "dv-983532b4ef8b4928978bfaeba42af3db", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -9067,7 +9407,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.11" + "code": "NC_000003.12" } ] } @@ -9106,8 +9446,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.11:32315654:A:G", - "display": "NC_000013.11:32315654:A:G" + "code": "NC_000003.12:37048782:C:T", + "display": "NC_000003.12:37048782:C:T" } ] } @@ -9139,7 +9479,7 @@ } ] }, - "valueString": "A" + "valueString": "C" }, { "code": { @@ -9151,7 +9491,7 @@ } ] }, - "valueString": "G" + "valueString": "T" }, { "code": { @@ -9185,7 +9525,7 @@ }, "valueRange": { "low": { - "value": 32315654 + "value": 37048782 } } } @@ -9196,7 +9536,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6675932091e78c13034", + "id": "dv-62fab6655932091e78c11615", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -9226,7 +9566,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-d35a9e4b945a443abf237057131c03e5" + "reference": "Observation/dv-e8e157f976b34a78ab1210328a2acd53" } ], "component": [ @@ -9288,11 +9628,11 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "91356" + "value": "89773" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000108367.2" + "value": "SCV000106243.2" } ] } @@ -9301,7 +9641,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-d35a9e4b945a443abf237057131c03e5", + "id": "dv-e8e157f976b34a78ab1210328a2acd53", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -9374,7 +9714,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "code": "NC_000003.12" } ] } @@ -9413,8 +9753,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:5999497:T:C", - "display": "NC_000007.14:5999497:T:C" + "code": "NC_000003.12:37031135:A:C", + "display": "NC_000003.12:37031135:A:C" } ] } @@ -9446,7 +9786,7 @@ } ] }, - "valueString": "T" + "valueString": "A" }, { "code": { @@ -9492,7 +9832,7 @@ }, "valueRange": { "low": { - "value": 5999497 + "value": 37031135 } } } @@ -9503,7 +9843,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab63a5932091e78bf6fe4", + "id": "dv-62fab66c5932091e78c15c01", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -9533,7 +9873,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-aab391f842a14a79865639fc25b95ff9" + "reference": "Observation/dv-edfe8714ceaf4687910f600e46f6806e" } ], "component": [ @@ -9571,8 +9911,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome" } ] } @@ -9588,30 +9928,30 @@ ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "text": "criteria provided, single submitter" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "36597" + "value": "126022" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000108224.2" + "value": "SCV002026093.2" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-aab391f842a14a79865639fc25b95ff9", + "id": "dv-62fab69e5932091e78c34f8c", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -9628,32 +9968,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/NB6TK329" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-b5fde7b61b29434bb495e2bca5859063" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -9661,8 +9996,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -9672,16 +10007,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0020445", + "display": "Familial hypercholesterolemia" } ] } @@ -9691,21 +10027,130 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "criteria provided, single submitter" } - }, + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "251936" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV001727625.2" + } + ] + } + }, + { + "name": "variant", + "resource": { + "resourceType": "Observation", + "id": "dv-b5fde7b61b29434bb495e2bca5859063", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "69548-6", + "display": "Genetic variant assessment" + } + ] + }, + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA9633-4", + "display": "present" + } + ] + }, + "component": [ + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "48002-0", + "display": "Genomic Source Class" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA6683-2", + "display": "germline" + } + ] + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "48013-7", + "display": "Genomic reference sequence ID" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://www.ncbi.nlm.nih.gov/nuccore", + "code": "NC_000019.10" + } + ] + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "53034-5", + "display": "Allelic state" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA6706-1", + "display": "heterozygous" + } + ] + } + }, { "code": { "coding": [ @@ -9720,8 +10165,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47795975:T:C", - "display": "NC_000002.12:47795975:T:C" + "code": "NC_000019.10:11116123:C:T", + "display": "NC_000019.10:11116123:C:T" } ] } @@ -9753,7 +10198,7 @@ } ] }, - "valueString": "T" + "valueString": "C" }, { "code": { @@ -9765,7 +10210,7 @@ } ] }, - "valueString": "C" + "valueString": "T" }, { "code": { @@ -9799,7 +10244,7 @@ }, "valueRange": { "low": { - "value": 47795975 + "value": 11116123 } } }, @@ -9814,7 +10259,7 @@ ] }, "valueQuantity": { - "value": 0.212977, + "value": 0.0756166, "system": "http://unitsofmeasure.org", "code": "1" } @@ -9826,7 +10271,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6645932091e78c10f67", + "id": "dv-62fab63a5932091e78bf7276", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -9856,7 +10301,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-db238eae873046a1bd607a546dc9381e" + "reference": "Observation/dv-5940367f4ed843f59a836f0cdce1dafe" } ], "component": [ @@ -9918,11 +10363,11 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "89410" + "value": "36693" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000108090.2" + "value": "SCV000108381.2" } ] } @@ -9931,7 +10376,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-db238eae873046a1bd607a546dc9381e", + "id": "dv-5940367f4ed843f59a836f0cdce1dafe", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -10004,7 +10449,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "NC_000007.14" } ] } @@ -10023,8 +10468,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "code": "LA6705-3", + "display": "homozygous" } ] } @@ -10043,8 +10488,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47805172:G:A", - "display": "NC_000002.12:47805172:G:A" + "code": "NC_000007.14:5997348:G:C", + "display": "NC_000007.14:5997348:G:C" } ] } @@ -10060,7 +10505,7 @@ ] }, "valueQuantity": { - "value": 0.5, + "value": 1.0, "unit": "relative frequency of a particular allele in the specimen", "system": "http://unitsofmeasure.org", "code": "1" @@ -10088,7 +10533,7 @@ } ] }, - "valueString": "A" + "valueString": "C" }, { "code": { @@ -10122,9 +10567,25 @@ }, "valueRange": { "low": { - "value": 47805172 + "value": 5997348 } } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "92821-8", + "display": "Population allele frequency" + } + ] + }, + "valueQuantity": { + "value": 0.8018, + "system": "http://unitsofmeasure.org", + "code": "1" + } } ] } @@ -10133,7 +10594,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cc2", + "id": "dv-62fab6645932091e78c10fbb", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -10163,7 +10624,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-c7c0803976fd4ab881f1588c713419ff" + "reference": "Observation/dv-32bc0d97fc48469c8f3bf615dc186530" } ], "component": [ @@ -10201,8 +10662,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" + "code": "C4552100", + "display": "Lynch syndrome" } ] } @@ -10218,18 +10679,18 @@ ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "reviewed by expert panel" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" + "value": "89432" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000494326.1" + "value": "SCV000108113.2" } ] } @@ -10238,7 +10699,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-c7c0803976fd4ab881f1588c713419ff", + "id": "dv-32bc0d97fc48469c8f3bf615dc186530", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -10311,7 +10772,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.11" + "code": "NC_000002.12" } ] } @@ -10350,8 +10811,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.11:32338917:A:G", - "display": "NC_000013.11:32338917:A:G" + "code": "NC_000002.12:47805797:T:C", + "display": "NC_000002.12:47805797:T:C" } ] } @@ -10383,7 +10844,7 @@ } ] }, - "valueString": "A" + "valueString": "T" }, { "code": { @@ -10395,7 +10856,7 @@ } ] }, - "valueString": "G" + "valueString": "C" }, { "code": { @@ -10429,25 +10890,9 @@ }, "valueRange": { "low": { - "value": 32338917 + "value": 47805797 } } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994359, - "system": "http://unitsofmeasure.org", - "code": "1" - } } ] } @@ -10456,7 +10901,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6645932091e78c11177", + "id": "dv-62fab66f5932091e78c17cc2", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -10486,7 +10931,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-1aa0fdfa74344f23b55e811414e4dcdf" + "reference": "Observation/dv-c7c0803976fd4ab881f1588c713419ff" } ], "component": [ @@ -10524,8 +10969,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome" } ] } @@ -10541,30 +10986,30 @@ ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "text": "criteria provided, single submitter" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "89521" + "value": "132779" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000108207.2" + "value": "SCV000494326.1" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-1aa0fdfa74344f23b55e811414e4dcdf", + "id": "dv-62fab63a5932091e78bf6f6f", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -10581,32 +11026,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/NB6TK329" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-db2c78d7a2d84f6a9a8927fb296cb567" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -10614,8 +11054,118 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign" + } + ] + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "81259-4", + "display": "predicted phenotype" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C4552100", + "display": "Lynch syndrome" + } + ] + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "93044-6", + "display": "Level of evidence" + } + ] + }, + "valueCodeableConcept": { + "text": "reviewed by expert panel" + } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "36584" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000107898.2" + } + ] + } + }, + { + "name": "variant", + "resource": { + "resourceType": "Observation", + "id": "dv-db2c78d7a2d84f6a9a8927fb296cb567", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "69548-6", + "display": "Genetic variant assessment" + } + ] + }, + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA9633-4", + "display": "present" + } + ] + }, + "component": [ + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "48002-0", + "display": "Genomic Source Class" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA6683-2", + "display": "germline" } ] } @@ -10673,8 +11223,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47792345:T:C", - "display": "NC_000002.12:47792345:T:C" + "code": "NC_000002.12:47783418:C:A", + "display": "NC_000002.12:47783418:C:A" } ] } @@ -10706,7 +11256,7 @@ } ] }, - "valueString": "T" + "valueString": "C" }, { "code": { @@ -10718,7 +11268,7 @@ } ] }, - "valueString": "C" + "valueString": "A" }, { "code": { @@ -10752,9 +11302,25 @@ }, "valueRange": { "low": { - "value": 47792345 + "value": 47783418 } } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "92821-8", + "display": "Population allele frequency" + } + ] + }, + "valueQuantity": { + "value": 0.14442, + "system": "http://unitsofmeasure.org", + "code": "1" + } } ] } @@ -10763,7 +11329,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6645932091e78c11178", + "id": "dv-62fab66e5932091e78c176b0", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -10793,7 +11359,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-234ee4ca3da04ab39f5ebfed027792dd" + "reference": "Observation/dv-719286980a454cc792902098a0122614" } ], "component": [ @@ -10831,8 +11397,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" + "code": "C0020445", + "display": "Familial hypercholesterolemia" } ] } @@ -10848,18 +11414,18 @@ ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "text": "criteria provided, single submitter" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "89525" + "value": "128416" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000108211.2" + "value": "SCV000902556.1" } ] } @@ -10868,7 +11434,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-234ee4ca3da04ab39f5ebfed027792dd", + "id": "dv-719286980a454cc792902098a0122614", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -10980,8 +11546,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47791516:T:C", - "display": "NC_000002.12:47791516:T:C" + "code": "NC_000002.12:21005954:C:T", + "display": "NC_000002.12:21005954:C:T" } ] } @@ -11013,7 +11579,7 @@ } ] }, - "valueString": "T" + "valueString": "C" }, { "code": { @@ -11025,7 +11591,7 @@ } ] }, - "valueString": "C" + "valueString": "T" }, { "code": { @@ -11059,9 +11625,25 @@ }, "valueRange": { "low": { - "value": 47791516 + "value": 21005954 } } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "92821-8", + "display": "Population allele frequency" + } + ] + }, + "valueQuantity": { + "value": 0.0700284, + "system": "http://unitsofmeasure.org", + "code": "1" + } } ] } @@ -11070,7 +11652,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6645932091e78c10fbb", + "id": "dv-62fab6995932091e78c31f8b", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -11100,7 +11682,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-32bc0d97fc48469c8f3bf615dc186530" + "reference": "Observation/dv-9bd8faa16b7f4b1d9a8d4c14b358b7db" } ], "component": [ @@ -11138,8 +11720,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" + "code": "C0020445", + "display": "Familial hypercholesterolemia" } ] } @@ -11155,18 +11737,18 @@ ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "text": "criteria provided, single submitter" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "89432" + "value": "235043" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000108113.2" + "value": "SCV000912224.1" } ] } @@ -11175,7 +11757,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-32bc0d97fc48469c8f3bf615dc186530", + "id": "dv-9bd8faa16b7f4b1d9a8d4c14b358b7db", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -11248,7 +11830,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "NC_000001.11" } ] } @@ -11267,8 +11849,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "LA6706-1", + "display": "heterozygous" } ] } @@ -11287,8 +11869,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47805797:T:C", - "display": "NC_000002.12:47805797:T:C" + "code": "NC_000001.11:55039879:CTGCTGCTGCTGCTGCTGCTGCT:CTGCTGCTGCTGCTGCTGCTGCTGCT", + "display": "NC_000001.11:55039879:CTGCTGCTGCTGCTGCTGCTGCT:CTGCTGCTGCTGCTGCTGCTGCTGCT" } ] } @@ -11304,7 +11886,7 @@ ] }, "valueQuantity": { - "value": 1.0, + "value": 0.5, "unit": "relative frequency of a particular allele in the specimen", "system": "http://unitsofmeasure.org", "code": "1" @@ -11320,7 +11902,7 @@ } ] }, - "valueString": "T" + "valueString": "A" }, { "code": { @@ -11332,7 +11914,7 @@ } ] }, - "valueString": "C" + "valueString": "ACTG" }, { "code": { @@ -11366,9 +11948,25 @@ }, "valueRange": { "low": { - "value": 47805797 + "value": 55039878 } } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "92821-8", + "display": "Population allele frequency" + } + ] + }, + "valueQuantity": { + "value": 0.121721, + "system": "http://unitsofmeasure.org", + "code": "1" + } } ] } @@ -11377,7 +11975,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab63a5932091e78bf6f6f", + "id": "dv-62fab63a5932091e78bf6fe4", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -11407,7 +12005,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-db2c78d7a2d84f6a9a8927fb296cb567" + "reference": "Observation/dv-aab391f842a14a79865639fc25b95ff9" } ], "component": [ @@ -11469,11 +12067,11 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "36584" + "value": "36597" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000107898.2" + "value": "SCV000108224.2" } ] } @@ -11482,7 +12080,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-db2c78d7a2d84f6a9a8927fb296cb567", + "id": "dv-aab391f842a14a79865639fc25b95ff9", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -11594,8 +12192,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47783418:C:A", - "display": "NC_000002.12:47783418:C:A" + "code": "NC_000002.12:47795975:T:C", + "display": "NC_000002.12:47795975:T:C" } ] } @@ -11627,7 +12225,7 @@ } ] }, - "valueString": "C" + "valueString": "T" }, { "code": { @@ -11639,7 +12237,7 @@ } ] }, - "valueString": "A" + "valueString": "C" }, { "code": { @@ -11673,7 +12271,7 @@ }, "valueRange": { "low": { - "value": 47783418 + "value": 47795975 } } }, @@ -11688,7 +12286,7 @@ ] }, "valueQuantity": { - "value": 0.14442, + "value": 0.212977, "system": "http://unitsofmeasure.org", "code": "1" } @@ -11700,7 +12298,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6645932091e78c10f6f", + "id": "dv-62fab6675932091e78c13034", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -11730,7 +12328,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-3b3666df092d4e808a0d597a56a5022b" + "reference": "Observation/dv-d35a9e4b945a443abf237057131c03e5" } ], "component": [ @@ -11792,11 +12390,11 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "89411" + "value": "91356" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000108091.2" + "value": "SCV000108367.2" } ] } @@ -11805,7 +12403,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-3b3666df092d4e808a0d597a56a5022b", + "id": "dv-d35a9e4b945a443abf237057131c03e5", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -11878,7 +12476,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "NC_000007.14" } ] } @@ -11897,8 +12495,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "code": "LA6705-3", + "display": "homozygous" } ] } @@ -11917,8 +12515,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47805186:T:C", - "display": "NC_000002.12:47805186:T:C" + "code": "NC_000007.14:5999497:T:C", + "display": "NC_000007.14:5999497:T:C" } ] } @@ -11934,7 +12532,7 @@ ] }, "valueQuantity": { - "value": 0.5, + "value": 1.0, "unit": "relative frequency of a particular allele in the specimen", "system": "http://unitsofmeasure.org", "code": "1" @@ -11996,7 +12594,7 @@ }, "valueRange": { "low": { - "value": 47805186 + "value": 5999497 } } } @@ -12007,7 +12605,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab63a5932091e78bf6fd4", + "id": "dv-62fab6655932091e78c11493", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -12037,7 +12635,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-b8cc4e2fbe604134979c80e1aa8c4cee" + "reference": "Observation/dv-324e0f6400104fc4846edb4fa8d66008" } ], "component": [ @@ -12092,18 +12690,18 @@ ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "reviewed by expert panel" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "36594" + "value": "89625" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000052939.2" + "value": "SCV000106085.2" } ] } @@ -12112,7 +12710,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-b8cc4e2fbe604134979c80e1aa8c4cee", + "id": "dv-324e0f6400104fc4846edb4fa8d66008", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -12185,7 +12783,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "NC_000003.12" } ] } @@ -12224,8 +12822,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47806411:C:G", - "display": "NC_000002.12:47806411:C:G" + "code": "NC_000003.12:37025558:A:G", + "display": "NC_000003.12:37025558:A:G" } ] } @@ -12257,7 +12855,7 @@ } ] }, - "valueString": "C" + "valueString": "A" }, { "code": { @@ -12303,25 +12901,9 @@ }, "valueRange": { "low": { - "value": 47806411 + "value": 37025558 } } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.733985, - "system": "http://unitsofmeasure.org", - "code": "1" - } } ] } @@ -12330,7 +12912,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6395932091e78bf6bfd", + "id": "dv-62fab66f5932091e78c17ccc", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -12360,7 +12942,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-210349083123421e9899d9f21af3ef71" + "reference": "Observation/dv-d47c74da1d8340e3976b600eedc794ac" } ], "component": [ @@ -12398,8 +12980,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome" } ] } @@ -12415,18 +12997,18 @@ ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "text": "criteria provided, single submitter" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "36564" + "value": "132780" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000107047.2" + "value": "SCV002025800.2" } ] } @@ -12435,7 +13017,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-210349083123421e9899d9f21af3ef71", + "id": "dv-d47c74da1d8340e3976b600eedc794ac", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -12508,7 +13090,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "NC_000013.11" } ] } @@ -12527,8 +13109,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "code": "LA6705-3", + "display": "homozygous" } ] } @@ -12547,8 +13129,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47429661:G:A", - "display": "NC_000002.12:47429661:G:A" + "code": "NC_000013.11:32340867:G:C", + "display": "NC_000013.11:32340867:G:C" } ] } @@ -12564,7 +13146,7 @@ ] }, "valueQuantity": { - "value": 0.5, + "value": 1.0, "unit": "relative frequency of a particular allele in the specimen", "system": "http://unitsofmeasure.org", "code": "1" @@ -12592,7 +13174,7 @@ } ] }, - "valueString": "A" + "valueString": "C" }, { "code": { @@ -12626,9 +13208,25 @@ }, "valueRange": { "low": { - "value": 47429661 + "value": 32340867 } } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "92821-8", + "display": "Population allele frequency" + } + ] + }, + "valueQuantity": { + "value": 0.994199, + "system": "http://unitsofmeasure.org", + "code": "1" + } } ] } @@ -12637,7 +13235,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab63a5932091e78bf725d", + "id": "dv-62fab6645932091e78c10f67", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -12667,7 +13265,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-5940367f4ed843f59a836f0cdce1dafe" + "reference": "Observation/dv-db238eae873046a1bd607a546dc9381e" } ], "component": [ @@ -12722,18 +13320,18 @@ ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "reviewed by expert panel" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "36693" + "value": "89410" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000053039.2" + "value": "SCV000108090.2" } ] } @@ -12742,7 +13340,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-5940367f4ed843f59a836f0cdce1dafe", + "id": "dv-db238eae873046a1bd607a546dc9381e", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -12815,7 +13413,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "code": "NC_000002.12" } ] } @@ -12834,8 +13432,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "LA6706-1", + "display": "heterozygous" } ] } @@ -12854,8 +13452,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:5997348:G:C", - "display": "NC_000007.14:5997348:G:C" + "code": "NC_000002.12:47805172:G:A", + "display": "NC_000002.12:47805172:G:A" } ] } @@ -12871,7 +13469,7 @@ ] }, "valueQuantity": { - "value": 1.0, + "value": 0.5, "unit": "relative frequency of a particular allele in the specimen", "system": "http://unitsofmeasure.org", "code": "1" @@ -12899,7 +13497,7 @@ } ] }, - "valueString": "C" + "valueString": "A" }, { "code": { @@ -12933,25 +13531,9 @@ }, "valueRange": { "low": { - "value": 5997348 + "value": 47805172 } } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.8018, - "system": "http://unitsofmeasure.org", - "code": "1" - } } ] } @@ -12960,7 +13542,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab63a5932091e78bf7252", + "id": "dv-62fab6645932091e78c10f6f", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -12990,7 +13572,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-4435221b91444669b3f6237f6b6fa954" + "reference": "Observation/dv-3b3666df092d4e808a0d597a56a5022b" } ], "component": [ @@ -13045,18 +13627,18 @@ ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "reviewed by expert panel" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "36692" + "value": "89411" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000053038.2" + "value": "SCV000108091.2" } ] } @@ -13065,7 +13647,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-4435221b91444669b3f6237f6b6fa954", + "id": "dv-3b3666df092d4e808a0d597a56a5022b", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -13138,7 +13720,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "code": "NC_000002.12" } ] } @@ -13157,8 +13739,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "LA6706-1", + "display": "heterozygous" } ] } @@ -13177,8 +13759,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:5999090:T:C", - "display": "NC_000007.14:5999090:T:C" + "code": "NC_000002.12:47805186:T:C", + "display": "NC_000002.12:47805186:T:C" } ] } @@ -13194,7 +13776,7 @@ ] }, "valueQuantity": { - "value": 1.0, + "value": 0.5, "unit": "relative frequency of a particular allele in the specimen", "system": "http://unitsofmeasure.org", "code": "1" @@ -13256,25 +13838,9 @@ }, "valueRange": { "low": { - "value": 5999090 + "value": 47805186 } } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.368213, - "system": "http://unitsofmeasure.org", - "code": "1" - } } ] } @@ -13283,7 +13849,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6645932091e78c11181", + "id": "dv-62fab6645932091e78c10b92", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -13313,7 +13879,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-49c6c5a200fb42fba2c02268d74d00a3" + "reference": "Observation/dv-fc120b4aab9444d0b262a5d3036026b9" } ], "component": [ @@ -13375,11 +13941,11 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "89526" + "value": "89294" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000108213.2" + "value": "SCV000107969.2" } ] } @@ -13388,7 +13954,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-49c6c5a200fb42fba2c02268d74d00a3", + "id": "dv-fc120b4aab9444d0b262a5d3036026b9", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -13500,8 +14066,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47791174:T:A", - "display": "NC_000002.12:47791174:T:A" + "code": "NC_000002.12:47785706:C:T", + "display": "NC_000002.12:47785706:C:T" } ] } @@ -13533,7 +14099,7 @@ } ] }, - "valueString": "T" + "valueString": "C" }, { "code": { @@ -13545,7 +14111,7 @@ } ] }, - "valueString": "A" + "valueString": "T" }, { "code": { @@ -13579,7 +14145,7 @@ }, "valueRange": { "low": { - "value": 47791174 + "value": 47785706 } } } @@ -13590,7 +14156,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6725932091e78c1a029", + "id": "dv-62fab6645932091e78c10fb4", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -13620,7 +14186,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-57863b6706444b2e9fabc5d5808df40a" + "reference": "Observation/dv-a71417cfb7164f2090e77f29a9ead21a" } ], "component": [ @@ -13658,8 +14224,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" + "code": "C4552100", + "display": "Lynch syndrome" } ] } @@ -13675,18 +14241,18 @@ ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "reviewed by expert panel" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "137691" + "value": "89429" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002505088.1" + "value": "SCV000108111.2" } ] } @@ -13695,7 +14261,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-57863b6706444b2e9fabc5d5808df40a", + "id": "dv-a71417cfb7164f2090e77f29a9ead21a", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -13768,7 +14334,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000017.11" + "code": "NC_000002.12" } ] } @@ -13807,8 +14373,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000017.11:7676482:G:C", - "display": "NC_000017.11:7676482:G:C" + "code": "NC_000002.12:47805735:CTATCTATCT:CTATCT", + "display": "NC_000002.12:47805735:CTATCTATCT:CTATCT" } ] } @@ -13840,7 +14406,7 @@ } ] }, - "valueString": "G" + "valueString": "ACTAT" }, { "code": { @@ -13852,7 +14418,7 @@ } ] }, - "valueString": "C" + "valueString": "A" }, { "code": { @@ -13886,7 +14452,7 @@ }, "valueRange": { "low": { - "value": 7676482 + "value": 47805734 } } }, @@ -13901,7 +14467,7 @@ ] }, "valueQuantity": { - "value": 0.673405, + "value": 0.6847, "system": "http://unitsofmeasure.org", "code": "1" } @@ -13913,7 +14479,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15bf3", + "id": "dv-62fab68a5932091e78c28ec6", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -13943,7 +14509,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-edfe8714ceaf4687910f600e46f6806e" + "reference": "Observation/dv-f2d0de4c461c487fa0d7b2b0a9034361" } ], "component": [ @@ -13981,8 +14547,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" + "code": "C0020445", + "display": "Familial hypercholesterolemia" } ] } @@ -14005,20 +14571,125 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "200916" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001000460.4" + "value": "SCV001729839.2" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-edfe8714ceaf4687910f600e46f6806e", + "id": "dv-62fab6705932091e78c186e7", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/NB6TK329" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-c05bb5adae894ebc865a6808c7685992" + } + ], + "component": [ + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "53037-8", + "display": "Genetic variation clinical significance" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA6675-8", + "display": "Benign" + } + ] + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "81259-4", + "display": "predicted phenotype" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome" + } + ] + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "93044-6", + "display": "Level of evidence" + } + ] + }, + "valueCodeableConcept": { + "text": "criteria provided, single submitter" + } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "133738" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV001000149.4" + } + ] + } + }, + { + "name": "variant", + "resource": { + "resourceType": "Observation", + "id": "dv-c05bb5adae894ebc865a6808c7685992", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -14130,8 +14801,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.11:32338161:T:C", - "display": "NC_000013.11:32338161:T:C" + "code": "NC_000013.11:32355249:T:C", + "display": "NC_000013.11:32355249:T:C" } ] } @@ -14209,7 +14880,7 @@ }, "valueRange": { "low": { - "value": 32338161 + "value": 32355249 } } }, @@ -14224,7 +14895,7 @@ ] }, "valueQuantity": { - "value": 0.174603, + "value": 0.994876, "system": "http://unitsofmeasure.org", "code": "1" } @@ -14236,7 +14907,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6665932091e78c1220d", + "id": "dv-62fab6725932091e78c1a029", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -14266,7 +14937,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-e33b1b39b9074c3ab87f3695f3beb087" + "reference": "Observation/dv-57863b6706444b2e9fabc5d5808df40a" } ], "component": [ @@ -14304,8 +14975,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome" } ] } @@ -14321,18 +14992,18 @@ ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "text": "criteria provided, single submitter" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "90607" + "value": "137691" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000107124.2" + "value": "SCV002505088.1" } ] } @@ -14341,7 +15012,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-e33b1b39b9074c3ab87f3695f3beb087", + "id": "dv-57863b6706444b2e9fabc5d5808df40a", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -14414,7 +15085,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "NC_000017.11" } ] } @@ -14453,8 +15124,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47439698:T:C", - "display": "NC_000002.12:47439698:T:C" + "code": "NC_000017.11:7676482:G:C", + "display": "NC_000017.11:7676482:G:C" } ] } @@ -14486,7 +15157,7 @@ } ] }, - "valueString": "T" + "valueString": "G" }, { "code": { @@ -14532,9 +15203,25 @@ }, "valueRange": { "low": { - "value": 47439698 + "value": 7676482 } } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "92821-8", + "display": "Population allele frequency" + } + ] + }, + "valueQuantity": { + "value": 0.673405, + "system": "http://unitsofmeasure.org", + "code": "1" + } } ] } @@ -14543,7 +15230,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6335932091e78bf3e30", + "id": "dv-62fab6655932091e78c11bb9", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -14573,7 +15260,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-3bbaa1e62567438db8586df47ee86d51" + "reference": "Observation/dv-aa7bc4cb064c41b8939860b917dde5af" } ], "component": [ @@ -14611,8 +15298,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" + "code": "C4552100", + "display": "Lynch syndrome" } ] } @@ -14628,18 +15315,18 @@ ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "reviewed by expert panel" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "12351" + "value": "90146" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002505076.1" + "value": "SCV000106634.2" } ] } @@ -14648,7 +15335,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-3bbaa1e62567438db8586df47ee86d51", + "id": "dv-aa7bc4cb064c41b8939860b917dde5af", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -14721,7 +15408,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000017.11" + "code": "NC_000003.12" } ] } @@ -14740,8 +15427,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "code": "LA6705-3", + "display": "homozygous" } ] } @@ -14760,8 +15447,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000017.11:7676153:G:C", - "display": "NC_000017.11:7676153:G:C" + "code": "NC_000003.12:37001468:A:C", + "display": "NC_000003.12:37001468:A:C" } ] } @@ -14777,7 +15464,7 @@ ] }, "valueQuantity": { - "value": 0.5, + "value": 1.0, "unit": "relative frequency of a particular allele in the specimen", "system": "http://unitsofmeasure.org", "code": "1" @@ -14793,7 +15480,7 @@ } ] }, - "valueString": "G" + "valueString": "A" }, { "code": { @@ -14839,25 +15526,9 @@ }, "valueRange": { "low": { - "value": 7676153 + "value": 37001468 } } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.668165, - "system": "http://unitsofmeasure.org", - "code": "1" - } } ] } @@ -14866,7 +15537,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab63a5932091e78bf6f98", + "id": "dv-62fab63a5932091e78bf6fd4", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -14896,7 +15567,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-70b3a31ae2224e559d8be65a11a9eddb" + "reference": "Observation/dv-b8cc4e2fbe604134979c80e1aa8c4cee" } ], "component": [ @@ -14958,23 +15629,23 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "36587" + "value": "36594" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000052932.2" + "value": "SCV000052939.2" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-70b3a31ae2224e559d8be65a11a9eddb", + "id": "dv-62fab63a5932091e78bf6fdb", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -14991,32 +15662,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/NB6TK329" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-aab391f842a14a79865639fc25b95ff9" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -15024,8 +15690,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -15035,16 +15701,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C4552100", + "display": "Lynch syndrome" } ] } @@ -15054,133 +15721,24 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47790941:A:G", - "display": "NC_000002.12:47790941:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] + "text": "criteria provided, single submitter" } - }, + } + ], + "identifier": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 47790941 - } - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "36597" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.134727, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000052942.2" } ] } @@ -15189,7 +15747,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6665932091e78c1245b", + "id": "dv-62fab6665932091e78c12386", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -15219,7 +15777,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-ddbfcfdb118b4385a9dad7e38d9b6da5" + "reference": "Observation/dv-7dcdefbf50b7446eb461e5d998247478" } ], "component": [ @@ -15281,11 +15839,11 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "90687" + "value": "90599" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000107200.2" + "value": "SCV000107117.2" } ] } @@ -15294,7 +15852,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-ddbfcfdb118b4385a9dad7e38d9b6da5", + "id": "dv-7dcdefbf50b7446eb461e5d998247478", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -15406,8 +15964,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47465141:C:T", - "display": "NC_000002.12:47465141:C:T" + "code": "NC_000002.12:47445429:G:A", + "display": "NC_000002.12:47445429:G:A" } ] } @@ -15439,7 +15997,7 @@ } ] }, - "valueString": "C" + "valueString": "G" }, { "code": { @@ -15451,7 +16009,7 @@ } ] }, - "valueString": "T" + "valueString": "A" }, { "code": { @@ -15485,7 +16043,7 @@ }, "valueRange": { "low": { - "value": 47465141 + "value": 47445429 } } } @@ -15496,7 +16054,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6655932091e78c11bb9", + "id": "dv-62fab66e5932091e78c17717", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -15526,7 +16084,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-aa7bc4cb064c41b8939860b917dde5af" + "reference": "Observation/dv-1692d4f52d4944a391a1e1e57347d8eb" } ], "component": [ @@ -15564,8 +16122,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" + "code": "C0020445", + "display": "Familial hypercholesterolemia" } ] } @@ -15581,30 +16139,30 @@ ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "text": "criteria provided, single submitter" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "90146" + "value": "128422" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000106634.2" + "value": "SCV000902527.1" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-aa7bc4cb064c41b8939860b917dde5af", + "id": "dv-62fab66c5932091e78c15bf3", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -15621,32 +16179,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/NB6TK329" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-edfe8714ceaf4687910f600e46f6806e" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -15654,8 +16207,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -15665,16 +16218,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000003.12" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome" } ] } @@ -15684,117 +16238,24 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] + "text": "criteria provided, single submitter" } - }, + } + ], + "identifier": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000003.12:37001468:A:C", - "display": "NC_000003.12:37001468:A:C" - } - ] - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "126022" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 37001468 - } - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV001000460.4" } ] } @@ -15803,7 +16264,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6705932091e78c186e3", + "id": "dv-62fab7095932091e78c75e4d", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -15833,7 +16294,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-c05bb5adae894ebc865a6808c7685992" + "reference": "Observation/dv-f2bfcff0b23a4c15a74aaeaef5faec4f" } ], "component": [ @@ -15871,8 +16332,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" + "code": "C0020445", + "display": "Familial hypercholesterolemia" } ] } @@ -15895,11 +16356,11 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "133738" + "value": "1168905" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002025816.2" + "value": "SCV002053227.1" } ] } @@ -15908,7 +16369,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-c05bb5adae894ebc865a6808c7685992", + "id": "dv-f2bfcff0b23a4c15a74aaeaef5faec4f", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -15981,7 +16442,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.11" + "code": "NC_000002.12" } ] } @@ -16020,8 +16481,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.11:32355249:T:C", - "display": "NC_000013.11:32355249:T:C" + "code": "NC_000002.12:21009930:T:C", + "display": "NC_000002.12:21009930:T:C" } ] } @@ -16099,7 +16560,7 @@ }, "valueRange": { "low": { - "value": 32355249 + "value": 21009930 } } }, @@ -16114,7 +16575,7 @@ ] }, "valueQuantity": { - "value": 0.994876, + "value": 0.995763, "system": "http://unitsofmeasure.org", "code": "1" } @@ -16126,7 +16587,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15c01", + "id": "dv-62fab6905932091e78c2c79a", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -16156,7 +16617,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-edfe8714ceaf4687910f600e46f6806e" + "reference": "Observation/dv-e28737e34fd843fbbe1717b56b96d1f8" } ], "component": [ @@ -16194,8 +16655,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" + "code": "C4552100", + "display": "Lynch syndrome" } ] } @@ -16218,11 +16679,116 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "218461" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002026093.2" + "value": "SCV000257707.2" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab6395932091e78bf6b0a", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/NB6TK329" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-437c728d910a46189036896c9a3fe97f" + } + ], + "component": [ + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "53037-8", + "display": "Genetic variation clinical significance" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA6675-8", + "display": "Benign" + } + ] + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "81259-4", + "display": "predicted phenotype" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C4552100", + "display": "Lynch syndrome" + } + ] + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "93044-6", + "display": "Level of evidence" + } + ] + }, + "valueCodeableConcept": { + "text": "criteria provided, single submitter" + } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "36542" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000052882.2" } ] } @@ -16231,7 +16797,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-edfe8714ceaf4687910f600e46f6806e", + "id": "dv-437c728d910a46189036896c9a3fe97f", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -16304,7 +16870,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.11" + "code": "NC_000003.12" } ] } @@ -16343,8 +16909,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.11:32338161:T:C", - "display": "NC_000013.11:32338161:T:C" + "code": "NC_000003.12:37042248:A:G", + "display": "NC_000003.12:37042248:A:G" } ] } @@ -16376,7 +16942,7 @@ } ] }, - "valueString": "T" + "valueString": "A" }, { "code": { @@ -16388,7 +16954,7 @@ } ] }, - "valueString": "C" + "valueString": "G" }, { "code": { @@ -16422,7 +16988,7 @@ }, "valueRange": { "low": { - "value": 32338161 + "value": 37042248 } } }, @@ -16437,7 +17003,7 @@ ] }, "valueQuantity": { - "value": 0.174603, + "value": 0.370828, "system": "http://unitsofmeasure.org", "code": "1" } @@ -16449,7 +17015,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6645932091e78c10df7", + "id": "dv-62fab63a5932091e78bf725d", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -16479,7 +17045,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-2439d4f778564bdd88dc95b2864fac18" + "reference": "Observation/dv-5940367f4ed843f59a836f0cdce1dafe" } ], "component": [ @@ -16534,30 +17100,30 @@ ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "text": "criteria provided, single submitter" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "89345" + "value": "36693" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000108022.2" + "value": "SCV000053039.2" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-2439d4f778564bdd88dc95b2864fac18", + "id": "dv-62fab6655932091e78c1146d", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -16574,33 +17140,138 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/NB6TK329" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-89eb7b13687a4828baa470fb82be0c0d" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } + "code": "53037-8", + "display": "Genetic variation clinical significance" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA6675-8", + "display": "Benign" + } + ] + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "81259-4", + "display": "predicted phenotype" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C4552100", + "display": "Lynch syndrome" + } + ] + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "93044-6", + "display": "Level of evidence" + } + ] + }, + "valueCodeableConcept": { + "text": "reviewed by expert panel" + } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "89615" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000106073.2" + } + ] + } + }, + { + "name": "variant", + "resource": { + "resourceType": "Observation", + "id": "dv-89eb7b13687a4828baa470fb82be0c0d", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "69548-6", + "display": "Genetic variant assessment" + } + ] + }, + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA9633-4", + "display": "present" + } + ] + }, + "component": [ + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "48002-0", + "display": "Genomic Source Class" + } ] }, "valueCodeableConcept": { @@ -16627,7 +17298,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "NC_000003.12" } ] } @@ -16666,8 +17337,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47803318:G:C", - "display": "NC_000002.12:47803318:G:C" + "code": "NC_000003.12:37020548:T:C", + "display": "NC_000003.12:37020548:T:C" } ] } @@ -16699,7 +17370,7 @@ } ] }, - "valueString": "G" + "valueString": "T" }, { "code": { @@ -16745,7 +17416,7 @@ }, "valueRange": { "low": { - "value": 47803318 + "value": 37020548 } } } @@ -17063,7 +17734,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab69e5932091e78c3549d", + "id": "dv-62fab6655932091e78c11695", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -17093,7 +17764,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-37304b7e844c41258d4a25a6dffada5b" + "reference": "Observation/dv-86d0233b22f3488197627b36c7594a73" } ], "component": [ @@ -17131,8 +17802,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0020445", - "display": "Familial hypercholesterolemia" + "code": "C4552100", + "display": "Lynch syndrome" } ] } @@ -17148,18 +17819,18 @@ ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "reviewed by expert panel" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "252262" + "value": "89830" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001717062.2" + "value": "SCV000106300.2" } ] } @@ -17168,7 +17839,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-37304b7e844c41258d4a25a6dffada5b", + "id": "dv-86d0233b22f3488197627b36c7594a73", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -17241,7 +17912,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.10" + "code": "NC_000003.12" } ] } @@ -17280,8 +17951,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.10:11123264:A:G", - "display": "NC_000019.10:11123264:A:G" + "code": "NC_000003.12:37041382:T:C", + "display": "NC_000003.12:37041382:T:C" } ] } @@ -17313,7 +17984,7 @@ } ] }, - "valueString": "A" + "valueString": "T" }, { "code": { @@ -17325,7 +17996,7 @@ } ] }, - "valueString": "G" + "valueString": "C" }, { "code": { @@ -17359,25 +18030,9 @@ }, "valueRange": { "low": { - "value": 11123264 + "value": 37041382 } } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.781146, - "system": "http://unitsofmeasure.org", - "code": "1" - } } ] } @@ -17386,7 +18041,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6665932091e78c1262d", + "id": "dv-62fab66e5932091e78c17733", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -17416,7 +18071,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-acb6861a2ae345cdae082be1563a4a66" + "reference": "Observation/dv-b96b0bdcbc3a4a68913378136736b773" } ], "component": [ @@ -17454,8 +18109,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" + "code": "C0020445", + "display": "Familial hypercholesterolemia" } ] } @@ -17471,18 +18126,18 @@ ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "text": "criteria provided, single submitter" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "90846" + "value": "128425" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000107374.2" + "value": "SCV000902523.1" } ] } @@ -17491,7 +18146,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-acb6861a2ae345cdae082be1563a4a66", + "id": "dv-b96b0bdcbc3a4a68913378136736b773", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -17603,8 +18258,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47476101:A:G", - "display": "NC_000002.12:47476101:A:G" + "code": "NC_000002.12:21009322:G:A", + "display": "NC_000002.12:21009322:G:A" } ] } @@ -17636,7 +18291,7 @@ } ] }, - "valueString": "A" + "valueString": "G" }, { "code": { @@ -17648,7 +18303,7 @@ } ] }, - "valueString": "G" + "valueString": "A" }, { "code": { @@ -17682,9 +18337,25 @@ }, "valueRange": { "low": { - "value": 47476101 + "value": 21009322 } } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "92821-8", + "display": "Population allele frequency" + } + ] + }, + "valueQuantity": { + "value": 0.388555, + "system": "http://unitsofmeasure.org", + "code": "1" + } } ] } @@ -17693,7 +18364,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15b7b", + "id": "dv-62fab6645932091e78c10df7", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -17723,7 +18394,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-99d2b1819c554636b70c366c3f79f914" + "reference": "Observation/dv-2439d4f778564bdd88dc95b2864fac18" } ], "component": [ @@ -17761,8 +18432,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" + "code": "C4552100", + "display": "Lynch syndrome" } ] } @@ -17778,18 +18449,18 @@ ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "reviewed by expert panel" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "125991" + "value": "89345" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001719551.2" + "value": "SCV000108022.2" } ] } @@ -17798,7 +18469,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-99d2b1819c554636b70c366c3f79f914", + "id": "dv-2439d4f778564bdd88dc95b2864fac18", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -17871,7 +18542,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.11" + "code": "NC_000002.12" } ] } @@ -17890,8 +18561,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "code": "LA6705-3", + "display": "homozygous" } ] } @@ -17910,8 +18581,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.11:32316588:T:G", - "display": "NC_000013.11:32316588:T:G" + "code": "NC_000002.12:47803318:G:C", + "display": "NC_000002.12:47803318:G:C" } ] } @@ -17927,7 +18598,7 @@ ] }, "valueQuantity": { - "value": 0.5, + "value": 1.0, "unit": "relative frequency of a particular allele in the specimen", "system": "http://unitsofmeasure.org", "code": "1" @@ -17943,7 +18614,7 @@ } ] }, - "valueString": "T" + "valueString": "G" }, { "code": { @@ -17955,7 +18626,7 @@ } ] }, - "valueString": "G" + "valueString": "C" }, { "code": { @@ -17989,7 +18660,7 @@ }, "valueRange": { "low": { - "value": 32316588 + "value": 47803318 } } } @@ -18000,7 +18671,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6665932091e78c11f9b", + "id": "dv-62fab6655932091e78c11c6a", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -18030,7 +18701,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-994f4ecf114a4bbb92bdb40776afc9b3" + "reference": "Observation/dv-fcf9e127dc524dbab17c34123fd5aaf0" } ], "component": [ @@ -18092,11 +18763,11 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "90366" + "value": "90227" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000106871.2" + "value": "SCV000106721.2" } ] } @@ -18105,7 +18776,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-994f4ecf114a4bbb92bdb40776afc9b3", + "id": "dv-fcf9e127dc524dbab17c34123fd5aaf0", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -18217,9 +18888,9 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000003.12:37015498:C:A", - "display": "NC_000003.12:37015498:C:A" - } + "code": "NC_000003.12:37007141:A:G", + "display": "NC_000003.12:37007141:A:G" + } ] } }, @@ -18250,7 +18921,7 @@ } ] }, - "valueString": "C" + "valueString": "A" }, { "code": { @@ -18262,7 +18933,7 @@ } ] }, - "valueString": "A" + "valueString": "G" }, { "code": { @@ -18296,7 +18967,7 @@ }, "valueRange": { "low": { - "value": 37015498 + "value": 37007141 } } } @@ -18307,7 +18978,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cb2", + "id": "dv-62fab6705932091e78c186e3", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -18337,7 +19008,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-c7c0803976fd4ab881f1588c713419ff" + "reference": "Observation/dv-c05bb5adae894ebc865a6808c7685992" } ], "component": [ @@ -18399,23 +19070,23 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" + "value": "133738" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002026104.2" + "value": "SCV002025816.2" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-c7c0803976fd4ab881f1588c713419ff", + "id": "dv-62fab69e5932091e78c3549c", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -18432,71 +19103,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/NB6TK329" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, + "derivedFrom": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.11" - } - ] - } - }, + "reference": "Observation/dv-37304b7e844c41258d4a25a6dffada5b" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -18504,8 +19131,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -18515,36 +19142,19 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.11:32338917:A:G", - "display": "NC_000013.11:32338917:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0020445", + "display": "Familial hypercholesterolemia" } ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" } }, { @@ -18552,76 +19162,24 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] + "text": "no assertion criteria provided" } - }, + } + ], + "identifier": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32338917 - } - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "252262" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994359, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV001461329.1" } ] } @@ -18630,7 +19188,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6645932091e78c10b9c", + "id": "dv-62fab6335932091e78bf3e30", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -18660,7 +19218,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-6b10bc016d794b2d891a2da2b7b49512" + "reference": "Observation/dv-3bbaa1e62567438db8586df47ee86d51" } ], "component": [ @@ -18698,8 +19256,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome" } ] } @@ -18715,18 +19273,18 @@ ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "text": "criteria provided, single submitter" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "89300" + "value": "12351" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000107976.2" + "value": "SCV002505076.1" } ] } @@ -18735,7 +19293,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-6b10bc016d794b2d891a2da2b7b49512", + "id": "dv-3bbaa1e62567438db8586df47ee86d51", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -18808,7 +19366,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "NC_000017.11" } ] } @@ -18847,8 +19405,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47789756:G:T", - "display": "NC_000002.12:47789756:G:T" + "code": "NC_000017.11:7676153:G:C", + "display": "NC_000017.11:7676153:G:C" } ] } @@ -18892,7 +19450,7 @@ } ] }, - "valueString": "T" + "valueString": "C" }, { "code": { @@ -18926,9 +19484,25 @@ }, "valueRange": { "low": { - "value": 47789756 + "value": 7676153 } } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "92821-8", + "display": "Population allele frequency" + } + ] + }, + "valueQuantity": { + "value": 0.668165, + "system": "http://unitsofmeasure.org", + "code": "1" + } } ] } @@ -18937,7 +19511,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6655932091e78c11695", + "id": "dv-62fab6395932091e78bf6bfe", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -18967,7 +19541,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-86d0233b22f3488197627b36c7594a73" + "reference": "Observation/dv-210349083123421e9899d9f21af3ef71" } ], "component": [ @@ -18995,5009 +19569,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "reviewed by expert panel" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "89830" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000106300.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-86d0233b22f3488197627b36c7594a73", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000003.12" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000003.12:37041382:T:C", - "display": "NC_000003.12:37041382:T:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 37041382 - } - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6305932091e78bf264e", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-5c81355782d446179e37701af154f50b" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0020445", - "display": "Familial hypercholesterolemia" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "2878" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000690958.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-5c81355782d446179e37701af154f50b", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000001.11" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000001.11:55039973:G:T", - "display": "NC_000001.11:55039973:G:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 55039973 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.0119305, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab68a5932091e78c28ec6", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f2d0de4c461c487fa0d7b2b0a9034361" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0020445", - "display": "Familial hypercholesterolemia" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "200916" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001729839.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-f2d0de4c461c487fa0d7b2b0a9034361", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.10:11113588:A:G", - "display": "NC_000019.10:11113588:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 11113588 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.632026, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6645932091e78c10fb4", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-a71417cfb7164f2090e77f29a9ead21a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "reviewed by expert panel" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "89429" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000108111.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-a71417cfb7164f2090e77f29a9ead21a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47805735:CTATCTATCT:CTATCT", - "display": "NC_000002.12:47805735:CTATCTATCT:CTATCT" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "ACTAT" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 47805734 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.6847, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab63a5932091e78bf6f6e", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-db2c78d7a2d84f6a9a8927fb296cb567" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "36584" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000052928.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-db2c78d7a2d84f6a9a8927fb296cb567", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47783418:C:A", - "display": "NC_000002.12:47783418:C:A" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 47783418 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.14442, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab69e5932091e78c34f8c", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-b5fde7b61b29434bb495e2bca5859063" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0020445", - "display": "Familial hypercholesterolemia" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "251936" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001727625.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-b5fde7b61b29434bb495e2bca5859063", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.10:11116123:C:T", - "display": "NC_000019.10:11116123:C:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 11116123 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.0756166, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6995932091e78c31f8b", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-9bd8faa16b7f4b1d9a8d4c14b358b7db" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0020445", - "display": "Familial hypercholesterolemia" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "235043" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000912224.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-9bd8faa16b7f4b1d9a8d4c14b358b7db", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000001.11" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000001.11:55039879:CTGCTGCTGCTGCTGCTGCTGCT:CTGCTGCTGCTGCTGCTGCTGCTGCT", - "display": "NC_000001.11:55039879:CTGCTGCTGCTGCTGCTGCTGCT:CTGCTGCTGCTGCTGCTGCTGCTGCT" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "ACTG" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 55039878 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.121721, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab63a5932091e78bf7276", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-5940367f4ed843f59a836f0cdce1dafe" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "reviewed by expert panel" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "36693" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000108381.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-5940367f4ed843f59a836f0cdce1dafe", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:5997348:G:C", - "display": "NC_000007.14:5997348:G:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 5997348 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.8018, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6645932091e78c10b95", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-49a4913593454c339fb981bd5144d9a6" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "reviewed by expert panel" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "89295" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000107970.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-49a4913593454c339fb981bd5144d9a6", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47783514:C:G", - "display": "NC_000002.12:47783514:C:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 47783514 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.13896, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17ccc", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-d47c74da1d8340e3976b600eedc794ac" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002025800.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-d47c74da1d8340e3976b600eedc794ac", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.11" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.11:32340867:G:C", - "display": "NC_000013.11:32340867:G:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32340867 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994199, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6905932091e78c2c79a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e28737e34fd843fbbe1717b56b96d1f8" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "218461" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000257707.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-e28737e34fd843fbbe1717b56b96d1f8", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:5997426:AAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAA", - "display": "NC_000007.14:5997426:AAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAA" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "GA" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 5997425 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.430816, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6655932091e78c11493", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-324e0f6400104fc4846edb4fa8d66008" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "reviewed by expert panel" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "89625" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000106085.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-324e0f6400104fc4846edb4fa8d66008", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000003.12" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000003.12:37025558:A:G", - "display": "NC_000003.12:37025558:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 37025558 - } - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6665932091e78c12386", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-7dcdefbf50b7446eb461e5d998247478" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "reviewed by expert panel" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "90599" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000107117.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-7dcdefbf50b7446eb461e5d998247478", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47445429:G:A", - "display": "NC_000002.12:47445429:G:A" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 47445429 - } - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6655932091e78c119bb", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-983532b4ef8b4928978bfaeba42af3db" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "reviewed by expert panel" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "89983" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000106463.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-983532b4ef8b4928978bfaeba42af3db", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000003.12" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000003.12:37048782:C:T", - "display": "NC_000003.12:37048782:C:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 37048782 - } - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66e5932091e78c17715", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-1692d4f52d4944a391a1e1e57347d8eb" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0020445", - "display": "Familial hypercholesterolemia" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "128422" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002524050.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-1692d4f52d4944a391a1e1e57347d8eb", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:21041027:G:A", - "display": "NC_000002.12:21041027:G:A" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 21041027 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.25802, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6645932091e78c10b92", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fc120b4aab9444d0b262a5d3036026b9" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "reviewed by expert panel" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "89294" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000107969.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-fc120b4aab9444d0b262a5d3036026b9", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47785706:C:T", - "display": "NC_000002.12:47785706:C:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "system": "http://loinc.org", + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C4552100", + "display": "Lynch syndrome" } ] } @@ -24007,17 +19590,25 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueRange": { - "low": { - "value": 47785706 - } + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "36564" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000052904.2" + } ] } }, @@ -24025,7 +19616,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6645932091e78c10b9e", + "id": "dv-62fab6665932091e78c1220d", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -24055,7 +19646,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-525568db5bbb42e79c7b9c4b5d27fd28" + "reference": "Observation/dv-e33b1b39b9074c3ab87f3695f3beb087" } ], "component": [ @@ -24117,11 +19708,11 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "89301" + "value": "90607" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000107977.2" + "value": "SCV000107124.2" } ] } @@ -24130,7 +19721,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-525568db5bbb42e79c7b9c4b5d27fd28", + "id": "dv-e33b1b39b9074c3ab87f3695f3beb087", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -24242,8 +19833,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47790890:A:G", - "display": "NC_000002.12:47790890:A:G" + "code": "NC_000002.12:47439698:T:C", + "display": "NC_000002.12:47439698:T:C" } ] } @@ -24275,7 +19866,7 @@ } ] }, - "valueString": "A" + "valueString": "T" }, { "code": { @@ -24287,7 +19878,7 @@ } ] }, - "valueString": "G" + "valueString": "C" }, { "code": { @@ -24321,8 +19912,69 @@ }, "valueRange": { "low": { - "value": 47790890 + "value": 47439698 + } + } + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab6395932091e78bf6afa", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/NB6TK329" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-437c728d910a46189036896c9a3fe97f" + } + ], + "component": [ + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "53037-8", + "display": "Genetic variation clinical significance" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA6675-8", + "display": "Benign" + } + ] } }, { @@ -24330,17 +19982,45 @@ "coding": [ { "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueQuantity": { - "value": 0.0372618, - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C4552100", + "display": "Lynch syndrome" + } + ] + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "93044-6", + "display": "Level of evidence" + } + ] + }, + "valueCodeableConcept": { + "text": "reviewed by expert panel" } } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "36542" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000106295.2" + } ] } }, @@ -24348,7 +20028,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6655932091e78c11631", + "id": "dv-62fab6665932091e78c11f9b", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -24378,7 +20058,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-e7a8dac6a6aa45c5b219fea9973e34ab" + "reference": "Observation/dv-994f4ecf114a4bbb92bdb40776afc9b3" } ], "component": [ @@ -24440,11 +20120,11 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "89785" + "value": "90366" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000106257.2" + "value": "SCV000106871.2" } ] } @@ -24453,7 +20133,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-e7a8dac6a6aa45c5b219fea9973e34ab", + "id": "dv-994f4ecf114a4bbb92bdb40776afc9b3", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -24565,8 +20245,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000003.12:37037014:A:G", - "display": "NC_000003.12:37037014:A:G" + "code": "NC_000003.12:37015498:C:A", + "display": "NC_000003.12:37015498:C:A" } ] } @@ -24598,7 +20278,7 @@ } ] }, - "valueString": "A" + "valueString": "C" }, { "code": { @@ -24610,7 +20290,7 @@ } ] }, - "valueString": "G" + "valueString": "A" }, { "code": { @@ -24644,7 +20324,7 @@ }, "valueRange": { "low": { - "value": 37037014 + "value": 37015498 } } } @@ -24655,7 +20335,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab66e5932091e78c17717", + "id": "dv-62fab6305932091e78bf264e", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -24685,7 +20365,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-1692d4f52d4944a391a1e1e57347d8eb" + "reference": "Observation/dv-5c81355782d446179e37701af154f50b" } ], "component": [ @@ -24747,11 +20427,11 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "128422" + "value": "2878" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000902527.1" + "value": "SCV000690958.2" } ] } @@ -24760,7 +20440,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-1692d4f52d4944a391a1e1e57347d8eb", + "id": "dv-5c81355782d446179e37701af154f50b", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -24833,7 +20513,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "NC_000001.11" } ] } @@ -24872,8 +20552,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:21041027:G:A", - "display": "NC_000002.12:21041027:G:A" + "code": "NC_000001.11:55039973:G:T", + "display": "NC_000001.11:55039973:G:T" } ] } @@ -24917,7 +20597,7 @@ } ] }, - "valueString": "A" + "valueString": "T" }, { "code": { @@ -24951,7 +20631,7 @@ }, "valueRange": { "low": { - "value": 21041027 + "value": 55039973 } } }, @@ -24966,7 +20646,7 @@ ] }, "valueQuantity": { - "value": 0.25802, + "value": 0.0119305, "system": "http://unitsofmeasure.org", "code": "1" } @@ -24978,7 +20658,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6705932091e78c186e7", + "id": "dv-62fab6665932091e78c1262d", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -25008,7 +20688,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-c05bb5adae894ebc865a6808c7685992" + "reference": "Observation/dv-acb6861a2ae345cdae082be1563a4a66" } ], "component": [ @@ -25046,8 +20726,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" + "code": "C4552100", + "display": "Lynch syndrome" } ] } @@ -25063,18 +20743,18 @@ ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "reviewed by expert panel" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "133738" + "value": "90846" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001000149.4" + "value": "SCV000107374.2" } ] } @@ -25083,7 +20763,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-c05bb5adae894ebc865a6808c7685992", + "id": "dv-acb6861a2ae345cdae082be1563a4a66", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -25156,7 +20836,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.11" + "code": "NC_000002.12" } ] } @@ -25175,8 +20855,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "LA6706-1", + "display": "heterozygous" } ] } @@ -25195,8 +20875,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.11:32355249:T:C", - "display": "NC_000013.11:32355249:T:C" + "code": "NC_000002.12:47476101:A:G", + "display": "NC_000002.12:47476101:A:G" } ] } @@ -25212,7 +20892,7 @@ ] }, "valueQuantity": { - "value": 1.0, + "value": 0.5, "unit": "relative frequency of a particular allele in the specimen", "system": "http://unitsofmeasure.org", "code": "1" @@ -25228,7 +20908,7 @@ } ] }, - "valueString": "T" + "valueString": "A" }, { "code": { @@ -25240,7 +20920,7 @@ } ] }, - "valueString": "C" + "valueString": "G" }, { "code": { @@ -25274,25 +20954,9 @@ }, "valueRange": { "low": { - "value": 32355249 + "value": 47476101 } } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994876, - "system": "http://unitsofmeasure.org", - "code": "1" - } } ] } @@ -25301,7 +20965,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6645932091e78c111bb", + "id": "dv-62fab6435932091e78bfc9ac", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -25331,7 +20995,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-37cd8d0c069d43cca4761374a718b6e8" + "reference": "Observation/dv-5071403516aa4a17871949bf246b8b5d" } ], "component": [ @@ -25393,11 +21057,11 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "89543" + "value": "42471" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000108232.2" + "value": "SCV000108065.2" } ] } @@ -25406,7 +21070,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-37cd8d0c069d43cca4761374a718b6e8", + "id": "dv-5071403516aa4a17871949bf246b8b5d", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -25498,8 +21162,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "code": "LA6705-3", + "display": "homozygous" } ] } @@ -25518,8 +21182,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47798554:C:T", - "display": "NC_000002.12:47798554:C:T" + "code": "NC_000002.12:47803698:A:T", + "display": "NC_000002.12:47803698:A:T" } ] } @@ -25535,7 +21199,7 @@ ] }, "valueQuantity": { - "value": 0.5, + "value": 1.0, "unit": "relative frequency of a particular allele in the specimen", "system": "http://unitsofmeasure.org", "code": "1" @@ -25551,7 +21215,7 @@ } ] }, - "valueString": "C" + "valueString": "A" }, { "code": { @@ -25597,9 +21261,25 @@ }, "valueRange": { "low": { - "value": 47798554 + "value": 47803698 } } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "92821-8", + "display": "Population allele frequency" + } + ] + }, + "valueQuantity": { + "value": 0.411752, + "system": "http://unitsofmeasure.org", + "code": "1" + } } ] } @@ -25608,7 +21288,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6905932091e78c2c798", + "id": "dv-62fab66f5932091e78c17cbd", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -25638,7 +21318,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-e28737e34fd843fbbe1717b56b96d1f8" + "reference": "Observation/dv-c7c0803976fd4ab881f1588c713419ff" } ], "component": [ @@ -25676,8 +21356,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome" } ] } @@ -25700,23 +21380,23 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "218461" + "value": "132779" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000257705.2" + "value": "SCV000635377.5" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-e28737e34fd843fbbe1717b56b96d1f8", + "id": "dv-62fab63a5932091e78bf6f6e", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -25733,71 +21413,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/NB6TK329" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, + "derivedFrom": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, + "reference": "Observation/dv-db2c78d7a2d84f6a9a8927fb296cb567" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -25805,8 +21441,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -25816,36 +21452,19 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:5997426:AAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAA", - "display": "NC_000007.14:5997426:AAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAA" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C4552100", + "display": "Lynch syndrome" } ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" } }, { @@ -25853,76 +21472,24 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "GA" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] + "text": "criteria provided, single submitter" } - }, + } + ], + "identifier": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 5997425 - } - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "36584" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.430816, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000052928.2" } ] } @@ -25931,7 +21498,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab7095932091e78c75e4d", + "id": "dv-62fab6655932091e78c11355", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -25961,7 +21528,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-f2bfcff0b23a4c15a74aaeaef5faec4f" + "reference": "Observation/dv-8154922662b44a9aa5260207fea8d5b6" } ], "component": [ @@ -25999,8 +21566,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0020445", - "display": "Familial hypercholesterolemia" + "code": "C4552100", + "display": "Lynch syndrome" } ] } @@ -26016,18 +21583,18 @@ ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "reviewed by expert panel" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "1168905" + "value": "89544" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002053227.1" + "value": "SCV000108233.2" } ] } @@ -26036,7 +21603,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-f2bfcff0b23a4c15a74aaeaef5faec4f", + "id": "dv-8154922662b44a9aa5260207fea8d5b6", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -26148,8 +21715,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:21009930:T:C", - "display": "NC_000002.12:21009930:T:C" + "code": "NC_000002.12:47797736:C:T", + "display": "NC_000002.12:47797736:C:T" } ] } @@ -26181,7 +21748,7 @@ } ] }, - "valueString": "T" + "valueString": "C" }, { "code": { @@ -26193,7 +21760,7 @@ } ] }, - "valueString": "C" + "valueString": "T" }, { "code": { @@ -26222,29 +21789,13 @@ "system": "http://loinc.org", "code": "81254-5", "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 21009930 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.995763, - "system": "http://unitsofmeasure.org", - "code": "1" + } + ] + }, + "valueRange": { + "low": { + "value": 47797736 + } } } ] @@ -26254,7 +21805,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6655932091e78c1145b", + "id": "dv-62fab66f5932091e78c17ce1", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -26284,7 +21835,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-0c3e9547181e4b789c13b04121a9ced8" + "reference": "Observation/dv-d47c74da1d8340e3976b600eedc794ac" } ], "component": [ @@ -26322,8 +21873,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome" } ] } @@ -26339,30 +21890,30 @@ ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "text": "criteria provided, single submitter" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "89611" + "value": "132780" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000106069.2" + "value": "SCV000494339.1" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-0c3e9547181e4b789c13b04121a9ced8", + "id": "dv-62fab66f5932091e78c17cd7", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -26379,32 +21930,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/NB6TK329" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-d47c74da1d8340e3976b600eedc794ac" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -26412,27 +21958,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000003.12" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -26442,17 +21969,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome" } ] } @@ -26462,97 +21989,24 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000003.12:37021467:G:T", - "display": "NC_000003.12:37021467:G:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "text": "criteria provided, single submitter" } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, + } + ], + "identifier": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "132780" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 37021467 - } - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000635514.5" } ] } @@ -26561,7 +22015,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6645932091e78c10b9a", + "id": "dv-62fab6645932091e78c10b95", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -26591,7 +22045,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-d83d284e564e4106a409fcd7bb222eb9" + "reference": "Observation/dv-49a4913593454c339fb981bd5144d9a6" } ], "component": [ @@ -26653,11 +22107,11 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "89296" + "value": "89295" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000107958.2" + "value": "SCV000107970.2" } ] } @@ -26666,7 +22120,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-d83d284e564e4106a409fcd7bb222eb9", + "id": "dv-49a4913593454c339fb981bd5144d9a6", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -26778,8 +22232,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47785959:A:G", - "display": "NC_000002.12:47785959:A:G" + "code": "NC_000002.12:47783514:C:G", + "display": "NC_000002.12:47783514:C:G" } ] } @@ -26811,7 +22265,7 @@ } ] }, - "valueString": "A" + "valueString": "C" }, { "code": { @@ -26857,9 +22311,25 @@ }, "valueRange": { "low": { - "value": 47785959 + "value": 47783514 } } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "92821-8", + "display": "Population allele frequency" + } + ] + }, + "valueQuantity": { + "value": 0.13896, + "system": "http://unitsofmeasure.org", + "code": "1" + } } ] } @@ -26868,7 +22338,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab63a5932091e78bf6fdb", + "id": "dv-62fab6655932091e78c11a58", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -26898,7 +22368,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-aab391f842a14a79865639fc25b95ff9" + "reference": "Observation/dv-396515d9058748f2a3ce8d4e5149620b" } ], "component": [ @@ -26953,18 +22423,18 @@ ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "reviewed by expert panel" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "36597" + "value": "90024" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000052942.2" + "value": "SCV000106504.2" } ] } @@ -26973,7 +22443,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-aab391f842a14a79865639fc25b95ff9", + "id": "dv-396515d9058748f2a3ce8d4e5149620b", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -27046,7 +22516,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "NC_000003.12" } ] } @@ -27065,8 +22535,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "code": "LA6705-3", + "display": "homozygous" } ] } @@ -27085,8 +22555,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47795975:T:C", - "display": "NC_000002.12:47795975:T:C" + "code": "NC_000003.12:36997279:C:T", + "display": "NC_000003.12:36997279:C:T" } ] } @@ -27102,7 +22572,7 @@ ] }, "valueQuantity": { - "value": 0.5, + "value": 1.0, "unit": "relative frequency of a particular allele in the specimen", "system": "http://unitsofmeasure.org", "code": "1" @@ -27118,7 +22588,7 @@ } ] }, - "valueString": "T" + "valueString": "C" }, { "code": { @@ -27130,7 +22600,7 @@ } ] }, - "valueString": "C" + "valueString": "T" }, { "code": { @@ -27164,25 +22634,9 @@ }, "valueRange": { "low": { - "value": 47795975 + "value": 36997279 } } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.212977, - "system": "http://unitsofmeasure.org", - "code": "1" - } } ] } diff --git a/tests/expected_outputs/find_subject_dx_implications/4.json b/tests/expected_outputs/find_subject_dx_implications/4.json index d82535dbe..dc8e014fb 100644 --- a/tests/expected_outputs/find_subject_dx_implications/4.json +++ b/tests/expected_outputs/find_subject_dx_implications/4.json @@ -5,7 +5,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6305932091e78bf2316", + "id": "dv-62fab6305932091e78bf2329", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -90,7 +90,7 @@ ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], @@ -101,7 +101,7 @@ }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000245789.1" + "value": "SCV001251532.1" } ] } @@ -328,7 +328,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6305932091e78bf232f", + "id": "dv-62fab6305932091e78bf2317", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -413,7 +413,7 @@ ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], @@ -424,19 +424,19 @@ }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000020169.4" + "value": "SCV001368348.2" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-e6b9e50014b24ebe81a0504cbba79282", + "id": "dv-62fab6305932091e78bf230e", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -453,32 +453,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG02657" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -486,8 +481,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6668-3", + "display": "Pathogenic" } ] } @@ -497,16 +492,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000006.11" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C3469186", + "display": "Hemochromatosis type 1" } ] } @@ -516,98 +512,102 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "criteria provided, single submitter" } - }, + } + ], + "identifier": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000006.11:26091178:C:G", - "display": "NC_000006.11:26091178:C:G" - } - ] - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "10" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV001137061.1" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab6305932091e78bf231b", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } - }, + ] + }, + "subject": { + "reference": "Patient/HG02657" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, - "valueString": "C" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6668-3", + "display": "Pathogenic" } ] - }, - "valueString": "G" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C3469186", + "display": "Hemochromatosis type 1" } ] } @@ -617,32 +617,24 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueRange": { - "low": { - "value": 26091178 - } + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "10" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.10924, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000693430.2" } ] } @@ -651,7 +643,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6305932091e78bf2330", + "id": "dv-62fab6305932091e78bf232b", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -747,19 +739,19 @@ }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000206973.2" + "value": "SCV001523197.1" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-e6b9e50014b24ebe81a0504cbba79282", + "id": "dv-62fab6305932091e78bf2330", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -776,32 +768,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG02657" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -809,8 +796,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6668-3", + "display": "Pathogenic" } ] } @@ -820,16 +807,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000006.11" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C3469186", + "display": "Hemochromatosis type 1" } ] } @@ -839,37 +827,82 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "criteria provided, single submitter" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "10" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000206973.2" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab6305932091e78bf2316", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG02657" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000006.11:26091178:C:G", - "display": "NC_000006.11:26091178:C:G" + "system": "http://loinc.org", + "code": "LA6668-3", + "display": "Pathogenic" } ] } @@ -879,49 +912,93 @@ "coding": [ { "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C3469186", + "display": "Hemochromatosis type 1" } ] - }, - "valueString": "C" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueString": "G" + "valueCodeableConcept": { + "text": "no assertion criteria provided" + } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "10" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000245789.1" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab6305932091e78bf232f", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG02657" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -929,8 +1006,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "LA6668-3", + "display": "Pathogenic" } ] } @@ -940,15 +1017,19 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueRange": { - "low": { - "value": 26091178 - } + "valueCodeableConcept": { + "coding": [ + { + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C3469186", + "display": "Hemochromatosis type 1" + } + ] } }, { @@ -956,17 +1037,25 @@ "coding": [ { "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueQuantity": { - "value": 0.10924, - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "text": "no assertion criteria provided" } } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "10" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000020169.4" + } ] } }, @@ -974,7 +1063,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6305932091e78bf231b", + "id": "dv-62fab6305932091e78bf232c", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -1070,19 +1159,19 @@ }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000693430.2" + "value": "SCV000223933.2" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-e6b9e50014b24ebe81a0504cbba79282", + "id": "dv-62fab6305932091e78bf231e", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -1099,32 +1188,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG02657" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -1132,8 +1216,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6668-3", + "display": "Pathogenic" } ] } @@ -1143,16 +1227,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000006.11" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C3469186", + "display": "Hemochromatosis t" } ] } @@ -1162,133 +1247,24 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "criteria provided, single submitter" } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000006.11:26091178:C:G", - "display": "NC_000006.11:26091178:C:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, + } + ], + "identifier": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 26091178 - } - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "10" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.10924, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000893709.1" } ] } @@ -1297,7 +1273,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6305932091e78bf2326", + "id": "dv-62fab6305932091e78bf231f", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -1393,19 +1369,19 @@ }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001519563.1" + "value": "SCV002028310.1" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-e6b9e50014b24ebe81a0504cbba79282", + "id": "dv-62fab6305932091e78bf2326", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -1422,2817 +1398,15 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG02657" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000006.11" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000006.11:26091178:C:G", - "display": "NC_000006.11:26091178:C:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 26091178 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.10924, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6305932091e78bf2317", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG02657" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C3469186", - "display": "Hemochromatosis type 1" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "10" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001368348.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-e6b9e50014b24ebe81a0504cbba79282", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG02657" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000006.11" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000006.11:26091178:C:G", - "display": "NC_000006.11:26091178:C:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 26091178 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.10924, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6305932091e78bf2312", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG02657" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C3469186", - "display": "Hemochromatosis type 1" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "10" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002499222.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-e6b9e50014b24ebe81a0504cbba79282", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG02657" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000006.11" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000006.11:26091178:C:G", - "display": "NC_000006.11:26091178:C:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 26091178 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.10924, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6305932091e78bf230d", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG02657" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C3469186", - "display": "Hemochromatosis type 1" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "10" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002038504.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-e6b9e50014b24ebe81a0504cbba79282", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG02657" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000006.11" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000006.11:26091178:C:G", - "display": "NC_000006.11:26091178:C:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 26091178 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.10924, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6305932091e78bf2329", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG02657" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C3469186", - "display": "Hemochromatosis type 1" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "10" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001251532.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-e6b9e50014b24ebe81a0504cbba79282", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG02657" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000006.11" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000006.11:26091178:C:G", - "display": "NC_000006.11:26091178:C:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 26091178 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.10924, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6305932091e78bf232c", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG02657" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C3469186", - "display": "Hemochromatosis type 1" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "10" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000223933.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-e6b9e50014b24ebe81a0504cbba79282", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG02657" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000006.11" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000006.11:26091178:C:G", - "display": "NC_000006.11:26091178:C:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 26091178 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.10924, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6305932091e78bf231f", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG02657" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C3469186", - "display": "Hemochromatosis type 1" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "10" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002028310.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-e6b9e50014b24ebe81a0504cbba79282", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG02657" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000006.11" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000006.11:26091178:C:G", - "display": "NC_000006.11:26091178:C:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 26091178 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.10924, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6305932091e78bf2322", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG02657" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C3469186", - "display": "Hemochromatosis type 1" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "10" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001194094.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-e6b9e50014b24ebe81a0504cbba79282", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG02657" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000006.11" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000006.11:26091178:C:G", - "display": "NC_000006.11:26091178:C:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 26091178 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.10924, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6305932091e78bf230e", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG02657" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C3469186", - "display": "Hemochromatosis type 1" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "10" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001137061.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-e6b9e50014b24ebe81a0504cbba79282", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG02657" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000006.11" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000006.11:26091178:C:G", - "display": "NC_000006.11:26091178:C:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 26091178 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.10924, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6305932091e78bf231e", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG02657" - }, - "derivedFrom": [ + "derivedFrom": [ { "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" } @@ -4243,247 +1417,37 @@ "coding": [ { "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C3469186", - "display": "Hemochromatosis t" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "10" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000893709.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-e6b9e50014b24ebe81a0504cbba79282", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG02657" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000006.11" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000006.11:26091178:C:G", - "display": "NC_000006.11:26091178:C:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, - "valueString": "C" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6668-3", + "display": "Pathogenic" } ] - }, - "valueString": "G" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C3469186", + "display": "Hemochromatosis type 1" } ] } @@ -4493,32 +1457,24 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueRange": { - "low": { - "value": 26091178 - } + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "10" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.10924, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV001519563.1" } ] } @@ -4527,7 +1483,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6305932091e78bf232b", + "id": "dv-62fab6305932091e78bf230d", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -4623,19 +1579,19 @@ }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001523197.1" + "value": "SCV002038504.1" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-e6b9e50014b24ebe81a0504cbba79282", + "id": "dv-62fab6305932091e78bf2312", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -4652,32 +1608,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG02657" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -4685,8 +1636,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6668-3", + "display": "Pathogenic" } ] } @@ -4696,16 +1647,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000006.11" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C3469186", + "display": "Hemochromatosis type 1" } ] } @@ -4715,98 +1667,102 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "criteria provided, single submitter" } - }, + } + ], + "identifier": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000006.11:26091178:C:G", - "display": "NC_000006.11:26091178:C:G" - } - ] - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "10" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV002499222.1" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab6305932091e78bf2322", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } - }, + ] + }, + "subject": { + "reference": "Patient/HG02657" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, - "valueString": "C" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6668-3", + "display": "Pathogenic" } ] - }, - "valueString": "G" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C3469186", + "display": "Hemochromatosis type 1" } ] } @@ -4816,32 +1772,24 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueRange": { - "low": { - "value": 26091178 - } + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "10" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.10924, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV001194094.2" } ] } diff --git a/tests/expected_outputs/find_subject_dx_implications/5.json b/tests/expected_outputs/find_subject_dx_implications/5.json index 6e6ece7aa..df76b8c23 100644 --- a/tests/expected_outputs/find_subject_dx_implications/5.json +++ b/tests/expected_outputs/find_subject_dx_implications/5.json @@ -430,13 +430,13 @@ } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-c2f729c9baee4e9290dfc7dae09d497f", + "id": "dv-62fab66c5932091e78c15bf3", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -453,32 +453,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -486,8 +481,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -497,16 +492,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome" } ] } @@ -516,98 +512,102 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "criteria provided, single submitter" } - }, + } + ], + "identifier": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32912298:T:C", - "display": "NC_000013.10:32912298:T:C" - } - ] - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "126022" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV001000460.4" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab66c5932091e78c15bf5", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } - }, + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, - "valueString": "T" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6675-8", + "display": "Benign" } ] - }, - "valueString": "C" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN169374", + "display": "not specified" } ] } @@ -617,32 +617,24 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueRange": { - "low": { - "value": 32912298 - } + "valueCodeableConcept": { + "text": "no assertion criteria provided" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "126022" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.174603, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV001551831.1" } ] } @@ -651,7 +643,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15bf3", + "id": "dv-62fab66c5932091e78c15bf9", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -719,8 +711,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" + "code": "CN169374", + "display": "not specified" } ] } @@ -747,19 +739,19 @@ }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001000460.4" + "value": "SCV000693636.1" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-c2f729c9baee4e9290dfc7dae09d497f", + "id": "dv-62fab66c5932091e78c15c04", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -776,32 +768,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -809,8 +796,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -820,16 +807,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2" } ] } @@ -839,37 +827,82 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "criteria provided, single submitter" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "126022" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000744444.1" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab66c5932091e78c15c05", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32912298:T:C", - "display": "NC_000013.10:32912298:T:C" + "system": "http://loinc.org", + "code": "LA6675-8", + "display": "Benign" } ] } @@ -879,49 +912,93 @@ "coding": [ { "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0027672", + "display": "Hereditary cancer-predisposing syndrome" } ] - }, - "valueString": "T" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueString": "C" + "valueCodeableConcept": { + "text": "criteria provided, single submitter" + } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "126022" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000185213.5" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab66c5932091e78c15c08", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -929,8 +1006,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -940,15 +1017,19 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueRange": { - "low": { - "value": 32912298 - } + "valueCodeableConcept": { + "coding": [ + { + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2" + } + ] } }, { @@ -956,17 +1037,25 @@ "coding": [ { "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueQuantity": { - "value": 0.174603, - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "126022" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000743289.1" + } ] } }, @@ -974,7 +1063,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15bf5", + "id": "dv-62fab66c5932091e78c15bf2", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -1042,8 +1131,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "CN517202", + "display": "not provided" } ] } @@ -1070,19 +1159,19 @@ }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001551831.1" + "value": "SCV000778666.1" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-c2f729c9baee4e9290dfc7dae09d497f", + "id": "dv-62fab66c5932091e78c15bf6", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -1099,32 +1188,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -1132,8 +1216,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -1143,16 +1227,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN169374", + "display": "not specified" } ] } @@ -1162,98 +1247,102 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "criteria provided, single submitter" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "126022" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32912298:T:C", - "display": "NC_000013.10:32912298:T:C" - } - ] - } - }, + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000301763.1" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab66c5932091e78c15bf7", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } - }, + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, - "valueString": "T" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6675-8", + "display": "Benign" } ] - }, - "valueString": "C" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2" } ] } @@ -1263,32 +1352,24 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueRange": { - "low": { - "value": 32912298 - } + "valueCodeableConcept": { + "text": "no assertion criteria provided" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "126022" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.174603, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000733249.1" } ] } @@ -1297,7 +1378,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15bf9", + "id": "dv-62fab66c5932091e78c15bfa", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -1365,8 +1446,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2" } ] } @@ -1393,19 +1474,19 @@ }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000693636.1" + "value": "SCV000195977.1" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-c2f729c9baee4e9290dfc7dae09d497f", + "id": "dv-62fab66c5932091e78c15bfd", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -1422,71 +1503,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, + "derivedFrom": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -1494,8 +1531,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -1505,36 +1542,19 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32912298:T:C", - "display": "NC_000013.10:32912298:T:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN517202", + "display": "not provided" } ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" } }, { @@ -1542,76 +1562,24 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] + "text": "criteria provided, single submitter" } - }, + } + ], + "identifier": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32912298 - } - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "126022" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.174603, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000602744.6" } ] } @@ -1620,7 +1588,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15c04", + "id": "dv-62fab66c5932091e78c15bff", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -1688,8 +1656,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" + "code": "C0027672", + "display": "Hereditary cancer-predisposing syndrome" } ] } @@ -1716,19 +1684,19 @@ }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000744444.1" + "value": "SCV002533822.1" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-c2f729c9baee4e9290dfc7dae09d497f", + "id": "dv-62fab66c5932091e78c15c00", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -1745,71 +1713,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, + "derivedFrom": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -1817,8 +1741,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -1828,36 +1752,19 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32912298:T:C", - "display": "NC_000013.10:32912298:T:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome" } ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" } }, { @@ -1865,76 +1772,24 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] + "text": "criteria provided, single submitter" } - }, + } + ], + "identifier": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32912298 - } - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "126022" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.174603, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000494320.1" } ] } @@ -1943,7 +1798,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15c05", + "id": "dv-62fab66c5932091e78c15c02", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -2011,8 +1866,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0027672", - "display": "Hereditary cancer-predisposing syndrome" + "code": "CN169374", + "display": "not specified" } ] } @@ -2028,7 +1883,7 @@ ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion criteria provided" } } ], @@ -2039,19 +1894,19 @@ }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000185213.5" + "value": "SCV001953719.1" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-c2f729c9baee4e9290dfc7dae09d497f", + "id": "dv-62fab66c5932091e78c15bed", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -2068,32 +1923,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -2101,8 +1951,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -2112,16 +1962,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2" } ] } @@ -2131,98 +1982,102 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "criteria provided, single submitter" } - }, + } + ], + "identifier": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32912298:T:C", - "display": "NC_000013.10:32912298:T:C" - } - ] - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "126022" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000154051.1" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab66c5932091e78c15bf0", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } - }, + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, - "valueString": "T" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6675-8", + "display": "Benign" } ] - }, - "valueString": "C" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0346153", + "display": "Familial cancer of breast" } ] } @@ -2232,32 +2087,24 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueRange": { - "low": { - "value": 32912298 - } + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "126022" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.174603, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000541022.1" } ] } @@ -2266,7 +2113,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15c08", + "id": "dv-62fab66c5932091e78c15bf8", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -2334,8 +2181,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" + "code": "CN169374", + "display": "not specified" } ] } @@ -2362,19 +2209,19 @@ }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000743289.1" + "value": "SCV000538459.1" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-c2f729c9baee4e9290dfc7dae09d497f", + "id": "dv-62fab66c5932091e78c15bfc", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -2391,32 +2238,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -2424,8 +2266,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -2435,16 +2277,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN169374", + "display": "not specified" } ] } @@ -2454,37 +2297,82 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "no assertion criteria provided" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "126022" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV001906228.1" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab66c5932091e78c15bfe", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32912298:T:C", - "display": "NC_000013.10:32912298:T:C" + "system": "http://loinc.org", + "code": "LA6675-8", + "display": "Benign" } ] } @@ -2494,49 +2382,93 @@ "coding": [ { "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN169374", + "display": "not specified" } ] - }, - "valueString": "T" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueString": "C" + "valueCodeableConcept": { + "text": "criteria provided, single submitter" + } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "126022" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000586945.1" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab66c5932091e78c15beb", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -2544,8 +2476,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -2555,15 +2487,19 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueRange": { - "low": { - "value": 32912298 - } + "valueCodeableConcept": { + "coding": [ + { + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2" + } + ] } }, { @@ -2571,17 +2507,25 @@ "coding": [ { "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueQuantity": { - "value": 0.174603, - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "text": "no assertion criteria provided" } } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "126022" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000189304.1" + } ] } }, @@ -2589,7 +2533,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15bf2", + "id": "dv-62fab66c5932091e78c15bee", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -2657,8 +2601,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN517202", - "display": "not provided" + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2" } ] } @@ -2674,7 +2618,7 @@ ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "reviewed by expert panel" } } ], @@ -2685,19 +2629,19 @@ }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000778666.1" + "value": "SCV000245028.1" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-c2f729c9baee4e9290dfc7dae09d497f", + "id": "dv-62fab66c5932091e78c15bf4", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -2714,32 +2658,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -2747,8 +2686,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -2758,16 +2697,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0027672", + "display": "Hereditary cancer-predisposing syndrome" } ] } @@ -2777,98 +2717,102 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "criteria provided, single submitter" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "126022" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32912298:T:C", - "display": "NC_000013.10:32912298:T:C" - } - ] - } - }, + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000537340.1" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab66c5932091e78c15bfb", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } - }, + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, - "valueString": "T" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6675-8", + "display": "Benign" } ] - }, - "valueString": "C" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C1838457", + "display": "Fanconi anemia complementation group D1" } ] } @@ -2878,32 +2822,24 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueRange": { - "low": { - "value": 32912298 - } + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "126022" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.174603, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000383688.3" } ] } @@ -2912,7 +2848,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15bf6", + "id": "dv-62fab66c5932091e78c15c01", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -2980,8 +2916,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome" } ] } @@ -3008,19 +2944,19 @@ }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000301763.1" + "value": "SCV002026093.2" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-c2f729c9baee4e9290dfc7dae09d497f", + "id": "dv-62fab66c5932091e78c15c03", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -3037,71 +2973,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, + "derivedFrom": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -3109,8 +3001,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -3120,36 +3012,19 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32912298:T:C", - "display": "NC_000013.10:32912298:T:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2" } ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" } }, { @@ -3157,76 +3032,24 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] + "text": "criteria provided, single submitter" } - }, + } + ], + "identifier": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32912298 - } - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "126022" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.174603, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000383687.3" } ] } @@ -3235,7 +3058,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15bf7", + "id": "dv-62fab66f5932091e78c17cb5", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -3265,7 +3088,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" } ], "component": [ @@ -3303,8 +3126,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" + "code": "C1838457", + "display": "Fanconi anemia complementation group D1" } ] } @@ -3320,18 +3143,18 @@ ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "132779" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000733249.1" + "value": "SCV000383699.3" } ] } @@ -3340,7 +3163,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-c2f729c9baee4e9290dfc7dae09d497f", + "id": "dv-fd6337f92b2a42dbb2c3410bdfcd9c27", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -3432,8 +3255,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "code": "LA6705-3", + "display": "homozygous" } ] } @@ -3452,8 +3275,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32912298:T:C", - "display": "NC_000013.10:32912298:T:C" + "code": "NC_000013.10:32913054:A:G", + "display": "NC_000013.10:32913054:A:G" } ] } @@ -3469,7 +3292,7 @@ ] }, "valueQuantity": { - "value": 0.5, + "value": 1.0, "unit": "relative frequency of a particular allele in the specimen", "system": "http://unitsofmeasure.org", "code": "1" @@ -3485,7 +3308,7 @@ } ] }, - "valueString": "T" + "valueString": "A" }, { "code": { @@ -3497,7 +3320,7 @@ } ] }, - "valueString": "C" + "valueString": "G" }, { "code": { @@ -3531,7 +3354,7 @@ }, "valueRange": { "low": { - "value": 32912298 + "value": 32913054 } } }, @@ -3546,7 +3369,7 @@ ] }, "valueQuantity": { - "value": 0.174603, + "value": 0.994359, "system": "http://unitsofmeasure.org", "code": "1" } @@ -3558,7 +3381,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15bfa", + "id": "dv-62fab66f5932091e78c17cb7", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -3588,7 +3411,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" } ], "component": [ @@ -3650,23 +3473,23 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "132779" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000195977.1" + "value": "SCV000743299.1" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-c2f729c9baee4e9290dfc7dae09d497f", + "id": "dv-62fab66f5932091e78c17cb8", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -3683,32 +3506,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -3716,8 +3534,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -3727,16 +3545,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2" } ] } @@ -3746,98 +3565,102 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "criteria provided, single submitter" } - }, + } + ], + "identifier": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32912298:T:C", - "display": "NC_000013.10:32912298:T:C" - } - ] - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "132779" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000383698.3" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab66f5932091e78c17cb9", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } - }, + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, - "valueString": "T" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6675-8", + "display": "Benign" } ] - }, - "valueString": "C" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0027672", + "display": "Hereditary cancer-predisposing syndrome" } ] } @@ -3847,32 +3670,24 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueRange": { - "low": { - "value": 32912298 - } + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "132779" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.174603, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000537315.1" } ] } @@ -3881,7 +3696,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15bfd", + "id": "dv-62fab66f5932091e78c17cba", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -3911,7 +3726,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" } ], "component": [ @@ -3949,8 +3764,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN517202", - "display": "not provided" + "code": "CN169374", + "display": "not specified" } ] } @@ -3973,23 +3788,23 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "132779" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000602744.6" + "value": "SCV000693637.1" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-c2f729c9baee4e9290dfc7dae09d497f", + "id": "dv-62fab66f5932091e78c17cbf", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -4006,32 +3821,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -4039,8 +3849,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -4050,16 +3860,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2" } ] } @@ -4069,37 +3880,82 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "criteria provided, single submitter" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "132779" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000154035.1" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab66f5932091e78c17cc1", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32912298:T:C", - "display": "NC_000013.10:32912298:T:C" + "system": "http://loinc.org", + "code": "LA6675-8", + "display": "Benign" } ] } @@ -4109,49 +3965,93 @@ "coding": [ { "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN169374", + "display": "not specified" } ] - }, - "valueString": "T" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueString": "C" + "valueCodeableConcept": { + "text": "criteria provided, single submitter" + } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "132779" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000301764.1" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab66f5932091e78c17cb0", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -4159,8 +4059,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -4170,15 +4070,19 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueRange": { - "low": { - "value": 32912298 - } + "valueCodeableConcept": { + "coding": [ + { + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN169374", + "display": "not specified" + } + ] } }, { @@ -4186,17 +4090,25 @@ "coding": [ { "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueQuantity": { - "value": 0.174603, - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "text": "no assertion criteria provided" } } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "132779" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV001905911.1" + } ] } }, @@ -4204,7 +4116,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15bff", + "id": "dv-62fab66f5932091e78c17cb1", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -4234,7 +4146,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" } ], "component": [ @@ -4272,8 +4184,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0027672", - "display": "Hereditary cancer-predisposing syndrome" + "code": "CN517202", + "display": "not provided" } ] } @@ -4296,23 +4208,23 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "132779" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002533822.1" + "value": "SCV000602737.6" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-c2f729c9baee4e9290dfc7dae09d497f", + "id": "dv-62fab66f5932091e78c17cb2", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -4329,32 +4241,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -4362,8 +4269,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -4373,16 +4280,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome" } ] } @@ -4392,37 +4300,82 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "criteria provided, single submitter" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "132779" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV002026104.2" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab66f5932091e78c17cc3", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32912298:T:C", - "display": "NC_000013.10:32912298:T:C" + "system": "http://loinc.org", + "code": "LA6675-8", + "display": "Benign" } ] } @@ -4432,49 +4385,93 @@ "coding": [ { "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN169374", + "display": "not specified" } ] - }, - "valueString": "T" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueString": "C" + "valueCodeableConcept": { + "text": "criteria provided, single submitter" + } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "132779" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000202287.7" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab66f5932091e78c17cc6", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -4482,8 +4479,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -4493,15 +4490,19 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueRange": { - "low": { - "value": 32912298 - } + "valueCodeableConcept": { + "coding": [ + { + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2" + } + ] } }, { @@ -4509,17 +4510,25 @@ "coding": [ { "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueQuantity": { - "value": 0.174603, - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "132779" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV002097617.1" + } ] } }, @@ -4527,7 +4536,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15c00", + "id": "dv-62fab66f5932091e78c17cb3", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -4557,7 +4566,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" } ], "component": [ @@ -4595,8 +4604,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" + "code": "CN517202", + "display": "not provided" } ] } @@ -4612,30 +4621,30 @@ ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion criteria provided" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "132779" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000494320.1" + "value": "SCV000778675.1" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-c2f729c9baee4e9290dfc7dae09d497f", + "id": "dv-62fab66f5932091e78c17cb4", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -4652,32 +4661,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -4685,8 +4689,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -4696,16 +4700,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN169374", + "display": "not specified" } ] } @@ -4715,37 +4720,82 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "no assertion criteria provided" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "132779" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV001951903.1" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab66f5932091e78c17cb6", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32912298:T:C", - "display": "NC_000013.10:32912298:T:C" + "system": "http://loinc.org", + "code": "LA6675-8", + "display": "Benign" } ] } @@ -4755,49 +4805,93 @@ "coding": [ { "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0027672", + "display": "Hereditary cancer-predisposing syndrome" } ] - }, - "valueString": "T" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueString": "C" + "valueCodeableConcept": { + "text": "criteria provided, single submitter" + } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "132779" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000187248.5" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab66f5932091e78c17cc0", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -4805,8 +4899,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -4816,15 +4910,19 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueRange": { - "low": { - "value": 32912298 - } + "valueCodeableConcept": { + "coding": [ + { + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0346153", + "display": "Familial cancer of breast" + } + ] } }, { @@ -4832,17 +4930,25 @@ "coding": [ { "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueQuantity": { - "value": 0.174603, - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "132779" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000541017.1" + } ] } }, @@ -4850,7 +4956,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15c02", + "id": "dv-62fab66f5932091e78c17cc2", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -4880,7 +4986,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" } ], "component": [ @@ -4918,8 +5024,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome" } ] } @@ -4935,30 +5041,30 @@ ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "132779" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001953719.1" + "value": "SCV000494326.1" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-c2f729c9baee4e9290dfc7dae09d497f", + "id": "dv-62fab66f5932091e78c17cc7", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -4975,32 +5081,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -5008,8 +5109,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -5019,16 +5120,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0006142", + "display": "Malignant tumor of breast" } ] } @@ -5038,37 +5140,82 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "no assertion criteria provided" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "132779" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000591909.2" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab66f5932091e78c17cc8", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32912298:T:C", - "display": "NC_000013.10:32912298:T:C" + "system": "http://loinc.org", + "code": "LA6675-8", + "display": "Benign" } ] } @@ -5078,49 +5225,93 @@ "coding": [ { "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN169374", + "display": "not specified" } ] - }, - "valueString": "T" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueString": "C" + "valueCodeableConcept": { + "text": "criteria provided, single submitter" + } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "132779" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000586951.1" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab66f5932091e78c17cbb", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -5128,8 +5319,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -5139,15 +5330,19 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueRange": { - "low": { - "value": 32912298 - } + "valueCodeableConcept": { + "coding": [ + { + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2" + } + ] } }, { @@ -5155,17 +5350,25 @@ "coding": [ { "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueQuantity": { - "value": 0.174603, - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "132779" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000195985.1" + } ] } }, @@ -5173,7 +5376,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15bed", + "id": "dv-62fab66f5932091e78c17cbc", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -5203,7 +5406,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" } ], "component": [ @@ -5258,30 +5461,30 @@ ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "reviewed by expert panel" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "132779" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000154051.1" + "value": "SCV000245032.1" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-c2f729c9baee4e9290dfc7dae09d497f", + "id": "dv-62fab66f5932091e78c17cbd", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -5298,32 +5501,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -5331,8 +5529,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -5342,16 +5540,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome" } ] } @@ -5361,37 +5560,82 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "criteria provided, single submitter" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "132779" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000635377.5" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab66f5932091e78c17cbe", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32912298:T:C", - "display": "NC_000013.10:32912298:T:C" + "system": "http://loinc.org", + "code": "LA6675-8", + "display": "Benign" } ] } @@ -5401,49 +5645,93 @@ "coding": [ { "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN169374", + "display": "not specified" } ] - }, - "valueString": "T" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueString": "C" + "valueCodeableConcept": { + "text": "criteria provided, single submitter" + } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "132779" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000167365.11" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab66f5932091e78c17cc4", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -5451,8 +5739,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -5462,15 +5750,19 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueRange": { - "low": { - "value": 32912298 - } + "valueCodeableConcept": { + "coding": [ + { + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2" + } + ] } }, { @@ -5478,17 +5770,25 @@ "coding": [ { "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueQuantity": { - "value": 0.174603, - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "text": "no assertion criteria provided" } } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "132779" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000733258.1" + } ] } }, @@ -5496,7 +5796,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15bf0", + "id": "dv-62fab66f5932091e78c17cc5", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -5526,7 +5826,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" } ], "component": [ @@ -5564,8 +5864,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0346153", - "display": "Familial cancer of breast" + "code": "CN169374", + "display": "not specified" } ] } @@ -5588,23 +5888,23 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "132779" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000541022.1" + "value": "SCV000268809.3" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-c2f729c9baee4e9290dfc7dae09d497f", + "id": "dv-62fab66f5932091e78c17ccb", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -5621,32 +5921,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -5654,8 +5949,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -5665,16 +5960,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2" } ] } @@ -5684,238 +5980,24 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "no assertion criteria provided" } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32912298:T:C", - "display": "NC_000013.10:32912298:T:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32912298 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.174603, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15bf8", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ + } + ], + "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "132780" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000538459.1" + "value": "SCV000733283.1" } ] } @@ -5924,7 +6006,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-c2f729c9baee4e9290dfc7dae09d497f", + "id": "dv-f61ead8c31904509a974397555d4729d", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -6016,8 +6098,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "code": "LA6705-3", + "display": "homozygous" } ] } @@ -6036,8 +6118,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32912298:T:C", - "display": "NC_000013.10:32912298:T:C" + "code": "NC_000013.10:32915004:G:C", + "display": "NC_000013.10:32915004:G:C" } ] } @@ -6053,7 +6135,7 @@ ] }, "valueQuantity": { - "value": 0.5, + "value": 1.0, "unit": "relative frequency of a particular allele in the specimen", "system": "http://unitsofmeasure.org", "code": "1" @@ -6069,7 +6151,7 @@ } ] }, - "valueString": "T" + "valueString": "G" }, { "code": { @@ -6115,7 +6197,7 @@ }, "valueRange": { "low": { - "value": 32912298 + "value": 32915004 } } }, @@ -6130,7 +6212,7 @@ ] }, "valueQuantity": { - "value": 0.174603, + "value": 0.994199, "system": "http://unitsofmeasure.org", "code": "1" } @@ -6142,7 +6224,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15bfc", + "id": "dv-62fab66f5932091e78c17ccd", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -6172,7 +6254,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" } ], "component": [ @@ -6234,23 +6316,23 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "132780" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001906228.1" + "value": "SCV001958810.1" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-c2f729c9baee4e9290dfc7dae09d497f", + "id": "dv-62fab66f5932091e78c17ccf", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -6267,32 +6349,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -6300,8 +6377,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -6311,16 +6388,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN517202", + "display": "not provided" } ] } @@ -6330,98 +6408,102 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "no assertion criteria provided" } - }, + } + ], + "identifier": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32912298:T:C", - "display": "NC_000013.10:32912298:T:C" - } - ] - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "132780" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000778699.1" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab66f5932091e78c17cd2", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } - }, + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, - "valueString": "T" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6675-8", + "display": "Benign" } ] - }, - "valueString": "C" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2" } ] } @@ -6431,32 +6513,24 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueRange": { - "low": { - "value": 32912298 - } + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "132780" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.174603, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000743322.1" } ] } @@ -6465,7 +6539,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15bfe", + "id": "dv-62fab66f5932091e78c17cd4", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -6495,7 +6569,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" } ], "component": [ @@ -6533,8 +6607,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2" } ] } @@ -6557,23 +6631,23 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "132780" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000586945.1" + "value": "SCV000383747.3" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-c2f729c9baee4e9290dfc7dae09d497f", + "id": "dv-62fab66f5932091e78c17cd9", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -6590,32 +6664,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -6623,8 +6692,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -6634,16 +6703,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0006142", + "display": "Malignant tumor of breast" } ] } @@ -6653,98 +6723,102 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "no assertion criteria provided" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "132780" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32912298:T:C", - "display": "NC_000013.10:32912298:T:C" - } - ] - } - }, + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000592061.2" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab66f5932091e78c17cdb", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } - }, + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, - "valueString": "T" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6675-8", + "display": "Benign" } ] - }, - "valueString": "C" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0027672", + "display": "Hereditary cancer-predisposing syndrome" } ] } @@ -6754,32 +6828,24 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueRange": { - "low": { - "value": 32912298 - } + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "132780" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.174603, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000212687.4" } ] } @@ -6788,7 +6854,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15beb", + "id": "dv-62fab66f5932091e78c17cdc", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -6818,7 +6884,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" } ], "component": [ @@ -6856,8 +6922,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" + "code": "CN169374", + "display": "not specified" } ] } @@ -6873,30 +6939,30 @@ ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "132780" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000189304.1" + "value": "SCV000605771.2" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-c2f729c9baee4e9290dfc7dae09d497f", + "id": "dv-62fab66f5932091e78c17cdd", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -6913,71 +6979,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, + "derivedFrom": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -6985,8 +7007,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -6996,36 +7018,19 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32912298:T:C", - "display": "NC_000013.10:32912298:T:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0027672", + "display": "Hereditary cancer-predisposing syndrome" } ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" } }, { @@ -7033,76 +7038,24 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] + "text": "criteria provided, single submitter" } - }, + } + ], + "identifier": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32912298 - } - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "132780" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.174603, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000537316.1" } ] } @@ -7111,7 +7064,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15bee", + "id": "dv-62fab66f5932091e78c17ce0", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -7141,7 +7094,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" } ], "component": [ @@ -7196,30 +7149,30 @@ ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "text": "criteria provided, single submitter" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "132780" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000245028.1" + "value": "SCV000154059.1" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-c2f729c9baee4e9290dfc7dae09d497f", + "id": "dv-62fab66f5932091e78c17ce1", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -7236,71 +7189,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, + "derivedFrom": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -7308,8 +7217,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -7319,36 +7228,19 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32912298:T:C", - "display": "NC_000013.10:32912298:T:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome" } ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" } }, { @@ -7356,76 +7248,24 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] + "text": "criteria provided, single submitter" } - }, + } + ], + "identifier": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32912298 - } - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "132780" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.174603, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000494339.1" } ] } @@ -7434,7 +7274,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15bf4", + "id": "dv-62fab66f5932091e78c17ce2", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -7464,7 +7304,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" } ], "component": [ @@ -7502,8 +7342,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0027672", - "display": "Hereditary cancer-predisposing syndrome" + "code": "CN169374", + "display": "not specified" } ] } @@ -7519,30 +7359,30 @@ ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion criteria provided" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "132780" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000537340.1" + "value": "SCV001906399.1" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-c2f729c9baee4e9290dfc7dae09d497f", + "id": "dv-62fab66f5932091e78c17cc9", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -7559,32 +7399,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -7592,8 +7427,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -7603,16 +7438,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0346153", + "display": "Familial cancer of breast" } ] } @@ -7622,98 +7458,102 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "criteria provided, single submitter" } - }, + } + ], + "identifier": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32912298:T:C", - "display": "NC_000013.10:32912298:T:C" - } - ] - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "132780" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000541018.1" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab66f5932091e78c17ccc", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } - }, + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, - "valueString": "T" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6675-8", + "display": "Benign" } ] - }, - "valueString": "C" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome" } ] } @@ -7723,32 +7563,24 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueRange": { - "low": { - "value": 32912298 - } + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "132780" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.174603, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV002025800.2" } ] } @@ -7757,7 +7589,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15bfb", + "id": "dv-62fab66f5932091e78c17cd3", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -7787,7 +7619,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" } ], "component": [ @@ -7825,8 +7657,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C1838457", - "display": "Fanconi anemia complementation group D1" + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2" } ] } @@ -7849,23 +7681,23 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "132780" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000383688.3" + "value": "SCV002097618.1" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-c2f729c9baee4e9290dfc7dae09d497f", + "id": "dv-62fab66f5932091e78c17cd5", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -7882,32 +7714,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -7915,8 +7742,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -7926,16 +7753,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2" } ] } @@ -7945,37 +7773,82 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "reviewed by expert panel" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "132780" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000245036.1" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab66f5932091e78c17cdf", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32912298:T:C", - "display": "NC_000013.10:32912298:T:C" + "system": "http://loinc.org", + "code": "LA6675-8", + "display": "Benign" } ] } @@ -7985,49 +7858,93 @@ "coding": [ { "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN169374", + "display": "not specified" } ] - }, - "valueString": "T" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueString": "C" + "valueCodeableConcept": { + "text": "criteria provided, single submitter" + } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "132780" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000167382.11" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab66f5932091e78c17cca", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -8035,8 +7952,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -8046,15 +7963,19 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueRange": { - "low": { - "value": 32912298 - } + "valueCodeableConcept": { + "coding": [ + { + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN169374", + "display": "not specified" + } + ] } }, { @@ -8062,17 +7983,25 @@ "coding": [ { "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueQuantity": { - "value": 0.174603, - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "132780" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000202293.7" + } ] } }, @@ -8080,7 +8009,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15c01", + "id": "dv-62fab66f5932091e78c17cd1", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -8110,7 +8039,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" } ], "component": [ @@ -8148,8 +8077,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" + "code": "C0027672", + "display": "Hereditary cancer-predisposing syndrome" } ] } @@ -8172,23 +8101,23 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "132780" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002026093.2" + "value": "SCV002536241.1" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-c2f729c9baee4e9290dfc7dae09d497f", + "id": "dv-62fab66f5932091e78c17cd6", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -8205,32 +8134,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -8238,8 +8162,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -8249,16 +8173,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN517202", + "display": "not provided" } ] } @@ -8268,133 +8193,24 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "criteria provided, single submitter" } - }, + } + ], + "identifier": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32912298:T:C", - "display": "NC_000013.10:32912298:T:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32912298 - } - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "132780" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.174603, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000602743.6" } ] } @@ -8403,7 +8219,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15c03", + "id": "dv-62fab66f5932091e78c17cde", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -8433,7 +8249,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" } ], "component": [ @@ -8495,229 +8311,11 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "132780" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000383687.3" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-c2f729c9baee4e9290dfc7dae09d497f", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32912298:T:C", - "display": "NC_000013.10:32912298:T:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32912298 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.174603, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "value": "SCV000195998.1" } ] } @@ -8726,7 +8324,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cb5", + "id": "dv-62fab66f5932091e78c17cce", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -8756,7 +8354,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" } ], "component": [ @@ -8794,8 +8392,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C1838457", - "display": "Fanconi anemia complementation group D1" + "code": "CN169374", + "display": "not specified" } ] } @@ -8818,36910 +8416,20 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" + "value": "132780" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000383699.3" + "value": "SCV000586969.1" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-fd6337f92b2a42dbb2c3410bdfcd9c27", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32913054:A:G", - "display": "NC_000013.10:32913054:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32913054 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994359, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cb7", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000743299.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-fd6337f92b2a42dbb2c3410bdfcd9c27", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32913054:A:G", - "display": "NC_000013.10:32913054:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32913054 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994359, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cb8", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000383698.3" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-fd6337f92b2a42dbb2c3410bdfcd9c27", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32913054:A:G", - "display": "NC_000013.10:32913054:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32913054 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994359, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cb9", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0027672", - "display": "Hereditary cancer-predisposing syndrome" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000537315.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-fd6337f92b2a42dbb2c3410bdfcd9c27", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32913054:A:G", - "display": "NC_000013.10:32913054:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32913054 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994359, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cba", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000693637.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-fd6337f92b2a42dbb2c3410bdfcd9c27", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32913054:A:G", - "display": "NC_000013.10:32913054:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32913054 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994359, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cbf", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000154035.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-fd6337f92b2a42dbb2c3410bdfcd9c27", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32913054:A:G", - "display": "NC_000013.10:32913054:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32913054 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994359, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cc1", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000301764.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-fd6337f92b2a42dbb2c3410bdfcd9c27", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32913054:A:G", - "display": "NC_000013.10:32913054:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32913054 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994359, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cb0", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "no assertion criteria provided" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001905911.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-fd6337f92b2a42dbb2c3410bdfcd9c27", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32913054:A:G", - "display": "NC_000013.10:32913054:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32913054 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994359, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cb1", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN517202", - "display": "not provided" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000602737.6" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-fd6337f92b2a42dbb2c3410bdfcd9c27", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32913054:A:G", - "display": "NC_000013.10:32913054:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32913054 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994359, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cb2", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002026104.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-fd6337f92b2a42dbb2c3410bdfcd9c27", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32913054:A:G", - "display": "NC_000013.10:32913054:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32913054 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994359, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cc3", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000202287.7" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-fd6337f92b2a42dbb2c3410bdfcd9c27", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32913054:A:G", - "display": "NC_000013.10:32913054:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32913054 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994359, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cc6", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002097617.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-fd6337f92b2a42dbb2c3410bdfcd9c27", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32913054:A:G", - "display": "NC_000013.10:32913054:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32913054 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994359, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cb3", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN517202", - "display": "not provided" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "no assertion criteria provided" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000778675.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-fd6337f92b2a42dbb2c3410bdfcd9c27", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32913054:A:G", - "display": "NC_000013.10:32913054:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32913054 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994359, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cb4", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "no assertion criteria provided" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001951903.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-fd6337f92b2a42dbb2c3410bdfcd9c27", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32913054:A:G", - "display": "NC_000013.10:32913054:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32913054 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994359, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cb6", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0027672", - "display": "Hereditary cancer-predisposing syndrome" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000187248.5" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-fd6337f92b2a42dbb2c3410bdfcd9c27", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32913054:A:G", - "display": "NC_000013.10:32913054:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32913054 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994359, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cc0", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0346153", - "display": "Familial cancer of breast" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000541017.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-fd6337f92b2a42dbb2c3410bdfcd9c27", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32913054:A:G", - "display": "NC_000013.10:32913054:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32913054 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994359, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cc2", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000494326.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-fd6337f92b2a42dbb2c3410bdfcd9c27", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32913054:A:G", - "display": "NC_000013.10:32913054:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32913054 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994359, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cc7", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0006142", - "display": "Malignant tumor of breast" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "no assertion criteria provided" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000591909.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-fd6337f92b2a42dbb2c3410bdfcd9c27", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32913054:A:G", - "display": "NC_000013.10:32913054:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32913054 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994359, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cc8", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000586951.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-fd6337f92b2a42dbb2c3410bdfcd9c27", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32913054:A:G", - "display": "NC_000013.10:32913054:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32913054 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994359, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cbb", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000195985.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-fd6337f92b2a42dbb2c3410bdfcd9c27", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32913054:A:G", - "display": "NC_000013.10:32913054:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32913054 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994359, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cbc", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "reviewed by expert panel" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000245032.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-fd6337f92b2a42dbb2c3410bdfcd9c27", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32913054:A:G", - "display": "NC_000013.10:32913054:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32913054 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994359, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cbd", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000635377.5" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-fd6337f92b2a42dbb2c3410bdfcd9c27", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32913054:A:G", - "display": "NC_000013.10:32913054:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32913054 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994359, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cbe", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000167365.11" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-fd6337f92b2a42dbb2c3410bdfcd9c27", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32913054:A:G", - "display": "NC_000013.10:32913054:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32913054 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994359, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cc4", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "no assertion criteria provided" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000733258.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-fd6337f92b2a42dbb2c3410bdfcd9c27", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32913054:A:G", - "display": "NC_000013.10:32913054:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32913054 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994359, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cc5", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000268809.3" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-fd6337f92b2a42dbb2c3410bdfcd9c27", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32913054:A:G", - "display": "NC_000013.10:32913054:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32913054 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994359, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17ccb", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "no assertion criteria provided" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000733283.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-f61ead8c31904509a974397555d4729d", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32915004:G:C", - "display": "NC_000013.10:32915004:G:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32915004 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994199, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17ccd", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "no assertion criteria provided" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001958810.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-f61ead8c31904509a974397555d4729d", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32915004:G:C", - "display": "NC_000013.10:32915004:G:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32915004 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994199, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17ccf", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN517202", - "display": "not provided" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "no assertion criteria provided" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000778699.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-f61ead8c31904509a974397555d4729d", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32915004:G:C", - "display": "NC_000013.10:32915004:G:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32915004 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994199, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cd2", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000743322.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-f61ead8c31904509a974397555d4729d", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32915004:G:C", - "display": "NC_000013.10:32915004:G:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32915004 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994199, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cd4", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000383747.3" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-f61ead8c31904509a974397555d4729d", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32915004:G:C", - "display": "NC_000013.10:32915004:G:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32915004 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994199, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cd9", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0006142", - "display": "Malignant tumor of breast" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "no assertion criteria provided" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000592061.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-f61ead8c31904509a974397555d4729d", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32915004:G:C", - "display": "NC_000013.10:32915004:G:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32915004 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994199, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cdb", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0027672", - "display": "Hereditary cancer-predisposing syndrome" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000212687.4" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-f61ead8c31904509a974397555d4729d", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32915004:G:C", - "display": "NC_000013.10:32915004:G:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32915004 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994199, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cdc", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000605771.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-f61ead8c31904509a974397555d4729d", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32915004:G:C", - "display": "NC_000013.10:32915004:G:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32915004 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994199, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cdd", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0027672", - "display": "Hereditary cancer-predisposing syndrome" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000537316.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-f61ead8c31904509a974397555d4729d", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32915004:G:C", - "display": "NC_000013.10:32915004:G:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32915004 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994199, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17ce0", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000154059.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-f61ead8c31904509a974397555d4729d", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32915004:G:C", - "display": "NC_000013.10:32915004:G:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32915004 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994199, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17ce1", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000494339.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-f61ead8c31904509a974397555d4729d", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32915004:G:C", - "display": "NC_000013.10:32915004:G:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32915004 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994199, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17ce2", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "no assertion criteria provided" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001906399.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-f61ead8c31904509a974397555d4729d", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32915004:G:C", - "display": "NC_000013.10:32915004:G:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32915004 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994199, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cc9", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0346153", - "display": "Familial cancer of breast" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000541018.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-f61ead8c31904509a974397555d4729d", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32915004:G:C", - "display": "NC_000013.10:32915004:G:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32915004 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994199, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17ccc", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002025800.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-f61ead8c31904509a974397555d4729d", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32915004:G:C", - "display": "NC_000013.10:32915004:G:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32915004 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994199, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cd3", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002097618.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-f61ead8c31904509a974397555d4729d", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32915004:G:C", - "display": "NC_000013.10:32915004:G:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32915004 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994199, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cd5", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "reviewed by expert panel" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000245036.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-f61ead8c31904509a974397555d4729d", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32915004:G:C", - "display": "NC_000013.10:32915004:G:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32915004 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994199, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cdf", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000167382.11" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-f61ead8c31904509a974397555d4729d", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32915004:G:C", - "display": "NC_000013.10:32915004:G:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32915004 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994199, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cca", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000202293.7" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-f61ead8c31904509a974397555d4729d", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32915004:G:C", - "display": "NC_000013.10:32915004:G:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32915004 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994199, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cd1", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0027672", - "display": "Hereditary cancer-predisposing syndrome" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002536241.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-f61ead8c31904509a974397555d4729d", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32915004:G:C", - "display": "NC_000013.10:32915004:G:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32915004 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994199, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cd6", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN517202", - "display": "not provided" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000602743.6" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-f61ead8c31904509a974397555d4729d", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32915004:G:C", - "display": "NC_000013.10:32915004:G:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32915004 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994199, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cde", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000195998.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-f61ead8c31904509a974397555d4729d", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32915004:G:C", - "display": "NC_000013.10:32915004:G:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32915004 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994199, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cce", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000586969.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-f61ead8c31904509a974397555d4729d", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32915004:G:C", - "display": "NC_000013.10:32915004:G:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32915004 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994199, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cd0", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C1838457", - "display": "Fanconi anemia complementation group D1" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000383746.3" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-f61ead8c31904509a974397555d4729d", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32915004:G:C", - "display": "NC_000013.10:32915004:G:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32915004 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994199, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cd7", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000635514.5" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-f61ead8c31904509a974397555d4729d", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32915004:G:C", - "display": "NC_000013.10:32915004:G:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32915004 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994199, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cd8", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000693639.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-f61ead8c31904509a974397555d4729d", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32915004:G:C", - "display": "NC_000013.10:32915004:G:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32915004 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994199, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cda", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000301767.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-f61ead8c31904509a974397555d4729d", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32915004:G:C", - "display": "NC_000013.10:32915004:G:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32915004 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994199, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6705932091e78c186e2", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "text": "not provided" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "no assertion provided" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "133738" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000084509.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-e2e6891735854abd8abb5a30cc6cc0e0", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32929386:T:C", - "display": "NC_000013.10:32929386:T:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32929386 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994876, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6705932091e78c186f5", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "133738" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001139178.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-e2e6891735854abd8abb5a30cc6cc0e0", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32929386:T:C", - "display": "NC_000013.10:32929386:T:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32929386 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994876, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6705932091e78c186e0", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "no assertion criteria provided" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "133738" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001930871.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-e2e6891735854abd8abb5a30cc6cc0e0", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32929386:T:C", - "display": "NC_000013.10:32929386:T:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32929386 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994876, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6705932091e78c186e1", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "no assertion criteria provided" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "133738" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001550303.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-e2e6891735854abd8abb5a30cc6cc0e0", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32929386:T:C", - "display": "NC_000013.10:32929386:T:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32929386 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994876, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6705932091e78c186e5", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA26333-7", - "display": "Uncertain significance" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C1527349", - "display": "Ductal breast carcinoma" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "no assertion criteria provided" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "133738" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000258682.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-e2e6891735854abd8abb5a30cc6cc0e0", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32929386:T:C", - "display": "NC_000013.10:32929386:T:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32929386 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994876, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6705932091e78c186e6", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "no assertion criteria provided" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "133738" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001906256.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-e2e6891735854abd8abb5a30cc6cc0e0", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32929386:T:C", - "display": "NC_000013.10:32929386:T:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32929386 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994876, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6705932091e78c186ec", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "133738" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000202300.7" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-e2e6891735854abd8abb5a30cc6cc0e0", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32929386:T:C", - "display": "NC_000013.10:32929386:T:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32929386 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994876, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6705932091e78c186f3", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "133738" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002097591.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-e2e6891735854abd8abb5a30cc6cc0e0", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32929386:T:C", - "display": "NC_000013.10:32929386:T:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32929386 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994876, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6705932091e78c186e4", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN517202", - "display": "not provided" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "133738" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000602752.5" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-e2e6891735854abd8abb5a30cc6cc0e0", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32929386:T:C", - "display": "NC_000013.10:32929386:T:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32929386 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994876, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6705932091e78c186e7", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "133738" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001000149.4" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-e2e6891735854abd8abb5a30cc6cc0e0", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32929386:T:C", - "display": "NC_000013.10:32929386:T:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32929386 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994876, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6705932091e78c186e9", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "no assertion criteria provided" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "133738" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001979638.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-e2e6891735854abd8abb5a30cc6cc0e0", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32929386:T:C", - "display": "NC_000013.10:32929386:T:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32929386 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994876, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6705932091e78c186ea", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "133738" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000268811.3" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-e2e6891735854abd8abb5a30cc6cc0e0", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32929386:T:C", - "display": "NC_000013.10:32929386:T:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32929386 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994876, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6705932091e78c186e3", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "133738" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002025816.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-e2e6891735854abd8abb5a30cc6cc0e0", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32929386:T:C", - "display": "NC_000013.10:32929386:T:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32929386 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994876, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6705932091e78c186e8", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "no assertion criteria provided" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "133738" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001744232.3" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-e2e6891735854abd8abb5a30cc6cc0e0", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32929386:T:C", - "display": "NC_000013.10:32929386:T:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32929386 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994876, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15a82", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-b49765544a4f4ffdb9856882d59ea768" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "125927" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000383816.3" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-b49765544a4f4ffdb9856882d59ea768", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32973011:A:C", - "display": "NC_000013.10:32973011:A:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32973011 - } - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15a84", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-b49765544a4f4ffdb9856882d59ea768" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA26333-7", - "display": "Uncertain significance" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "no assertion criteria provided" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "125927" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000145775.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-b49765544a4f4ffdb9856882d59ea768", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32973011:A:C", - "display": "NC_000013.10:32973011:A:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32973011 - } - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15a86", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-b49765544a4f4ffdb9856882d59ea768" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "no assertion criteria provided" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "125927" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001906326.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-b49765544a4f4ffdb9856882d59ea768", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32973011:A:C", - "display": "NC_000013.10:32973011:A:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32973011 - } - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15a8b", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-b49765544a4f4ffdb9856882d59ea768" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "reviewed by expert panel" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "125927" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000245315.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-b49765544a4f4ffdb9856882d59ea768", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32973011:A:C", - "display": "NC_000013.10:32973011:A:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32973011 - } - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15a87", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-b49765544a4f4ffdb9856882d59ea768" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "no assertion criteria provided" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "125927" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001548650.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-b49765544a4f4ffdb9856882d59ea768", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32973011:A:C", - "display": "NC_000013.10:32973011:A:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32973011 - } - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15a89", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-b49765544a4f4ffdb9856882d59ea768" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN517202", - "display": "not provided" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "125927" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000883471.4" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-b49765544a4f4ffdb9856882d59ea768", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32973011:A:C", - "display": "NC_000013.10:32973011:A:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32973011 - } - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15a88", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-b49765544a4f4ffdb9856882d59ea768" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "125927" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000693649.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-b49765544a4f4ffdb9856882d59ea768", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32973011:A:C", - "display": "NC_000013.10:32973011:A:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32973011 - } - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15a83", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-b49765544a4f4ffdb9856882d59ea768" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C1838457", - "display": "Fanconi anemia complementation group D1" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "125927" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000383815.3" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-b49765544a4f4ffdb9856882d59ea768", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32973011:A:C", - "display": "NC_000013.10:32973011:A:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32973011 - } - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15a85", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-b49765544a4f4ffdb9856882d59ea768" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "125927" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000743532.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-b49765544a4f4ffdb9856882d59ea768", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32973011:A:C", - "display": "NC_000013.10:32973011:A:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32973011 - } - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6455932091e78bfda01", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "42942" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000170522.11" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-45d90d04eaf548d5b98b6528f6fdc045", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000014.8" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000014.8:23892887:A:G", - "display": "NC_000014.8:23892887:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 23892887 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.308092, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6455932091e78bfda04", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552004", - "display": "MYH7-related skeletal myopathy" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "42942" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000386097.3" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-45d90d04eaf548d5b98b6528f6fdc045", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000014.8" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000014.8:23892887:A:G", - "display": "NC_000014.8:23892887:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 23892887 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.308092, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6455932091e78bfda06", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "42942" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000151919.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-45d90d04eaf548d5b98b6528f6fdc045", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000014.8" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000014.8:23892887:A:G", - "display": "NC_000014.8:23892887:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 23892887 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.308092, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6455932091e78bfda09", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C1842160", - "display": "Myosin storage myopathy" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "42942" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000386099.3" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-45d90d04eaf548d5b98b6528f6fdc045", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000014.8" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000014.8:23892887:A:G", - "display": "NC_000014.8:23892887:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 23892887 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.308092, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6455932091e78bfda0a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C1834481", - "display": "Dilated cardiomyopathy 1S" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "42942" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000386095.3" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-45d90d04eaf548d5b98b6528f6fdc045", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000014.8" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000014.8:23892887:A:G", - "display": "NC_000014.8:23892887:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 23892887 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.308092, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6455932091e78bfda0c", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C3495498", - "display": "Hypertrophic cardiomyopathy 1" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "42942" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000386098.3" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-45d90d04eaf548d5b98b6528f6fdc045", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000014.8" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000014.8:23892887:A:G", - "display": "NC_000014.8:23892887:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 23892887 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.308092, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6455932091e78bfda17", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA26333-7", - "display": "Uncertain significance" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN517202", - "display": "not provided" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "no assertion criteria provided" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "42942" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001551199.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-45d90d04eaf548d5b98b6528f6fdc045", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000014.8" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000014.8:23892887:A:G", - "display": "NC_000014.8:23892887:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 23892887 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.308092, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6455932091e78bfda19", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "no assertion criteria provided" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "42942" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001920413.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-45d90d04eaf548d5b98b6528f6fdc045", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000014.8" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000014.8:23892887:A:G", - "display": "NC_000014.8:23892887:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 23892887 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.308092, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6455932091e78bfda02", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "no assertion criteria provided" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "42942" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001930264.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-45d90d04eaf548d5b98b6528f6fdc045", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000014.8" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000014.8:23892887:A:G", - "display": "NC_000014.8:23892887:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 23892887 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.308092, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6455932091e78bfda08", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "no assertion criteria provided" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "42942" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001951128.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-45d90d04eaf548d5b98b6528f6fdc045", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000014.8" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000014.8:23892887:A:G", - "display": "NC_000014.8:23892887:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 23892887 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.308092, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6455932091e78bfda0f", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "no assertion criteria provided" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "42942" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001975767.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-45d90d04eaf548d5b98b6528f6fdc045", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000014.8" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000014.8:23892887:A:G", - "display": "NC_000014.8:23892887:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 23892887 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.308092, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6455932091e78bfda14", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "42942" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000303219.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-45d90d04eaf548d5b98b6528f6fdc045", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000014.8" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000014.8:23892887:A:G", - "display": "NC_000014.8:23892887:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 23892887 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.308092, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6455932091e78bfda0e", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "42942" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001433073.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-45d90d04eaf548d5b98b6528f6fdc045", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000014.8" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000014.8:23892887:A:G", - "display": "NC_000014.8:23892887:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 23892887 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.308092, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6455932091e78bfda12", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0878544", - "display": "Cardiomyopathy" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "reviewed by expert panel" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "42942" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000564487.4" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-45d90d04eaf548d5b98b6528f6fdc045", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000014.8" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000014.8:23892887:A:G", - "display": "NC_000014.8:23892887:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 23892887 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.308092, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6455932091e78bfda15", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "42942" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000059486.5" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-45d90d04eaf548d5b98b6528f6fdc045", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000014.8" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000014.8:23892887:A:G", - "display": "NC_000014.8:23892887:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 23892887 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.308092, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6455932091e78bfda18", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0007194", - "display": "Hypertrophic cardiomyopathy" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "42942" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001000422.4" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-45d90d04eaf548d5b98b6528f6fdc045", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000014.8" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000014.8:23892887:A:G", - "display": "NC_000014.8:23892887:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 23892887 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.308092, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6455932091e78bfda03", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4021133", - "display": "Left ventricular noncompaction cardiomyopathy" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "42942" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000386100.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-45d90d04eaf548d5b98b6528f6fdc045", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000014.8" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000014.8:23892887:A:G", - "display": "NC_000014.8:23892887:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 23892887 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.308092, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6455932091e78bfda07", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "no assertion criteria provided" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "42942" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001742640.3" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-45d90d04eaf548d5b98b6528f6fdc045", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000014.8" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000014.8:23892887:A:G", - "display": "NC_000014.8:23892887:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 23892887 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.308092, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6455932091e78bfda0d", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN230736", - "display": "Cardiovascular phenotype" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "42942" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000317659.5" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-45d90d04eaf548d5b98b6528f6fdc045", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000014.8" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000014.8:23892887:A:G", - "display": "NC_000014.8:23892887:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 23892887 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.308092, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6455932091e78bfda16", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0878544", - "display": "Cardiomyopathy" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "42942" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000902546.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-45d90d04eaf548d5b98b6528f6fdc045", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000014.8" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000014.8:23892887:A:G", - "display": "NC_000014.8:23892887:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 23892887 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.308092, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6355932091e78bf4ad5", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN517202", - "display": "not provided" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "no assertion criteria provided" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "14095" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001972763.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-0e81b678f2aa4151b1cba965d0fbaab7", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000014.8" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000014.8:23895022:G:A", - "display": "NC_000014.8:23895022:G:A" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 23895022 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 1.1942e-05, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6355932091e78bf4ad7", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C3495498", - "display": "Hypertrophic cardiomyopathy 1" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "14095" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000212630.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-0e81b678f2aa4151b1cba965d0fbaab7", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000014.8" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000014.8:23895022:G:A", - "display": "NC_000014.8:23895022:G:A" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 23895022 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 1.1942e-05, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6355932091e78bf4ae5", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN230736", - "display": "Cardiovascular phenotype" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "14095" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000318794.5" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-0e81b678f2aa4151b1cba965d0fbaab7", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000014.8" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000014.8:23895022:G:A", - "display": "NC_000014.8:23895022:G:A" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 23895022 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 1.1942e-05, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6355932091e78bf4ae6", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN517202", - "display": "not provided" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "14095" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001249810.10" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-0e81b678f2aa4151b1cba965d0fbaab7", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000014.8" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000014.8:23895022:G:A", - "display": "NC_000014.8:23895022:G:A" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 23895022 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 1.1942e-05, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6355932091e78bf4aea", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0007194", - "display": "Hypertrophic cardiomyopathy" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "reviewed by expert panel" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "14095" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000564425.4" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-0e81b678f2aa4151b1cba965d0fbaab7", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000014.8" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000014.8:23895022:G:A", - "display": "NC_000014.8:23895022:G:A" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 23895022 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 1.1942e-05, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6355932091e78bf4aef", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C3495498", - "display": "Hypertrophic cardiomyopathy 1" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "14095" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002538613.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-0e81b678f2aa4151b1cba965d0fbaab7", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000014.8" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000014.8:23895022:G:A", - "display": "NC_000014.8:23895022:G:A" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 23895022 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 1.1942e-05, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6355932091e78bf4afb", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA26332-9", - "display": "Likely pathogenic" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN517202", - "display": "not provided" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "no assertion criteria provided" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "14095" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001739623.3" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-0e81b678f2aa4151b1cba965d0fbaab7", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000014.8" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000014.8:23895022:G:A", - "display": "NC_000014.8:23895022:G:A" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 23895022 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 1.1942e-05, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6355932091e78bf4ad6", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA26332-9", - "display": "Likely pathogenic" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0949658", - "display": "Primary familial hypertrophic cardiomyopathy" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "no assertion criteria provided" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "14095" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000188798.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-0e81b678f2aa4151b1cba965d0fbaab7", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000014.8" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000014.8:23895022:G:A", - "display": "NC_000014.8:23895022:G:A" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 23895022 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 1.1942e-05, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6355932091e78bf4add", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN517202", - "display": "not provided" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "no assertion criteria provided" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "14095" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000280314.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-0e81b678f2aa4151b1cba965d0fbaab7", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000014.8" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000014.8:23895022:G:A", - "display": "NC_000014.8:23895022:G:A" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 23895022 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 1.1942e-05, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6355932091e78bf4ade", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN517202", - "display": "not provided" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "no assertion criteria provided" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "14095" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002017675.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-0e81b678f2aa4151b1cba965d0fbaab7", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000014.8" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000014.8:23895022:G:A", - "display": "NC_000014.8:23895022:G:A" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 23895022 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 1.1942e-05, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6355932091e78bf4adf", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0007194", - "display": "Hypertrophic cardiomyopathy" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "14095" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000546190.6" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-0e81b678f2aa4151b1cba965d0fbaab7", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000014.8" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000014.8:23895022:G:A", - "display": "NC_000014.8:23895022:G:A" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 23895022 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 1.1942e-05, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6355932091e78bf4b17", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0878544", - "display": "Cardiomyopathy" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "14095" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001352585.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-0e81b678f2aa4151b1cba965d0fbaab7", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000014.8" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000014.8:23895022:G:A", - "display": "NC_000014.8:23895022:G:A" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 23895022 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 1.1942e-05, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6355932091e78bf4b1a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN517202", - "display": "not provided" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "no assertion criteria provided" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "14095" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001959712.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-0e81b678f2aa4151b1cba965d0fbaab7", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000014.8" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000014.8:23895022:G:A", - "display": "NC_000014.8:23895022:G:A" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 23895022 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 1.1942e-05, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6355932091e78bf4ae3", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0007194", - "display": "Hypertrophic cardiomyopathy" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "14095" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000059423.7" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-0e81b678f2aa4151b1cba965d0fbaab7", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000014.8" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000014.8:23895022:G:A", - "display": "NC_000014.8:23895022:G:A" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 23895022 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 1.1942e-05, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6355932091e78bf4ad8", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C3495498", - "display": "Hypertrophic cardiomyopathy 1" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "no assertion criteria provided" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "14095" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000035408.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-0e81b678f2aa4151b1cba965d0fbaab7", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000014.8" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000014.8:23895022:G:A", - "display": "NC_000014.8:23895022:G:A" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 23895022 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 1.1942e-05, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6355932091e78bf4ae4", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN517202", - "display": "not provided" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "14095" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000208451.14" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-0e81b678f2aa4151b1cba965d0fbaab7", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000014.8" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000014.8:23895022:G:A", - "display": "NC_000014.8:23895022:G:A" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 23895022 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 1.1942e-05, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6355932091e78bf4afa", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C3495498", - "display": "Hypertrophic cardiomyopathy 1" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "14095" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002059672.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-0e81b678f2aa4151b1cba965d0fbaab7", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000014.8" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000014.8:23895022:G:A", - "display": "NC_000014.8:23895022:G:A" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 23895022 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 1.1942e-05, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6315932091e78bf2a75", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "3683" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000294463.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-46597e63d927405d8818e0867d0e521c", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11210927:C:T", - "display": "NC_000019.9:11210927:C:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 11210927 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 7.96318e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6315932091e78bf2a79", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "reviewed by expert panel" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "3683" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002506409.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-46597e63d927405d8818e0867d0e521c", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11210927:C:T", - "display": "NC_000019.9:11210927:C:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 11210927 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 7.96318e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6315932091e78bf2a7b", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "3683" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000588484.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-46597e63d927405d8818e0867d0e521c", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11210927:C:T", - "display": "NC_000019.9:11210927:C:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 11210927 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 7.96318e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6315932091e78bf2a7c", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "no assertion criteria provided" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "3683" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000606015.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-46597e63d927405d8818e0867d0e521c", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11210927:C:T", - "display": "NC_000019.9:11210927:C:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 11210927 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 7.96318e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6315932091e78bf2a7e", + "id": "dv-62fab66f5932091e78c17cd0", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -45751,7 +8459,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" } ], "component": [ @@ -45769,8 +8477,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -45789,8 +8497,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "C1838457", + "display": "Fanconi anemia complementation group D1" } ] } @@ -45813,23 +8521,23 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "3683" + "value": "132780" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000987040.1" + "value": "SCV000383746.3" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-46597e63d927405d8818e0867d0e521c", + "id": "dv-62fab66f5932091e78c17cd7", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -45846,32 +8554,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -45879,8 +8582,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -45890,16 +8593,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome" } ] } @@ -45909,37 +8613,82 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "criteria provided, single submitter" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "132780" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000635514.5" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab66f5932091e78c17cd8", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11210927:C:T", - "display": "NC_000019.9:11210927:C:T" + "system": "http://loinc.org", + "code": "LA6675-8", + "display": "Benign" } ] } @@ -45949,49 +8698,93 @@ "coding": [ { "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN169374", + "display": "not specified" } ] - }, - "valueString": "C" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueString": "T" + "valueCodeableConcept": { + "text": "criteria provided, single submitter" + } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "132780" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000693639.1" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab66f5932091e78c17cda", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -45999,8 +8792,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -46010,15 +8803,19 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueRange": { - "low": { - "value": 11210927 - } + "valueCodeableConcept": { + "coding": [ + { + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN169374", + "display": "not specified" + } + ] } }, { @@ -46026,17 +8823,25 @@ "coding": [ { "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueQuantity": { - "value": 7.96318e-06, - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "132780" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000301767.1" + } ] } }, @@ -46044,7 +8849,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6315932091e78bf2a76", + "id": "dv-62fab6705932091e78c186e2", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -46074,7 +8879,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" + "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" } ], "component": [ @@ -46089,13 +8894,7 @@ ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" - } - ] + "text": "not provided" } }, { @@ -46112,8 +8911,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "CN169374", + "display": "not specified" } ] } @@ -46129,18 +8928,18 @@ ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "no assertion provided" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "3683" + "value": "133738" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002017112.1" + "value": "SCV000084509.1" } ] } @@ -46149,7 +8948,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-46597e63d927405d8818e0867d0e521c", + "id": "dv-e2e6891735854abd8abb5a30cc6cc0e0", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -46222,7 +9021,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000013.10" } ] } @@ -46241,8 +9040,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "code": "LA6705-3", + "display": "homozygous" } ] } @@ -46261,8 +9060,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11210927:C:T", - "display": "NC_000019.9:11210927:C:T" + "code": "NC_000013.10:32929386:T:C", + "display": "NC_000013.10:32929386:T:C" } ] } @@ -46278,7 +9077,7 @@ ] }, "valueQuantity": { - "value": 0.5, + "value": 1.0, "unit": "relative frequency of a particular allele in the specimen", "system": "http://unitsofmeasure.org", "code": "1" @@ -46294,7 +9093,7 @@ } ] }, - "valueString": "C" + "valueString": "T" }, { "code": { @@ -46306,7 +9105,7 @@ } ] }, - "valueString": "T" + "valueString": "C" }, { "code": { @@ -46340,7 +9139,7 @@ }, "valueRange": { "low": { - "value": 11210927 + "value": 32929386 } } }, @@ -46355,7 +9154,7 @@ ] }, "valueQuantity": { - "value": 7.96318e-06, + "value": 0.994876, "system": "http://unitsofmeasure.org", "code": "1" } @@ -46367,7 +9166,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6315932091e78bf2a7d", + "id": "dv-62fab6705932091e78c186f5", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -46397,7 +9196,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" + "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" } ], "component": [ @@ -46415,8 +9214,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -46435,8 +9234,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN517202", - "display": "not provided" + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2" } ] } @@ -46459,23 +9258,23 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "3683" + "value": "133738" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002027963.1" + "value": "SCV001139178.1" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-46597e63d927405d8818e0867d0e521c", + "id": "dv-62fab6705932091e78c186e0", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -46492,32 +9291,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -46525,8 +9319,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -46536,16 +9330,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN169374", + "display": "not specified" } ] } @@ -46555,37 +9350,82 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "no assertion criteria provided" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "133738" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV001930871.1" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab6705932091e78c186e1", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11210927:C:T", - "display": "NC_000019.9:11210927:C:T" + "system": "http://loinc.org", + "code": "LA6675-8", + "display": "Benign" } ] } @@ -46595,49 +9435,93 @@ "coding": [ { "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN169374", + "display": "not specified" } ] - }, - "valueString": "C" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueString": "T" + "valueCodeableConcept": { + "text": "no assertion criteria provided" + } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "133738" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV001550303.1" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab6705932091e78c186e5", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -46645,8 +9529,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "LA26333-7", + "display": "Uncertain significance" } ] } @@ -46656,15 +9540,19 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueRange": { - "low": { - "value": 11210927 - } + "valueCodeableConcept": { + "coding": [ + { + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C1527349", + "display": "Ductal breast carcinoma" + } + ] } }, { @@ -46672,17 +9560,25 @@ "coding": [ { "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueQuantity": { - "value": 7.96318e-06, - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "text": "no assertion criteria provided" } } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "133738" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000258682.1" + } ] } }, @@ -46690,7 +9586,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6315932091e78bf2a7f", + "id": "dv-62fab6705932091e78c186e6", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -46720,7 +9616,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" + "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" } ], "component": [ @@ -46738,8 +9634,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -46758,8 +9654,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "CN169374", + "display": "not specified" } ] } @@ -46775,30 +9671,30 @@ ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion criteria provided" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "3683" + "value": "133738" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000503101.1" + "value": "SCV001906256.1" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-46597e63d927405d8818e0867d0e521c", + "id": "dv-62fab6705932091e78c186ec", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -46815,32 +9711,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -46848,8 +9739,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -46859,16 +9750,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN169374", + "display": "not specified" } ] } @@ -46878,37 +9770,82 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "criteria provided, single submitter" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "133738" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000202300.7" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab6705932091e78c186f3", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11210927:C:T", - "display": "NC_000019.9:11210927:C:T" + "system": "http://loinc.org", + "code": "LA6675-8", + "display": "Benign" } ] } @@ -46918,49 +9855,93 @@ "coding": [ { "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2" } ] - }, - "valueString": "C" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueString": "T" + "valueCodeableConcept": { + "text": "criteria provided, single submitter" + } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "133738" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV002097591.1" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab6705932091e78c186e4", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -46968,8 +9949,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -46979,15 +9960,19 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueRange": { - "low": { - "value": 11210927 - } + "valueCodeableConcept": { + "coding": [ + { + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN517202", + "display": "not provided" + } + ] } }, { @@ -46995,17 +9980,25 @@ "coding": [ { "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueQuantity": { - "value": 7.96318e-06, - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "133738" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000602752.5" + } ] } }, @@ -47013,7 +10006,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6315932091e78bf2a71", + "id": "dv-62fab6705932091e78c186e7", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -47043,7 +10036,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" + "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" } ], "component": [ @@ -47061,8 +10054,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -47081,8 +10074,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0020445", - "display": "Familial hypercholesterolemia" + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome" } ] } @@ -47105,23 +10098,23 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "3683" + "value": "133738" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000544678.5" + "value": "SCV001000149.4" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-46597e63d927405d8818e0867d0e521c", + "id": "dv-62fab6705932091e78c186e9", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -47138,71 +10131,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, + "derivedFrom": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" - } - ] - } - }, + "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -47210,8 +10159,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -47221,36 +10170,19 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11210927:C:T", - "display": "NC_000019.9:11210927:C:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN169374", + "display": "not specified" } ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" } }, { @@ -47258,76 +10190,24 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] + "text": "no assertion criteria provided" } - }, + } + ], + "identifier": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 11210927 - } - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "133738" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 7.96318e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV001979638.1" } ] } @@ -47336,7 +10216,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6315932091e78bf2a78", + "id": "dv-62fab6705932091e78c186ea", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -47366,7 +10246,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" + "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" } ], "component": [ @@ -47384,8 +10264,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -47404,8 +10284,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "CN169374", + "display": "not specified" } ] } @@ -47428,23 +10308,23 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "3683" + "value": "133738" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000583630.1" + "value": "SCV000268811.3" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-46597e63d927405d8818e0867d0e521c", + "id": "dv-62fab6705932091e78c186e3", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -47461,32 +10341,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -47494,8 +10369,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -47505,16 +10380,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome" } ] } @@ -47524,98 +10400,102 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "criteria provided, single submitter" } - }, + } + ], + "identifier": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11210927:C:T", - "display": "NC_000019.9:11210927:C:T" - } - ] - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "133738" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV002025816.2" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab6705932091e78c186e8", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } - }, + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, - "valueString": "C" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6675-8", + "display": "Benign" } ] - }, - "valueString": "T" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN169374", + "display": "not specified" } ] } @@ -47625,32 +10505,24 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueRange": { - "low": { - "value": 11210927 - } + "valueCodeableConcept": { + "text": "no assertion criteria provided" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "133738" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 7.96318e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV001744232.3" } ] } @@ -47659,7 +10531,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6315932091e78bf2a7a", + "id": "dv-62fab66c5932091e78c15a82", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -47689,7 +10561,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" + "reference": "Observation/dv-b49765544a4f4ffdb9856882d59ea768" } ], "component": [ @@ -47707,8 +10579,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -47727,8 +10599,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2" } ] } @@ -47751,11 +10623,11 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "3683" + "value": "125927" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000607415.1" + "value": "SCV000383816.3" } ] } @@ -47764,7 +10636,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-46597e63d927405d8818e0867d0e521c", + "id": "dv-b49765544a4f4ffdb9856882d59ea768", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -47837,7 +10709,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000013.10" } ] } @@ -47856,8 +10728,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "code": "LA6705-3", + "display": "homozygous" } ] } @@ -47876,8 +10748,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11210927:C:T", - "display": "NC_000019.9:11210927:C:T" + "code": "NC_000013.10:32973011:A:C", + "display": "NC_000013.10:32973011:A:C" } ] } @@ -47893,7 +10765,7 @@ ] }, "valueQuantity": { - "value": 0.5, + "value": 1.0, "unit": "relative frequency of a particular allele in the specimen", "system": "http://unitsofmeasure.org", "code": "1" @@ -47909,7 +10781,7 @@ } ] }, - "valueString": "C" + "valueString": "A" }, { "code": { @@ -47921,7 +10793,7 @@ } ] }, - "valueString": "T" + "valueString": "C" }, { "code": { @@ -47937,8 +10809,85 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "LA30100-4", + "display": "0-based interval counting" + } + ] + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "81254-5", + "display": "Variant exact start-end" + } + ] + }, + "valueRange": { + "low": { + "value": 32973011 + } + } + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab66c5932091e78c15a84", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-b49765544a4f4ffdb9856882d59ea768" + } + ], + "component": [ + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "53037-8", + "display": "Genetic variation clinical significance" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA26333-7", + "display": "Uncertain significance" } ] } @@ -47948,15 +10897,19 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueRange": { - "low": { - "value": 11210927 - } + "valueCodeableConcept": { + "coding": [ + { + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2" + } + ] } }, { @@ -47964,17 +10917,25 @@ "coding": [ { "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueQuantity": { - "value": 7.96318e-06, - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "text": "no assertion criteria provided" } } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "125927" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000145775.1" + } ] } }, @@ -47982,7 +10943,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6315932091e78bf2a80", + "id": "dv-62fab66c5932091e78c15a86", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -48012,7 +10973,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" + "reference": "Observation/dv-b49765544a4f4ffdb9856882d59ea768" } ], "component": [ @@ -48030,8 +10991,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -48050,8 +11011,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0020445", - "display": "Familial hypercholesterolemia" + "code": "CN169374", + "display": "not specified" } ] } @@ -48074,23 +11035,23 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "3683" + "value": "125927" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002086359.1" + "value": "SCV001906326.1" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-46597e63d927405d8818e0867d0e521c", + "id": "dv-62fab66c5932091e78c15a8b", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -48107,32 +11068,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-b49765544a4f4ffdb9856882d59ea768" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -48140,8 +11096,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -48151,16 +11107,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2" } ] } @@ -48170,98 +11127,102 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "reviewed by expert panel" } - }, + } + ], + "identifier": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11210927:C:T", - "display": "NC_000019.9:11210927:C:T" - } - ] - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "125927" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000245315.1" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab66c5932091e78c15a87", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } - }, + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-b49765544a4f4ffdb9856882d59ea768" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, - "valueString": "C" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6675-8", + "display": "Benign" } ] - }, - "valueString": "T" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN169374", + "display": "not specified" } ] } @@ -48271,32 +11232,24 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueRange": { - "low": { - "value": 11210927 - } + "valueCodeableConcept": { + "text": "no assertion criteria provided" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "125927" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 7.96318e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV001548650.1" } ] } @@ -48305,7 +11258,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6315932091e78bf2a6e", + "id": "dv-62fab66c5932091e78c15a89", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -48335,7 +11288,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" + "reference": "Observation/dv-b49765544a4f4ffdb9856882d59ea768" } ], "component": [ @@ -48353,8 +11306,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -48373,8 +11326,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "CN517202", + "display": "not provided" } ] } @@ -48397,23 +11350,23 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "3683" + "value": "125927" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001653581.1" + "value": "SCV000883471.4" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-46597e63d927405d8818e0867d0e521c", + "id": "dv-62fab66c5932091e78c15a88", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -48430,32 +11383,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-b49765544a4f4ffdb9856882d59ea768" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -48463,8 +11411,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -48474,16 +11422,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN169374", + "display": "not specified" } ] } @@ -48493,37 +11442,82 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "criteria provided, single submitter" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "125927" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000693649.1" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab66c5932091e78c15a83", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-b49765544a4f4ffdb9856882d59ea768" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11210927:C:T", - "display": "NC_000019.9:11210927:C:T" + "system": "http://loinc.org", + "code": "LA6675-8", + "display": "Benign" } ] } @@ -48533,49 +11527,93 @@ "coding": [ { "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C1838457", + "display": "Fanconi anemia complementation group D1" } ] - }, - "valueString": "C" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueString": "T" + "valueCodeableConcept": { + "text": "criteria provided, single submitter" + } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "125927" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000383815.3" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab66c5932091e78c15a85", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-b49765544a4f4ffdb9856882d59ea768" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -48583,8 +11621,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -48594,15 +11632,19 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueRange": { - "low": { - "value": 11210927 - } + "valueCodeableConcept": { + "coding": [ + { + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2" + } + ] } }, { @@ -48610,17 +11652,25 @@ "coding": [ { "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueQuantity": { - "value": 7.96318e-06, - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "125927" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000743532.1" + } ] } }, @@ -48628,7 +11678,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6315932091e78bf2a77", + "id": "dv-62fab6455932091e78bfda01", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -48658,7 +11708,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" + "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" } ], "component": [ @@ -48676,8 +11726,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -48696,8 +11746,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN517202", - "display": "not provided" + "code": "CN169374", + "display": "not specified" } ] } @@ -48713,18 +11763,18 @@ ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "3683" + "value": "42942" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000925133.1" + "value": "SCV000170522.11" } ] } @@ -48733,7 +11783,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-46597e63d927405d8818e0867d0e521c", + "id": "dv-45d90d04eaf548d5b98b6528f6fdc045", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -48806,7 +11856,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000014.8" } ] } @@ -48845,8 +11895,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11210927:C:T", - "display": "NC_000019.9:11210927:C:T" + "code": "NC_000014.8:23892887:A:G", + "display": "NC_000014.8:23892887:A:G" } ] } @@ -48878,7 +11928,7 @@ } ] }, - "valueString": "C" + "valueString": "A" }, { "code": { @@ -48890,7 +11940,7 @@ } ] }, - "valueString": "T" + "valueString": "G" }, { "code": { @@ -48924,7 +11974,7 @@ }, "valueRange": { "low": { - "value": 11210927 + "value": 23892887 } } }, @@ -48939,7 +11989,7 @@ ] }, "valueQuantity": { - "value": 7.96318e-06, + "value": 0.308092, "system": "http://unitsofmeasure.org", "code": "1" } @@ -48951,7 +12001,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6315932091e78bf2a82", + "id": "dv-62fab6455932091e78bfda04", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -48981,7 +12031,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" + "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" } ], "component": [ @@ -48999,8 +12049,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -49019,8 +12069,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "C4552004", + "display": "MYH7-related skeletal myopathy" } ] } @@ -49036,30 +12086,30 @@ ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "3683" + "value": "42942" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000024033.3" + "value": "SCV000386097.3" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-46597e63d927405d8818e0867d0e521c", + "id": "dv-62fab6455932091e78bfda06", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -49076,32 +12126,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -49109,8 +12154,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -49120,16 +12165,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN169374", + "display": "not specified" } ] } @@ -49139,37 +12185,82 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "criteria provided, single submitter" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "42942" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000151919.1" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab6455932091e78bfda09", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11210927:C:T", - "display": "NC_000019.9:11210927:C:T" + "system": "http://loinc.org", + "code": "LA6675-8", + "display": "Benign" } ] } @@ -49179,49 +12270,93 @@ "coding": [ { "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C1842160", + "display": "Myosin storage myopathy" } ] - }, - "valueString": "C" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueString": "T" + "valueCodeableConcept": { + "text": "criteria provided, single submitter" + } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "42942" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000386099.3" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab6455932091e78bfda0a", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -49229,8 +12364,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -49240,15 +12375,19 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueRange": { - "low": { - "value": 11210927 - } + "valueCodeableConcept": { + "coding": [ + { + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C1834481", + "display": "Dilated cardiomyopathy 1S" + } + ] } }, { @@ -49256,17 +12395,25 @@ "coding": [ { "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueQuantity": { - "value": 7.96318e-06, - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "42942" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000386095.3" + } ] } }, @@ -49274,7 +12421,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab69e5932091e78c3549a", + "id": "dv-62fab6455932091e78bfda0c", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -49304,7 +12451,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" + "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" } ], "component": [ @@ -49342,8 +12489,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "C3495498", + "display": "Hypertrophic cardiomyopathy 1" } ] } @@ -49366,23 +12513,23 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "252262" + "value": "42942" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000295923.2" + "value": "SCV000386098.3" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-3f58c03ccc244f01820bf9445e076d69", + "id": "dv-62fab6455932091e78bfda17", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -49399,71 +12546,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, + "derivedFrom": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" - } - ] - } - }, + "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -49471,8 +12574,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "LA26333-7", + "display": "Uncertain significance" } ] } @@ -49482,36 +12585,19 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11233940:A:G", - "display": "NC_000019.9:11233940:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN517202", + "display": "not provided" } ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" } }, { @@ -49519,76 +12605,24 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] + "text": "no assertion criteria provided" } - }, + } + ], + "identifier": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 11233940 - } - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "42942" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.781146, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV001551199.1" } ] } @@ -49597,7 +12631,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab69e5932091e78c3549c", + "id": "dv-62fab6455932091e78bfda19", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -49627,7 +12661,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" + "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" } ], "component": [ @@ -49665,8 +12699,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0020445", - "display": "Familial hypercholesterolemia" + "code": "CN169374", + "display": "not specified" } ] } @@ -49689,23 +12723,23 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "252262" + "value": "42942" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001461329.1" + "value": "SCV001920413.1" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-3f58c03ccc244f01820bf9445e076d69", + "id": "dv-62fab6455932091e78bfda02", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -49722,71 +12756,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, + "derivedFrom": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" - } - ] - } - }, + "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -49794,8 +12784,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -49805,36 +12795,19 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11233940:A:G", - "display": "NC_000019.9:11233940:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN169374", + "display": "not specified" } ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" } }, { @@ -49842,76 +12815,24 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] + "text": "no assertion criteria provided" } - }, + } + ], + "identifier": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 11233940 - } - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "42942" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.781146, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV001930264.1" } ] } @@ -49920,7 +12841,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab69e5932091e78c3549f", + "id": "dv-62fab6455932091e78bfda08", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -49950,7 +12871,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" + "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" } ], "component": [ @@ -50005,30 +12926,30 @@ ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion criteria provided" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "252262" + "value": "42942" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000524334.4" + "value": "SCV001951128.1" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-3f58c03ccc244f01820bf9445e076d69", + "id": "dv-62fab6455932091e78bfda0f", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -50045,32 +12966,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -50078,8 +12994,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -50089,16 +13005,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN169374", + "display": "not specified" } ] } @@ -50108,98 +13025,102 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] + "text": "no assertion criteria provided" } - }, + } + ], + "identifier": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11233940:A:G", - "display": "NC_000019.9:11233940:A:G" - } - ] - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "42942" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV001975767.1" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab6455932091e78bfda14", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } - }, + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, - "valueString": "A" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6675-8", + "display": "Benign" } ] - }, - "valueString": "G" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN169374", + "display": "not specified" } ] } @@ -50209,32 +13130,24 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueRange": { - "low": { - "value": 11233940 - } + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "42942" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.781146, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000303219.1" } ] } @@ -50243,7 +13156,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab69e5932091e78c354a3", + "id": "dv-62fab6455932091e78bfda0e", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -50273,7 +13186,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" + "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" } ], "component": [ @@ -50328,30 +13241,30 @@ ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "252262" + "value": "42942" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001740479.3" + "value": "SCV001433073.1" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-3f58c03ccc244f01820bf9445e076d69", + "id": "dv-62fab6455932091e78bfda12", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -50368,32 +13281,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -50401,8 +13309,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -50412,16 +13320,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0878544", + "display": "Cardiomyopathy" } ] } @@ -50431,37 +13340,82 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] + "text": "reviewed by expert panel" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "42942" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000564487.4" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab6455932091e78bfda15", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11233940:A:G", - "display": "NC_000019.9:11233940:A:G" + "system": "http://loinc.org", + "code": "LA6675-8", + "display": "Benign" } ] } @@ -50471,49 +13425,93 @@ "coding": [ { "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN169374", + "display": "not specified" } ] - }, - "valueString": "A" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueString": "G" + "valueCodeableConcept": { + "text": "criteria provided, single submitter" + } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "42942" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000059486.5" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab6455932091e78bfda18", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -50521,8 +13519,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -50532,15 +13530,19 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueRange": { - "low": { - "value": 11233940 - } + "valueCodeableConcept": { + "coding": [ + { + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0007194", + "display": "Hypertrophic cardiomyopathy" + } + ] } }, { @@ -50548,17 +13550,25 @@ "coding": [ { "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueQuantity": { - "value": 0.781146, - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "42942" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV001000422.4" + } ] } }, @@ -50566,7 +13576,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab69e5932091e78c354a5", + "id": "dv-62fab6455932091e78bfda03", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -50596,7 +13606,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" + "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" } ], "component": [ @@ -50634,8 +13644,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "C4021133", + "display": "Left ventricular noncompaction cardiomyopathy" } ] } @@ -50658,23 +13668,23 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "252262" + "value": "42942" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000689775.1" + "value": "SCV000386100.2" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-3f58c03ccc244f01820bf9445e076d69", + "id": "dv-62fab6455932091e78bfda07", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -50691,32 +13701,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -50724,8 +13729,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -50735,16 +13740,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN169374", + "display": "not specified" } ] } @@ -50754,37 +13760,82 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] + "text": "no assertion criteria provided" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "42942" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV001742640.3" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab6455932091e78bfda0d", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11233940:A:G", - "display": "NC_000019.9:11233940:A:G" + "system": "http://loinc.org", + "code": "LA6675-8", + "display": "Benign" } ] } @@ -50794,49 +13845,93 @@ "coding": [ { "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN230736", + "display": "Cardiovascular phenotype" } ] - }, - "valueString": "A" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueString": "G" + "valueCodeableConcept": { + "text": "criteria provided, single submitter" + } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "42942" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000317659.5" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab6455932091e78bfda16", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -50844,8 +13939,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -50855,15 +13950,19 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueRange": { - "low": { - "value": 11233940 - } + "valueCodeableConcept": { + "coding": [ + { + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0878544", + "display": "Cardiomyopathy" + } + ] } }, { @@ -50871,17 +13970,25 @@ "coding": [ { "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueQuantity": { - "value": 0.781146, - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "42942" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000902546.1" + } ] } }, @@ -50889,7 +13996,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab69e5932091e78c35498", + "id": "dv-62fab6355932091e78bf4ad5", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -50919,7 +14026,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" + "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" } ], "component": [ @@ -50937,8 +14044,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6668-3", + "display": "Pathogenic" } ] } @@ -50974,18 +14081,18 @@ ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion criteria provided" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "252262" + "value": "14095" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002049746.2" + "value": "SCV001972763.1" } ] } @@ -50994,7 +14101,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-3f58c03ccc244f01820bf9445e076d69", + "id": "dv-0e81b678f2aa4151b1cba965d0fbaab7", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -51067,7 +14174,7 @@ "coding": [ { "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000014.8" } ] } @@ -51106,8 +14213,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11233940:A:G", - "display": "NC_000019.9:11233940:A:G" + "code": "NC_000014.8:23895022:G:A", + "display": "NC_000014.8:23895022:G:A" } ] } @@ -51139,7 +14246,7 @@ } ] }, - "valueString": "A" + "valueString": "G" }, { "code": { @@ -51151,7 +14258,7 @@ } ] }, - "valueString": "G" + "valueString": "A" }, { "code": { @@ -51185,7 +14292,7 @@ }, "valueRange": { "low": { - "value": 11233940 + "value": 23895022 } } }, @@ -51200,7 +14307,7 @@ ] }, "valueQuantity": { - "value": 0.781146, + "value": 1.1942e-05, "system": "http://unitsofmeasure.org", "code": "1" } @@ -51212,7 +14319,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab69e5932091e78c3549b", + "id": "dv-62fab6355932091e78bf4ad7", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -51242,7 +14349,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" + "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" } ], "component": [ @@ -51260,8 +14367,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6668-3", + "display": "Pathogenic" } ] } @@ -51280,8 +14387,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C3495498", + "display": "Hypertrophic cardiomyopathy 1" } ] } @@ -51297,30 +14404,30 @@ ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "252262" + "value": "14095" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001926076.1" + "value": "SCV000212630.1" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-3f58c03ccc244f01820bf9445e076d69", + "id": "dv-62fab6355932091e78bf4ae5", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -51337,32 +14444,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -51370,8 +14472,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6668-3", + "display": "Pathogenic" } ] } @@ -51381,16 +14483,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN230736", + "display": "Cardiovascular phenotype" } ] } @@ -51400,98 +14503,102 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] + "text": "criteria provided, single submitter" } - }, + } + ], + "identifier": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11233940:A:G", - "display": "NC_000019.9:11233940:A:G" - } - ] - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "14095" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000318794.5" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab6355932091e78bf4ae6", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } - }, + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, - "valueString": "A" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6668-3", + "display": "Pathogenic" } ] - }, - "valueString": "G" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN517202", + "display": "not provided" } ] } @@ -51501,32 +14608,24 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueRange": { - "low": { - "value": 11233940 - } + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "14095" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.781146, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV001249810.10" } ] } @@ -51535,7 +14634,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab69e5932091e78c3549d", + "id": "dv-62fab6355932091e78bf4aea", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -51565,7 +14664,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" + "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" } ], "component": [ @@ -51583,8 +14682,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6668-3", + "display": "Pathogenic" } ] } @@ -51603,8 +14702,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0020445", - "display": "Familial hypercholesterolemia" + "code": "C0007194", + "display": "Hypertrophic cardiomyopathy" } ] } @@ -51620,30 +14719,30 @@ ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "reviewed by expert panel" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "252262" + "value": "14095" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001717062.2" + "value": "SCV000564425.4" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-3f58c03ccc244f01820bf9445e076d69", + "id": "dv-62fab6355932091e78bf4aef", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -51660,32 +14759,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -51693,8 +14787,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6668-3", + "display": "Pathogenic" } ] } @@ -51704,16 +14798,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C3495498", + "display": "Hypertrophic cardiomyopathy 1" } ] } @@ -51723,37 +14818,82 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] + "text": "criteria provided, single submitter" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "14095" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV002538613.1" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab6355932091e78bf4afb", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11233940:A:G", - "display": "NC_000019.9:11233940:A:G" + "system": "http://loinc.org", + "code": "LA26332-9", + "display": "Likely pathogenic" } ] } @@ -51763,49 +14903,93 @@ "coding": [ { "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN517202", + "display": "not provided" } ] - }, - "valueString": "A" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueString": "G" + "valueCodeableConcept": { + "text": "no assertion criteria provided" + } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "14095" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV001739623.3" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab6355932091e78bf4ad6", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -51813,8 +14997,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "LA26332-9", + "display": "Likely pathogenic" } ] } @@ -51824,15 +15008,19 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueRange": { - "low": { - "value": 11233940 - } + "valueCodeableConcept": { + "coding": [ + { + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0949658", + "display": "Primary familial hypertrophic cardiomyopathy" + } + ] } }, { @@ -51840,17 +15028,25 @@ "coding": [ { "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueQuantity": { - "value": 0.781146, - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "text": "no assertion criteria provided" } } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "14095" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000188798.1" + } ] } }, @@ -51858,7 +15054,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab69e5932091e78c3549e", + "id": "dv-62fab6355932091e78bf4add", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -51888,7 +15084,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" + "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" } ], "component": [ @@ -51906,8 +15102,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6668-3", + "display": "Pathogenic" } ] } @@ -51926,8 +15122,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "CN517202", + "display": "not provided" } ] } @@ -51943,30 +15139,30 @@ ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion criteria provided" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "252262" + "value": "14095" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000410543.3" + "value": "SCV000280314.1" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-3f58c03ccc244f01820bf9445e076d69", + "id": "dv-62fab6355932091e78bf4ade", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -51983,32 +15179,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -52016,8 +15207,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6668-3", + "display": "Pathogenic" } ] } @@ -52027,16 +15218,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN517202", + "display": "not provided" } ] } @@ -52046,98 +15238,102 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] + "text": "no assertion criteria provided" } - }, + } + ], + "identifier": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11233940:A:G", - "display": "NC_000019.9:11233940:A:G" - } - ] - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "14095" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV002017675.1" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab6355932091e78bf4adf", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } - }, + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, - "valueString": "A" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6668-3", + "display": "Pathogenic" } ] - }, - "valueString": "G" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0007194", + "display": "Hypertrophic cardiomyopathy" } ] } @@ -52147,32 +15343,24 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueRange": { - "low": { - "value": 11233940 - } + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "14095" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.781146, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000546190.6" } ] } @@ -52181,7 +15369,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab69e5932091e78c354a0", + "id": "dv-62fab6355932091e78bf4b17", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -52211,7 +15399,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" + "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" } ], "component": [ @@ -52229,8 +15417,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6668-3", + "display": "Pathogenic" } ] } @@ -52249,8 +15437,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C0878544", + "display": "Cardiomyopathy" } ] } @@ -52273,23 +15461,23 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "252262" + "value": "14095" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000304691.1" + "value": "SCV001352585.2" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-3f58c03ccc244f01820bf9445e076d69", + "id": "dv-62fab6355932091e78bf4b1a", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -52306,32 +15494,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -52339,8 +15522,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6668-3", + "display": "Pathogenic" } ] } @@ -52350,16 +15533,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN517202", + "display": "not provided" } ] } @@ -52369,37 +15553,82 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] + "text": "no assertion criteria provided" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "14095" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV001959712.2" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab6355932091e78bf4ae3", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11233940:A:G", - "display": "NC_000019.9:11233940:A:G" + "system": "http://loinc.org", + "code": "LA6668-3", + "display": "Pathogenic" } ] } @@ -52409,49 +15638,93 @@ "coding": [ { "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0007194", + "display": "Hypertrophic cardiomyopathy" } ] - }, - "valueString": "A" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueString": "G" + "valueCodeableConcept": { + "text": "criteria provided, single submitter" + } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "14095" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000059423.7" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab6355932091e78bf4ad8", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -52459,8 +15732,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "LA6668-3", + "display": "Pathogenic" } ] } @@ -52470,15 +15743,19 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueRange": { - "low": { - "value": 11233940 - } + "valueCodeableConcept": { + "coding": [ + { + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C3495498", + "display": "Hypertrophic cardiomyopathy 1" + } + ] } }, { @@ -52486,17 +15763,25 @@ "coding": [ { "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueQuantity": { - "value": 0.781146, - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "text": "no assertion criteria provided" } } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "14095" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000035408.2" + } ] } }, @@ -52504,7 +15789,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab69e5932091e78c354a2", + "id": "dv-62fab6355932091e78bf4ae4", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -52534,7 +15819,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" + "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" } ], "component": [ @@ -52552,8 +15837,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6668-3", + "display": "Pathogenic" } ] } @@ -52572,8 +15857,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "CN517202", + "display": "not provided" } ] } @@ -52596,23 +15881,23 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "252262" + "value": "14095" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000711400.2" + "value": "SCV000208451.14" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-3f58c03ccc244f01820bf9445e076d69", + "id": "dv-62fab6355932091e78bf4afa", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -52629,71 +15914,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, + "derivedFrom": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" - } - ] - } - }, + "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -52701,8 +15942,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "LA6668-3", + "display": "Pathogenic" } ] } @@ -52712,36 +15953,19 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11233940:A:G", - "display": "NC_000019.9:11233940:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C3495498", + "display": "Hypertrophic cardiomyopathy 1" } ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" } }, { @@ -52749,76 +15973,24 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] + "text": "criteria provided, single submitter" } - }, + } + ], + "identifier": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 11233940 - } - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "14095" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.781146, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV002059672.1" } ] } @@ -52827,7 +15999,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab69e5932091e78c354ab", + "id": "dv-62fab6315932091e78bf2a75", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -52857,7 +16029,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" + "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" } ], "component": [ @@ -52875,8 +16047,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6668-3", + "display": "Pathogenic" } ] } @@ -52919,11 +16091,11 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "252262" + "value": "3683" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000987010.1" + "value": "SCV000294463.2" } ] } @@ -52932,7 +16104,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-3f58c03ccc244f01820bf9445e076d69", + "id": "dv-46597e63d927405d8818e0867d0e521c", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -53024,8 +16196,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "LA6706-1", + "display": "heterozygous" } ] } @@ -53044,8 +16216,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11233940:A:G", - "display": "NC_000019.9:11233940:A:G" + "code": "NC_000019.9:11210927:C:T", + "display": "NC_000019.9:11210927:C:T" } ] } @@ -53061,7 +16233,7 @@ ] }, "valueQuantity": { - "value": 1.0, + "value": 0.5, "unit": "relative frequency of a particular allele in the specimen", "system": "http://unitsofmeasure.org", "code": "1" @@ -53077,7 +16249,7 @@ } ] }, - "valueString": "A" + "valueString": "C" }, { "code": { @@ -53089,7 +16261,7 @@ } ] }, - "valueString": "G" + "valueString": "T" }, { "code": { @@ -53123,7 +16295,7 @@ }, "valueRange": { "low": { - "value": 11233940 + "value": 11210927 } } }, @@ -53138,7 +16310,7 @@ ] }, "valueQuantity": { - "value": 0.781146, + "value": 7.96318e-06, "system": "http://unitsofmeasure.org", "code": "1" } @@ -53150,7 +16322,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab69e5932091e78c354a4", + "id": "dv-62fab6315932091e78bf2a79", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -53180,7 +16352,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" + "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" } ], "component": [ @@ -53198,8 +16370,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6668-3", + "display": "Pathogenic" } ] } @@ -53235,30 +16407,30 @@ ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "reviewed by expert panel" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "252262" + "value": "3683" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001738025.1" + "value": "SCV002506409.1" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-3f58c03ccc244f01820bf9445e076d69", + "id": "dv-62fab6315932091e78bf2a7b", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -53275,32 +16447,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -53308,8 +16475,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6668-3", + "display": "Pathogenic" } ] } @@ -53319,16 +16486,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1" } ] } @@ -53338,37 +16506,82 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] + "text": "criteria provided, single submitter" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "3683" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000588484.1" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab6315932091e78bf2a7c", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11233940:A:G", - "display": "NC_000019.9:11233940:A:G" + "system": "http://loinc.org", + "code": "LA6668-3", + "display": "Pathogenic" } ] } @@ -53378,49 +16591,93 @@ "coding": [ { "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1" } ] - }, - "valueString": "A" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueString": "G" + "valueCodeableConcept": { + "text": "no assertion criteria provided" + } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "3683" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000606015.1" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab6315932091e78bf2a7e", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -53428,8 +16685,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "LA6668-3", + "display": "Pathogenic" } ] } @@ -53439,15 +16696,19 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueRange": { - "low": { - "value": 11233940 - } + "valueCodeableConcept": { + "coding": [ + { + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1" + } + ] } }, { @@ -53455,17 +16716,25 @@ "coding": [ { "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueQuantity": { - "value": 0.781146, - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "3683" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000987040.1" + } ] } }, @@ -53473,7 +16742,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab69e5932091e78c35499", + "id": "dv-62fab6315932091e78bf2a76", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -53503,7 +16772,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" + "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" } ], "component": [ @@ -53521,8 +16790,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6668-3", + "display": "Pathogenic" } ] } @@ -53558,30 +16827,30 @@ ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion criteria provided" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "252262" + "value": "3683" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000323005.1" + "value": "SCV002017112.1" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-3f58c03ccc244f01820bf9445e076d69", + "id": "dv-62fab6315932091e78bf2a7d", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -53598,32 +16867,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -53631,8 +16895,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6668-3", + "display": "Pathogenic" } ] } @@ -53642,16 +16906,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN517202", + "display": "not provided" } ] } @@ -53661,37 +16926,82 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] + "text": "criteria provided, single submitter" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "3683" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV002027963.1" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab6315932091e78bf2a7f", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11233940:A:G", - "display": "NC_000019.9:11233940:A:G" + "system": "http://loinc.org", + "code": "LA6668-3", + "display": "Pathogenic" } ] } @@ -53701,49 +17011,93 @@ "coding": [ { "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1" } ] - }, - "valueString": "A" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueString": "G" + "valueCodeableConcept": { + "text": "criteria provided, single submitter" + } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "3683" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000503101.1" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab6315932091e78bf2a71", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -53751,8 +17105,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "LA6668-3", + "display": "Pathogenic" } ] } @@ -53762,15 +17116,19 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueRange": { - "low": { - "value": 11233940 - } + "valueCodeableConcept": { + "coding": [ + { + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0020445", + "display": "Familial hypercholesterolemia" + } + ] } }, { @@ -53778,17 +17136,25 @@ "coding": [ { "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueQuantity": { - "value": 0.781146, - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "3683" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000544678.5" + } ] } }, @@ -53796,7 +17162,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab69e5932091e78c354a1", + "id": "dv-62fab6315932091e78bf2a78", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -53826,7 +17192,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" + "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" } ], "component": [ @@ -53844,8 +17210,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6668-3", + "display": "Pathogenic" } ] } @@ -53881,30 +17247,30 @@ ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "252262" + "value": "3683" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000606617.1" + "value": "SCV000583630.1" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-3f58c03ccc244f01820bf9445e076d69", + "id": "dv-62fab6315932091e78bf2a7a", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -53921,32 +17287,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -53954,8 +17315,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6668-3", + "display": "Pathogenic" } ] } @@ -53965,16 +17326,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1" } ] } @@ -53984,98 +17346,102 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] + "text": "criteria provided, single submitter" } - }, + } + ], + "identifier": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11233940:A:G", - "display": "NC_000019.9:11233940:A:G" - } - ] - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "3683" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000607415.1" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab6315932091e78bf2a80", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } - }, + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, - "valueString": "A" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6668-3", + "display": "Pathogenic" } ] - }, - "valueString": "G" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0020445", + "display": "Familial hypercholesterolemia" } ] } @@ -54085,32 +17451,24 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueRange": { - "low": { - "value": 11233940 - } + "valueCodeableConcept": { + "text": "no assertion criteria provided" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "3683" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.781146, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV002086359.1" } ] } @@ -54119,7 +17477,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6a25932091e78c37a93", + "id": "dv-62fab6315932091e78bf2a6e", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -54149,7 +17507,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-ec3a667068394825be063d587250d6e2" + "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" } ], "component": [ @@ -54167,8 +17525,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6668-3", + "display": "Pathogenic" } ] } @@ -54211,23 +17569,23 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "265910" + "value": "3683" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000323020.1" + "value": "SCV001653581.1" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-ec3a667068394825be063d587250d6e2", + "id": "dv-62fab6315932091e78bf2a77", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -54244,32 +17602,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -54277,8 +17630,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6668-3", + "display": "Pathogenic" } ] } @@ -54288,16 +17641,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN517202", + "display": "not provided" } ] } @@ -54307,98 +17661,102 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "no assertion criteria provided" } - }, + } + ], + "identifier": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11242043:G:A", - "display": "NC_000019.9:11242043:G:A" - } - ] - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "3683" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000925133.1" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab6315932091e78bf2a82", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } - }, + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, - "valueString": "G" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6668-3", + "display": "Pathogenic" } ] - }, - "valueString": "A" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1" } ] } @@ -54408,32 +17766,24 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueRange": { - "low": { - "value": 11242043 - } + "valueCodeableConcept": { + "text": "no assertion criteria provided" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "3683" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.243375, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000024033.3" } ] } @@ -54442,7 +17792,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6a25932091e78c37a92", + "id": "dv-62fab69e5932091e78c3549a", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -54472,7 +17822,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-ec3a667068394825be063d587250d6e2" + "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" } ], "component": [ @@ -54510,8 +17860,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN517202", - "display": "not provided" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1" } ] } @@ -54534,11 +17884,11 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "265910" + "value": "252262" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001935715.1" + "value": "SCV000295923.2" } ] } @@ -54547,7 +17897,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-ec3a667068394825be063d587250d6e2", + "id": "dv-3f58c03ccc244f01820bf9445e076d69", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -54639,8 +17989,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "code": "LA6705-3", + "display": "homozygous" } ] } @@ -54659,8 +18009,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11242043:G:A", - "display": "NC_000019.9:11242043:G:A" + "code": "NC_000019.9:11233940:A:G", + "display": "NC_000019.9:11233940:A:G" } ] } @@ -54676,7 +18026,7 @@ ] }, "valueQuantity": { - "value": 0.5, + "value": 1.0, "unit": "relative frequency of a particular allele in the specimen", "system": "http://unitsofmeasure.org", "code": "1" @@ -54692,7 +18042,7 @@ } ] }, - "valueString": "G" + "valueString": "A" }, { "code": { @@ -54704,7 +18054,7 @@ } ] }, - "valueString": "A" + "valueString": "G" }, { "code": { @@ -54738,7 +18088,7 @@ }, "valueRange": { "low": { - "value": 11242043 + "value": 11233940 } } }, @@ -54753,7 +18103,7 @@ ] }, "valueQuantity": { - "value": 0.243375, + "value": 0.781146, "system": "http://unitsofmeasure.org", "code": "1" } @@ -54765,7 +18115,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6a25932091e78c37a94", + "id": "dv-62fab69e5932091e78c3549c", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -54795,7 +18145,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-ec3a667068394825be063d587250d6e2" + "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" } ], "component": [ @@ -54833,8 +18183,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "C0020445", + "display": "Familial hypercholesterolemia" } ] } @@ -54850,30 +18200,30 @@ ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion criteria provided" } } ], "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "265910" + "value": "252262" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001738049.1" + "value": "SCV001461329.1" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-ec3a667068394825be063d587250d6e2", + "id": "dv-62fab69e5932091e78c3549f", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -54890,32 +18240,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -54923,27 +18268,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -54953,17 +18279,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN169374", + "display": "not specified" } ] } @@ -54973,69 +18299,73 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11242043:G:A", - "display": "NC_000019.9:11242043:G:A" - } - ] + "text": "criteria provided, single submitter" } - }, + } + ], + "identifier": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "252262" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000524334.4" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab69e5932091e78c354a3", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "A" - }, + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -55043,8 +18373,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -55054,15 +18384,19 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueRange": { - "low": { - "value": 11242043 - } + "valueCodeableConcept": { + "coding": [ + { + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN169374", + "display": "not specified" + } + ] } }, { @@ -55070,17 +18404,25 @@ "coding": [ { "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueQuantity": { - "value": 0.243375, - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "text": "no assertion criteria provided" } } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "252262" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV001740479.3" + } ] } }, @@ -55088,7 +18430,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6a25932091e78c37a95", + "id": "dv-62fab69e5932091e78c354a5", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -55118,7 +18460,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-ec3a667068394825be063d587250d6e2" + "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" } ], "component": [ @@ -55180,23 +18522,23 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "265910" + "value": "252262" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000410546.3" + "value": "SCV000689775.1" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-ec3a667068394825be063d587250d6e2", + "id": "dv-62fab69e5932091e78c35498", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -55213,32 +18555,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -55246,8 +18583,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -55257,16 +18594,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN517202", + "display": "not provided" } ] } @@ -55276,37 +18614,82 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "criteria provided, single submitter" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "252262" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV002049746.2" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab69e5932091e78c3549b", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11242043:G:A", - "display": "NC_000019.9:11242043:G:A" + "system": "http://loinc.org", + "code": "LA6675-8", + "display": "Benign" } ] } @@ -55316,49 +18699,93 @@ "coding": [ { "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN169374", + "display": "not specified" } ] - }, - "valueString": "G" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueString": "A" + "valueCodeableConcept": { + "text": "no assertion criteria provided" + } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "252262" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV001926076.1" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab69e5932091e78c3549d", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -55366,8 +18793,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -55377,15 +18804,19 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueRange": { - "low": { - "value": 11242043 - } + "valueCodeableConcept": { + "coding": [ + { + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0020445", + "display": "Familial hypercholesterolemia" + } + ] } }, { @@ -55393,17 +18824,25 @@ "coding": [ { "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueQuantity": { - "value": 0.243375, - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "252262" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV001717062.2" + } ] } }, @@ -55411,7 +18850,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6a25932091e78c37a96", + "id": "dv-62fab69e5932091e78c3549e", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -55441,7 +18880,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-ec3a667068394825be063d587250d6e2" + "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" } ], "component": [ @@ -55503,23 +18942,23 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "265910" + "value": "252262" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000987011.1" + "value": "SCV000410543.3" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-ec3a667068394825be063d587250d6e2", + "id": "dv-62fab69e5932091e78c354a0", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -55536,32 +18975,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -55569,8 +19003,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -55580,16 +19014,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN169374", + "display": "not specified" } ] } @@ -55599,98 +19034,102 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "criteria provided, single submitter" } - }, + } + ], + "identifier": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11242043:G:A", - "display": "NC_000019.9:11242043:G:A" - } - ] - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "252262" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000304691.1" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab69e5932091e78c354a2", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } - }, + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, - "valueString": "G" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6675-8", + "display": "Benign" } ] - }, - "valueString": "A" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "CN169374", + "display": "not specified" } ] } @@ -55700,32 +19139,24 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueRange": { - "low": { - "value": 11242043 - } + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "252262" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.243375, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000711400.2" } ] } @@ -55734,7 +19165,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6a85932091e78c3bb46", + "id": "dv-62fab69e5932091e78c354ab", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -55764,7 +19195,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-904b6ac36b25461ea7a2304093bc6fec" + "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" } ], "component": [ @@ -55802,8 +19233,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0020445", - "display": "Familial hypercholesterolemia" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1" } ] } @@ -55826,23 +19257,23 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "328058" + "value": "252262" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001717063.2" + "value": "SCV000987010.1" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-904b6ac36b25461ea7a2304093bc6fec", + "id": "dv-62fab69e5932091e78c354a4", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -55859,32 +19290,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -55892,8 +19318,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -55903,16 +19329,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1" } ] } @@ -55922,37 +19349,82 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] + "text": "criteria provided, single submitter" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "252262" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV001738025.1" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab69e5932091e78c35499", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11242306:G:C", - "display": "NC_000019.9:11242306:G:C" + "system": "http://loinc.org", + "code": "LA6675-8", + "display": "Benign" } ] } @@ -55962,49 +19434,93 @@ "coding": [ { "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1" } ] - }, - "valueString": "G" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueString": "C" + "valueCodeableConcept": { + "text": "criteria provided, single submitter" + } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "252262" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000323005.1" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab69e5932091e78c354a1", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -56012,8 +19528,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -56023,15 +19539,19 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueRange": { - "low": { - "value": 11242306 - } + "valueCodeableConcept": { + "coding": [ + { + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1" + } + ] } }, { @@ -56039,17 +19559,25 @@ "coding": [ { "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueQuantity": { - "value": 0.818994, - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "text": "no assertion criteria provided" } } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "252262" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000606617.1" + } ] } }, @@ -56057,7 +19585,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6a85932091e78c3bb47", + "id": "dv-62fab6a25932091e78c37a93", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -56087,7 +19615,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-904b6ac36b25461ea7a2304093bc6fec" + "reference": "Observation/dv-ec3a667068394825be063d587250d6e2" } ], "component": [ @@ -56149,11 +19677,11 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "328058" + "value": "265910" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000410549.3" + "value": "SCV000323020.1" } ] } @@ -56162,7 +19690,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-904b6ac36b25461ea7a2304093bc6fec", + "id": "dv-ec3a667068394825be063d587250d6e2", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -56254,8 +19782,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "LA6706-1", + "display": "heterozygous" } ] } @@ -56274,8 +19802,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11242306:G:C", - "display": "NC_000019.9:11242306:G:C" + "code": "NC_000019.9:11242043:G:A", + "display": "NC_000019.9:11242043:G:A" } ] } @@ -56291,7 +19819,7 @@ ] }, "valueQuantity": { - "value": 1.0, + "value": 0.5, "unit": "relative frequency of a particular allele in the specimen", "system": "http://unitsofmeasure.org", "code": "1" @@ -56319,7 +19847,7 @@ } ] }, - "valueString": "C" + "valueString": "A" }, { "code": { @@ -56353,7 +19881,7 @@ }, "valueRange": { "low": { - "value": 11242306 + "value": 11242043 } } }, @@ -56368,7 +19896,7 @@ ] }, "valueQuantity": { - "value": 0.818994, + "value": 0.243375, "system": "http://unitsofmeasure.org", "code": "1" } @@ -56380,7 +19908,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6a85932091e78c3bb4a", + "id": "dv-62fab6a25932091e78c37a92", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -56410,7 +19938,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-904b6ac36b25461ea7a2304093bc6fec" + "reference": "Observation/dv-ec3a667068394825be063d587250d6e2" } ], "component": [ @@ -56428,8 +19956,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA26334-5", - "display": "Likely benign" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -56448,8 +19976,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "CN517202", + "display": "not provided" } ] } @@ -56472,23 +20000,23 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "328058" + "value": "265910" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000987012.1" + "value": "SCV001935715.1" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-904b6ac36b25461ea7a2304093bc6fec", + "id": "dv-62fab6a25932091e78c37a94", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -56505,32 +20033,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-ec3a667068394825be063d587250d6e2" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -56538,8 +20061,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -56549,16 +20072,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1" } ] } @@ -56568,37 +20092,82 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] + "text": "criteria provided, single submitter" } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "265910" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV001738049.1" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab6a25932091e78c37a95", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-ec3a667068394825be063d587250d6e2" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11242306:G:C", - "display": "NC_000019.9:11242306:G:C" + "system": "http://loinc.org", + "code": "LA6675-8", + "display": "Benign" } ] } @@ -56608,49 +20177,93 @@ "coding": [ { "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1" } ] - }, - "valueString": "G" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueString": "C" + "valueCodeableConcept": { + "text": "criteria provided, single submitter" + } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "265910" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000410546.3" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab6a25932091e78c37a96", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-ec3a667068394825be063d587250d6e2" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -56658,8 +20271,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -56669,15 +20282,19 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "81259-4", + "display": "predicted phenotype" } ] }, - "valueRange": { - "low": { - "value": 11242306 - } + "valueCodeableConcept": { + "coding": [ + { + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1" + } + ] } }, { @@ -56685,17 +20302,25 @@ "coding": [ { "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueQuantity": { - "value": 0.818994, - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "265910" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000987011.1" + } ] } }, @@ -56703,7 +20328,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6a85932091e78c3bb4f", + "id": "dv-62fab6a85932091e78c3bb46", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -56733,7 +20358,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-25751058304a4b40a5254642589509ae" + "reference": "Observation/dv-904b6ac36b25461ea7a2304093bc6fec" } ], "component": [ @@ -56771,8 +20396,8 @@ "coding": [ { "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "C0020445", + "display": "Familial hypercholesterolemia" } ] } @@ -56795,11 +20420,11 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "328064" + "value": "328058" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000410555.3" + "value": "SCV001717063.2" } ] } @@ -56808,7 +20433,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-25751058304a4b40a5254642589509ae", + "id": "dv-904b6ac36b25461ea7a2304093bc6fec", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -56900,8 +20525,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "code": "LA6705-3", + "display": "homozygous" } ] } @@ -56920,8 +20545,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11242495:G:A", - "display": "NC_000019.9:11242495:G:A" + "code": "NC_000019.9:11242306:G:C", + "display": "NC_000019.9:11242306:G:C" } ] } @@ -56937,7 +20562,7 @@ ] }, "valueQuantity": { - "value": 0.5, + "value": 1.0, "unit": "relative frequency of a particular allele in the specimen", "system": "http://unitsofmeasure.org", "code": "1" @@ -56965,7 +20590,7 @@ } ] }, - "valueString": "A" + "valueString": "C" }, { "code": { @@ -56999,9 +20624,25 @@ }, "valueRange": { "low": { - "value": 11242495 + "value": 11242306 } } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "92821-8", + "display": "Population allele frequency" + } + ] + }, + "valueQuantity": { + "value": 0.818994, + "system": "http://unitsofmeasure.org", + "code": "1" + } } ] } @@ -57010,7 +20651,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6a85932091e78c3bb4e", + "id": "dv-62fab6a85932091e78c3bb47", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -57040,7 +20681,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-25751058304a4b40a5254642589509ae" + "reference": "Observation/dv-904b6ac36b25461ea7a2304093bc6fec" } ], "component": [ @@ -57058,8 +20699,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA26334-5", - "display": "Likely benign" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -57102,23 +20743,23 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "328064" + "value": "328058" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000987015.1" + "value": "SCV000410549.3" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-25751058304a4b40a5254642589509ae", + "id": "dv-62fab6a85932091e78c3bb4a", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, "status": "final", @@ -57135,32 +20776,27 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" } ] }, "subject": { "reference": "Patient/HG00403" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-904b6ac36b25461ea7a2304093bc6fec" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance" } ] }, @@ -57168,27 +20804,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "LA26334-5", + "display": "Likely benign" } ] } @@ -57198,17 +20815,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "81259-4", + "display": "predicted phenotype" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1" } ] } @@ -57218,97 +20835,24 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11242495:G:A", - "display": "NC_000019.9:11242495:G:A" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "text": "criteria provided, single submitter" } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "A" - }, + } + ], + "identifier": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "328058" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 11242495 - } - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000987012.1" } ] } @@ -57317,7 +20861,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6a85932091e78c3bb56", + "id": "dv-62fab6a85932091e78c3bb4f", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -57347,7 +20891,7 @@ }, "derivedFrom": [ { - "reference": "Observation/dv-57370e44f9884d8cb43661abf73c23c3" + "reference": "Observation/dv-25751058304a4b40a5254642589509ae" } ], "component": [ @@ -57365,8 +20909,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA26334-5", - "display": "Likely benign" + "code": "LA6675-8", + "display": "Benign" } ] } @@ -57409,11 +20953,11 @@ "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "328070" + "value": "328064" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000987013.1" + "value": "SCV000410555.3" } ] } @@ -57422,7 +20966,7 @@ "name": "variant", "resource": { "resourceType": "Observation", - "id": "dv-57370e44f9884d8cb43661abf73c23c3", + "id": "dv-25751058304a4b40a5254642589509ae", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" @@ -57514,8 +21058,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "LA6706-1", + "display": "heterozygous" } ] } @@ -57534,8 +21078,8 @@ "coding": [ { "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11242657:T:C", - "display": "NC_000019.9:11242657:T:C" + "code": "NC_000019.9:11242495:G:A", + "display": "NC_000019.9:11242495:G:A" } ] } @@ -57551,7 +21095,7 @@ ] }, "valueQuantity": { - "value": 1.0, + "value": 0.5, "unit": "relative frequency of a particular allele in the specimen", "system": "http://unitsofmeasure.org", "code": "1" @@ -57567,7 +21111,7 @@ } ] }, - "valueString": "T" + "valueString": "G" }, { "code": { @@ -57579,7 +21123,7 @@ } ] }, - "valueString": "C" + "valueString": "A" }, { "code": { @@ -57613,7 +21157,7 @@ }, "valueRange": { "low": { - "value": 11242657 + "value": 11242495 } } } @@ -57624,7 +21168,112 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-62fab6a85932091e78c3bb55", + "id": "dv-62fab6a85932091e78c3bb4e", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-25751058304a4b40a5254642589509ae" + } + ], + "component": [ + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "53037-8", + "display": "Genetic variation clinical significance" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA26334-5", + "display": "Likely benign" + } + ] + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "81259-4", + "display": "predicted phenotype" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1" + } + ] + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "93044-6", + "display": "Level of evidence" + } + ] + }, + "valueCodeableConcept": { + "text": "criteria provided, single submitter" + } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "328064" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000987015.1" + } + ] + } + }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab6a85932091e78c3bb56", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" @@ -57672,8 +21321,8 @@ "coding": [ { "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA26334-5", + "display": "Likely benign" } ] } @@ -57720,7 +21369,7 @@ }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000410561.3" + "value": "SCV000987013.1" } ] } @@ -57927,6 +21576,111 @@ ] } }, + { + "name": "implication", + "resource": { + "resourceType": "Observation", + "id": "dv-62fab6a85932091e78c3bb55", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "diagnostic-implication" + } + ] + }, + "subject": { + "reference": "Patient/HG00403" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-57370e44f9884d8cb43661abf73c23c3" + } + ], + "component": [ + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "53037-8", + "display": "Genetic variation clinical significance" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA6675-8", + "display": "Benign" + } + ] + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "81259-4", + "display": "predicted phenotype" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "https://www.ncbi.nlm.nih.gov/medgen", + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1" + } + ] + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "93044-6", + "display": "Level of evidence" + } + ] + }, + "valueCodeableConcept": { + "text": "criteria provided, single submitter" + } + } + ], + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "328070" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000410561.3" + } + ] + } + }, { "name": "implication", "resource": { @@ -58339,208 +22093,6 @@ ] } }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-930a27aa386d4cb8bff1e437040afb45", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11242764:A:G", - "display": "NC_000019.9:11242764:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 11242764 - } - } - } - ] - } - }, { "name": "implication", "resource": { diff --git a/tests/expected_outputs/find_subject_tx_implications/1.json b/tests/expected_outputs/find_subject_tx_implications/1.json index 058de23cf..08f78c74b 100644 --- a/tests/expected_outputs/find_subject_tx_implications/1.json +++ b/tests/expected_outputs/find_subject_tx_implications/1.json @@ -400,167 +400,6 @@ ] } }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, { "name": "implication", "resource": { @@ -699,167 +538,6 @@ } ] } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } } ] } \ No newline at end of file diff --git a/tests/expected_outputs/find_subject_tx_implications/3.json b/tests/expected_outputs/find_subject_tx_implications/3.json index 82cc3a5c9..fb03a14f5 100644 --- a/tests/expected_outputs/find_subject_tx_implications/3.json +++ b/tests/expected_outputs/find_subject_tx_implications/3.json @@ -5,7 +5,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d65", + "id": "dv-63287c9ff7c8d34d272a3d73", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -53,8 +53,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "8923", - "display": "Skin Melanoma" + "code": "1909", + "display": "Melanoma" } ] } @@ -115,7 +115,7 @@ }, { "system": "https://civicdb.org/evidence", - "value": "1410" + "value": "3757" } ] } @@ -285,7 +285,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a4086", + "id": "dv-63287c9ff7c8d34d272a3d75", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -333,8 +333,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "9256", - "display": "Colorectal Cancer" + "code": "50933", + "display": "Ovarian Serous Carcinoma" } ] } @@ -350,7 +350,7 @@ ] }, "valueCodeableConcept": { - "text": "D (Preclinical evidence)" + "text": "C (Case study)" } }, { @@ -395,19 +395,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "98" + "value": "3787" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a3d74", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -424,40 +424,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "6812", + "display": "Childhood Pilocytic Astrocytoma" } ] } @@ -467,19 +463,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "C (Case study)" } }, { @@ -487,41 +477,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1147220", + "display": "Vemurafenib" } ] } @@ -530,33 +496,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "3777" } ] } @@ -565,7 +523,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d86", + "id": "dv-63287c9ff7c8d34d272a3d7b", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -613,8 +571,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "7146", - "display": "Langerhans Cell Sarcoma" + "code": "8923", + "display": "Skin Melanoma" } ] } @@ -630,7 +588,7 @@ ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "text": "A (Validated association)" } }, { @@ -675,19 +633,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "7583" + "value": "1409" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a40d4", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -704,40 +662,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "9256", + "display": "Colorectal Cancer" } ] } @@ -747,19 +701,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "C (Case study)" } }, { @@ -767,41 +715,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1147220", + "display": "Vemurafenib" } ] } @@ -810,33 +734,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "1589" } ] } @@ -845,7 +761,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d6a", + "id": "dv-63287c9ff7c8d34d272a3d7a", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -893,8 +809,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "9538", - "display": "Multiple Myeloma" + "code": "3908", + "display": "Lung Non-small Cell Carcinoma" } ] } @@ -910,7 +826,7 @@ ] }, "valueCodeableConcept": { - "text": "C (Case study)" + "text": "B (Clinical evidence)" } }, { @@ -955,19 +871,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "1699" + "value": "5958" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a3d7f", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -984,40 +900,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "9256", + "display": "Colorectal Cancer" } ] } @@ -1027,19 +939,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "B (Clinical evidence)" } }, { @@ -1047,41 +953,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1147220", + "display": "Vemurafenib" } ] } @@ -1090,33 +972,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Does Not Support Sensitivity/Response" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "1405" } ] } @@ -1125,7 +999,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d69", + "id": "dv-63287c9ff7c8d34d272a3d84", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -1173,8 +1047,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "9538", - "display": "Multiple Myeloma" + "code": "3969", + "display": "Thyroid Gland Papillary Carcinoma" } ] } @@ -1190,7 +1064,7 @@ ] }, "valueCodeableConcept": { - "text": "C (Case study)" + "text": "B (Clinical evidence)" } }, { @@ -1235,19 +1109,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "1698" + "value": "9018" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a40f1", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -1264,40 +1138,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "9256", + "display": "Colorectal Cancer" } ] } @@ -1307,19 +1177,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "D (Preclinical evidence)" } }, { @@ -1327,41 +1191,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1147220", + "display": "Vemurafenib" } ] } @@ -1370,33 +1210,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "8507" } ] } @@ -1405,7 +1237,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d81", + "id": "dv-63287c9ff7c8d34d272a3d7e", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -1453,8 +1285,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "2394", - "display": "Ovarian Cancer" + "code": "9256", + "display": "Colorectal Cancer" } ] } @@ -1470,7 +1302,7 @@ ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "text": "C (Case study)" } }, { @@ -1515,19 +1347,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "5959" + "value": "5960" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a3d7d", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -1544,40 +1376,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "1909", + "display": "Melanoma" } ] } @@ -1587,19 +1415,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "B (Clinical evidence)" } }, { @@ -1607,41 +1429,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1147220", + "display": "Vemurafenib" } ] } @@ -1650,33 +1448,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "1398" } ] } @@ -1685,7 +1475,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d62", + "id": "dv-63287c9ff7c8d34d272a40a8", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -1733,8 +1523,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "9256", - "display": "Colorectal Cancer" + "code": "50626", + "display": "Gastrointestinal Neuroendocrine Tumor" } ] } @@ -1750,7 +1540,7 @@ ] }, "valueCodeableConcept": { - "text": "D (Preclinical evidence)" + "text": "C (Case study)" } }, { @@ -1795,19 +1585,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "99" + "value": "1430" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a3d6b", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -1824,40 +1614,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "1909", + "display": "Melanoma" } ] } @@ -1867,19 +1653,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "B (Clinical evidence)" } }, { @@ -1887,41 +1667,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1147220", + "display": "Vemurafenib" } ] } @@ -1930,33 +1686,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "1749" } ] } @@ -1965,7 +1713,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a40c9", + "id": "dv-63287c9ff7c8d34d272a3d66", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -2013,8 +1761,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "4947", - "display": "Cholangiocarcinoma" + "code": "3969", + "display": "Thyroid Gland Papillary Carcinoma" } ] } @@ -2075,19 +1823,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "5906" + "value": "1414" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a3d65", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -2104,40 +1852,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "8923", + "display": "Skin Melanoma" } ] } @@ -2147,19 +1891,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "B (Clinical evidence)" } }, { @@ -2167,41 +1905,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1147220", + "display": "Vemurafenib" } ] } @@ -2210,33 +1924,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "1410" } ] } @@ -2245,7 +1951,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d82", + "id": "dv-63287c9ff7c8d34d272a40ee", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -2293,8 +1999,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "2876", - "display": "Laryngeal Squamous Cell Carcinoma" + "code": "1909", + "display": "Melanoma" } ] } @@ -2310,7 +2016,7 @@ ] }, "valueCodeableConcept": { - "text": "C (Case study)" + "text": "B (Clinical evidence)" } }, { @@ -2355,19 +2061,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "5962" + "value": "1421" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a3d86", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -2384,40 +2090,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "7146", + "display": "Langerhans Cell Sarcoma" } ] } @@ -2427,19 +2129,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "B (Clinical evidence)" } }, { @@ -2447,41 +2143,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1147220", + "display": "Vemurafenib" } ] } @@ -2490,33 +2162,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "7583" } ] } @@ -2525,7 +2189,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d6b", + "id": "dv-63287c9ff7c8d34d272a3d62", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -2573,8 +2237,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "1909", - "display": "Melanoma" + "code": "9256", + "display": "Colorectal Cancer" } ] } @@ -2590,7 +2254,7 @@ ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "text": "D (Preclinical evidence)" } }, { @@ -2635,19 +2299,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "1749" + "value": "99" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a4090", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -2664,40 +2328,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "9256", + "display": "Colorectal Cancer" } ] } @@ -2707,19 +2367,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "D (Preclinical evidence)" } }, { @@ -2727,41 +2381,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1147220", + "display": "Vemurafenib" } ] } @@ -2770,33 +2400,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "1408" } ] } @@ -2805,7 +2427,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d72", + "id": "dv-63287c9ff7c8d34d272a40ca", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -2853,8 +2475,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "1909", - "display": "Melanoma" + "code": "9256", + "display": "Colorectal Cancer" } ] } @@ -2870,7 +2492,7 @@ ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "text": "D (Preclinical evidence)" } }, { @@ -2915,19 +2537,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "3755" + "value": "8506" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a40ef", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -2944,40 +2566,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "80522", + "display": "Thyroid Gland Anaplastic Carcinoma" } ] } @@ -2987,19 +2605,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "C (Case study)" } }, { @@ -3007,41 +2619,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1147220", + "display": "Vemurafenib" } ] } @@ -3050,33 +2638,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "5961" } ] } @@ -3085,7 +2665,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a40f1", + "id": "dv-63287c9ff7c8d34d272a3d81", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -3133,8 +2713,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "9256", - "display": "Colorectal Cancer" + "code": "2394", + "display": "Ovarian Cancer" } ] } @@ -3150,7 +2730,7 @@ ] }, "valueCodeableConcept": { - "text": "D (Preclinical evidence)" + "text": "B (Clinical evidence)" } }, { @@ -3195,19 +2775,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "8507" + "value": "5959" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a3d6a", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -3224,60 +2804,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ + "derivedFrom": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" + "system": "https://disease-ontology.org", + "code": "9538", + "display": "Multiple Myeloma" } ] } @@ -3287,41 +2843,31 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueString": "T" + "valueCodeableConcept": { + "text": "C (Case study)" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1147220", + "display": "Vemurafenib" } ] } @@ -3330,33 +2876,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "1699" } ] } @@ -3365,7 +2903,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a40ca", + "id": "dv-63287c9ff7c8d34d272a40c9", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -3413,8 +2951,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "9256", - "display": "Colorectal Cancer" + "code": "4947", + "display": "Cholangiocarcinoma" } ] } @@ -3430,7 +2968,7 @@ ] }, "valueCodeableConcept": { - "text": "D (Preclinical evidence)" + "text": "C (Case study)" } }, { @@ -3475,19 +3013,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "8506" + "value": "5906" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a4086", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -3504,40 +3042,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "9256", + "display": "Colorectal Cancer" } ] } @@ -3547,19 +3081,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "D (Preclinical evidence)" } }, { @@ -3567,41 +3095,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1147220", + "display": "Vemurafenib" } ] } @@ -3610,33 +3114,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "98" } ] } @@ -3645,7 +3141,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d80", + "id": "dv-63287c9ff7c8d34d272a3d69", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -3693,8 +3189,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "80522", - "display": "Thyroid Gland Anaplastic Carcinoma" + "code": "9538", + "display": "Multiple Myeloma" } ] } @@ -3710,7 +3206,7 @@ ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "text": "C (Case study)" } }, { @@ -3755,19 +3251,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "6045" + "value": "1698" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a40c8", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -3784,40 +3280,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } + "code": "81259-4", + "display": "phenotypic treatment context" + } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "9256", + "display": "Colorectal Cancer" } ] } @@ -3827,19 +3319,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "B (Clinical evidence)" } }, { @@ -3847,41 +3333,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1147220", + "display": "Vemurafenib" } ] } @@ -3890,33 +3352,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "1902" } ] } @@ -3925,7 +3379,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d68", + "id": "dv-63287c9ff7c8d34d272a3d80", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -3973,8 +3427,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "3969", - "display": "Thyroid Gland Papillary Carcinoma" + "code": "80522", + "display": "Thyroid Gland Anaplastic Carcinoma" } ] } @@ -4035,19 +3489,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "1591" + "value": "6045" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a3d67", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -4064,40 +3518,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "285", + "display": "Hairy Cell Leukemia" } ] } @@ -4107,19 +3557,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "B (Clinical evidence)" } }, { @@ -4127,41 +3571,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1147220", + "display": "Vemurafenib" } ] } @@ -4170,33 +3590,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "1579" } ] } @@ -4205,7 +3617,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d74", + "id": "dv-63287c9ff7c8d34d272a3d68", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -4253,8 +3665,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "6812", - "display": "Childhood Pilocytic Astrocytoma" + "code": "3969", + "display": "Thyroid Gland Papillary Carcinoma" } ] } @@ -4270,7 +3682,7 @@ ] }, "valueCodeableConcept": { - "text": "C (Case study)" + "text": "B (Clinical evidence)" } }, { @@ -4315,19 +3727,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "3777" + "value": "1591" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a40ed", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -4344,40 +3756,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "9256", + "display": "Colorectal Cancer" } ] } @@ -4387,19 +3795,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "B (Clinical evidence)" } }, { @@ -4407,41 +3809,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1147220", + "display": "Vemurafenib" } ] } @@ -4450,33 +3828,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Does Not Support Sensitivity/Response" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "1413" } ] } @@ -4485,7 +3855,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a40ee", + "id": "dv-63287c9ff7c8d34d272a3d82", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -4533,8 +3903,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "1909", - "display": "Melanoma" + "code": "2876", + "display": "Laryngeal Squamous Cell Carcinoma" } ] } @@ -4550,7 +3920,7 @@ ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "text": "C (Case study)" } }, { @@ -4595,19 +3965,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "1421" + "value": "5962" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a3d72", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -4624,40 +3994,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "1909", + "display": "Melanoma" } ] } @@ -4667,19 +4033,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "B (Clinical evidence)" } }, { @@ -4687,41 +4047,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1147220", + "display": "Vemurafenib" } ] } @@ -4730,33 +4066,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "3755" } ] } @@ -4765,7 +4093,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d7e", + "id": "dv-63287c9ff7c8d34d272a3d5e", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -4813,8 +4141,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "9256", - "display": "Colorectal Cancer" + "code": "1909", + "display": "Melanoma" } ] } @@ -4830,7 +4158,7 @@ ] }, "valueCodeableConcept": { - "text": "C (Case study)" + "text": "D (Preclinical evidence)" } }, { @@ -4864,7 +4192,7 @@ ] }, "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" + "text": "Supports Resistance" } } ], @@ -4875,19 +4203,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "5960" + "value": "90" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a3d71", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -4904,40 +4232,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "1909", + "display": "Melanoma" } ] } @@ -4947,4650 +4271,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a40a8", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "50626", - "display": "Gastrointestinal Neuroendocrine Tumor" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "C (Case study)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "1430" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d7b", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "8923", - "display": "Skin Melanoma" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "A (Validated association)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "1409" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a40d4", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "9256", - "display": "Colorectal Cancer" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "C (Case study)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "1589" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d84", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "3969", - "display": "Thyroid Gland Papillary Carcinoma" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "B (Clinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "9018" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d7f", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "9256", - "display": "Colorectal Cancer" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "B (Clinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Does Not Support Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "1405" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d66", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "3969", - "display": "Thyroid Gland Papillary Carcinoma" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "C (Case study)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "1414" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d73", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "1909", - "display": "Melanoma" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "B (Clinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "3757" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a40ed", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "9256", - "display": "Colorectal Cancer" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "B (Clinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Does Not Support Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "1413" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d71", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "1909", - "display": "Melanoma" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "B (Clinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "3750" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a40c8", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "9256", - "display": "Colorectal Cancer" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "B (Clinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "1902" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d7d", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "1909", - "display": "Melanoma" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "B (Clinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "1398" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a4090", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "9256", - "display": "Colorectal Cancer" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "D (Preclinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "1408" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d5e", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "1909", - "display": "Melanoma" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "D (Preclinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Resistance" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "90" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d67", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "285", - "display": "Hairy Cell Leukemia" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "B (Clinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "1579" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a40ef", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "80522", - "display": "Thyroid Gland Anaplastic Carcinoma" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "C (Case study)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "5961" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d7a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "3908", - "display": "Lung Non-small Cell Carcinoma" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "B (Clinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "5958" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d75", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "50933", - "display": "Ovarian Serous Carcinoma" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "C (Case study)" + "text": "B (Clinical evidence)" } }, { @@ -9635,168 +4322,7 @@ }, { "system": "https://civicdb.org/evidence", - "value": "3787" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "value": "3750" } ] } diff --git a/tests/expected_outputs/find_subject_tx_implications/5.json b/tests/expected_outputs/find_subject_tx_implications/5.json index 058de23cf..08f78c74b 100644 --- a/tests/expected_outputs/find_subject_tx_implications/5.json +++ b/tests/expected_outputs/find_subject_tx_implications/5.json @@ -400,167 +400,6 @@ ] } }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, { "name": "implication", "resource": { @@ -699,167 +538,6 @@ } ] } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } } ] } \ No newline at end of file diff --git a/tests/expected_outputs/find_subject_tx_implications/6.json b/tests/expected_outputs/find_subject_tx_implications/6.json index dd6e1f5ee..ff4705a06 100644 --- a/tests/expected_outputs/find_subject_tx_implications/6.json +++ b/tests/expected_outputs/find_subject_tx_implications/6.json @@ -401,13 +401,13 @@ } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a3d65", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -424,40 +424,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "8923", + "display": "Skin Melanoma" } ] } @@ -467,19 +463,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "B (Clinical evidence)" } }, { @@ -487,41 +477,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1147220", + "display": "Vemurafenib" } ] } @@ -530,33 +496,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "1410" } ] } @@ -565,7 +523,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d65", + "id": "dv-63287c9ff7c8d34d272a3d6a", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -613,8 +571,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "8923", - "display": "Skin Melanoma" + "code": "9538", + "display": "Multiple Myeloma" } ] } @@ -630,7 +588,7 @@ ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "text": "C (Case study)" } }, { @@ -675,19 +633,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "1410" + "value": "1699" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a3d6b", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -704,40 +662,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "1909", + "display": "Melanoma" } ] } @@ -747,19 +701,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "B (Clinical evidence)" } }, { @@ -767,41 +715,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1147220", + "display": "Vemurafenib" } ] } @@ -810,33 +734,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "1749" } ] } @@ -845,7 +761,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d6a", + "id": "dv-63287c9ff7c8d34d272a3d6c", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -893,8 +809,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "9538", - "display": "Multiple Myeloma" + "code": "9256", + "display": "Colorectal Cancer" } ] } @@ -910,7 +826,7 @@ ] }, "valueCodeableConcept": { - "text": "C (Case study)" + "text": "B (Clinical evidence)" } }, { @@ -927,8 +843,8 @@ "coding": [ { "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" + "code": "263034", + "display": "Panitumumab" } ] } @@ -944,7 +860,7 @@ ] }, "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" + "text": "Supports Resistance" } } ], @@ -955,19 +871,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "1699" + "value": "2115" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a3d6e", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -984,40 +900,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "9256", + "display": "Colorectal Cancer" } ] } @@ -1027,19 +939,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "B (Clinical evidence)" } }, { @@ -1047,41 +953,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "32592", + "display": "Oxaliplatin" } ] } @@ -1090,33 +972,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Resistance" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "2117" } ] } @@ -1125,7 +999,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d6b", + "id": "dv-63287c9ff7c8d34d272a3d7d", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -1235,19 +1109,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "1749" + "value": "1398" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a3d7f", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -1264,40 +1138,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "9256", + "display": "Colorectal Cancer" } ] } @@ -1307,19 +1177,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "B (Clinical evidence)" } }, { @@ -1327,41 +1191,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1147220", + "display": "Vemurafenib" } ] } @@ -1370,33 +1210,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Does Not Support Sensitivity/Response" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "1405" } ] } @@ -1405,7 +1237,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d6c", + "id": "dv-63287c9ff7c8d34d272a3d80", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -1453,8 +1285,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "9256", - "display": "Colorectal Cancer" + "code": "80522", + "display": "Thyroid Gland Anaplastic Carcinoma" } ] } @@ -1487,8 +1319,8 @@ "coding": [ { "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "263034", - "display": "Panitumumab" + "code": "1147220", + "display": "Vemurafenib" } ] } @@ -1504,7 +1336,7 @@ ] }, "valueCodeableConcept": { - "text": "Supports Resistance" + "text": "Supports Sensitivity/Response" } } ], @@ -1515,19 +1347,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "2115" + "value": "6045" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a3d82", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -1544,40 +1376,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "2876", + "display": "Laryngeal Squamous Cell Carcinoma" } ] } @@ -1587,19 +1415,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "C (Case study)" } }, { @@ -1607,41 +1429,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1147220", + "display": "Vemurafenib" } ] } @@ -1650,33 +1448,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "5962" } ] } @@ -1685,7 +1475,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d6e", + "id": "dv-63287c9ff7c8d34d272a3d60", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -1767,8 +1557,8 @@ "coding": [ { "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "32592", - "display": "Oxaliplatin" + "code": "318341", + "display": "Cetuximab" } ] } @@ -1795,19 +1585,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "2117" + "value": "126" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a3d69", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -1824,40 +1614,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "9538", + "display": "Multiple Myeloma" } ] } @@ -1867,19 +1653,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "C (Case study)" } }, { @@ -1887,41 +1667,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1147220", + "display": "Vemurafenib" } ] } @@ -1930,33 +1686,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "1698" } ] } @@ -1965,7 +1713,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d7d", + "id": "dv-63287c9ff7c8d34d272a3d6d", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -2013,8 +1761,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "1909", - "display": "Melanoma" + "code": "9256", + "display": "Colorectal Cancer" } ] } @@ -2047,8 +1795,8 @@ "coding": [ { "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" + "code": "318341", + "display": "Cetuximab" } ] } @@ -2064,7 +1812,7 @@ ] }, "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" + "text": "Supports Resistance" } } ], @@ -2075,19 +1823,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "1398" + "value": "2115" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a3d73", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -2104,40 +1852,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "1909", + "display": "Melanoma" } ] } @@ -2147,19 +1891,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "B (Clinical evidence)" } }, { @@ -2167,41 +1905,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1147220", + "display": "Vemurafenib" } ] } @@ -2210,33 +1924,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "3757" } ] } @@ -2245,7 +1951,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d7f", + "id": "dv-63287c9ff7c8d34d272a3d77", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -2327,8 +2033,8 @@ "coding": [ { "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" + "code": "263034", + "display": "Panitumumab" } ] } @@ -2344,7 +2050,7 @@ ] }, "valueCodeableConcept": { - "text": "Does Not Support Sensitivity/Response" + "text": "Does Not Support Resistance" } } ], @@ -2355,19 +2061,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "1405" + "value": "816" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a3d6f", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -2384,40 +2090,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "9256", + "display": "Colorectal Cancer" } ] } @@ -2427,19 +2129,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "B (Clinical evidence)" } }, { @@ -2447,41 +2143,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "51499", + "display": "Irinotecan" } ] } @@ -2490,33 +2162,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Resistance" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "2118" } ] } @@ -2525,7 +2189,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d80", + "id": "dv-63287c9ff7c8d34d272a3d7b", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -2573,8 +2237,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "80522", - "display": "Thyroid Gland Anaplastic Carcinoma" + "code": "8923", + "display": "Skin Melanoma" } ] } @@ -2590,7 +2254,7 @@ ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "text": "A (Validated association)" } }, { @@ -2635,19 +2299,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "6045" + "value": "1409" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a3d7a", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -2664,40 +2328,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "3908", + "display": "Lung Non-small Cell Carcinoma" } ] } @@ -2707,19 +2367,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "B (Clinical evidence)" } }, { @@ -2727,41 +2381,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1147220", + "display": "Vemurafenib" } ] } @@ -2770,33 +2400,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "5958" } ] } @@ -2805,7 +2427,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d82", + "id": "dv-63287c9ff7c8d34d272a3d81", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -2853,8 +2475,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "2876", - "display": "Laryngeal Squamous Cell Carcinoma" + "code": "2394", + "display": "Ovarian Cancer" } ] } @@ -2870,7 +2492,7 @@ ] }, "valueCodeableConcept": { - "text": "C (Case study)" + "text": "B (Clinical evidence)" } }, { @@ -2915,19 +2537,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "5962" + "value": "5959" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a3d5d", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -2944,40 +2566,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "1909", + "display": "Melanoma" } ] } @@ -2987,19 +2605,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "D (Preclinical evidence)" } }, { @@ -3007,41 +2619,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1425099", + "display": "Trametinib" } ] } @@ -3050,33 +2638,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Does Not Support Resistance" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "86" } ] } @@ -3085,7 +2665,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d60", + "id": "dv-63287c9ff7c8d34d272a3d5e", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -3133,8 +2713,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "9256", - "display": "Colorectal Cancer" + "code": "1909", + "display": "Melanoma" } ] } @@ -3150,7 +2730,7 @@ ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "text": "D (Preclinical evidence)" } }, { @@ -3167,8 +2747,8 @@ "coding": [ { "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "318341", - "display": "Cetuximab" + "code": "1147220", + "display": "Vemurafenib" } ] } @@ -3195,19 +2775,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "126" + "value": "90" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a3d71", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -3224,40 +2804,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "1909", + "display": "Melanoma" } ] } @@ -3267,19 +2843,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "B (Clinical evidence)" } }, { @@ -3287,41 +2857,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1147220", + "display": "Vemurafenib" } ] } @@ -3330,33 +2876,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "3750" } ] } @@ -3365,7 +2903,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d69", + "id": "dv-63287c9ff7c8d34d272a3d74", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -3413,8 +2951,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "9538", - "display": "Multiple Myeloma" + "code": "6812", + "display": "Childhood Pilocytic Astrocytoma" } ] } @@ -3475,19 +3013,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "1698" + "value": "3777" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a3d78", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -3504,40 +3042,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "1909", + "display": "Melanoma" } ] } @@ -3547,19 +3081,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "B (Clinical evidence)" } }, { @@ -3567,41 +3095,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "", + "display": "MEK Inhibitor RO4987655" } ] } @@ -3610,33 +3114,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Does Not Support Resistance" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "994" } ] } @@ -3645,7 +3141,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d6d", + "id": "dv-63287c9ff7c8d34d272a3d61", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -3693,8 +3189,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "9256", - "display": "Colorectal Cancer" + "code": "3908", + "display": "Lung Non-small Cell Carcinoma" } ] } @@ -3710,7 +3206,7 @@ ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "text": "C (Case study)" } }, { @@ -3727,8 +3223,8 @@ "coding": [ { "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "318341", - "display": "Cetuximab" + "code": "1424911", + "display": "Dabrafenib" } ] } @@ -3755,19 +3251,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "2115" + "value": "91" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a3d64", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -3784,40 +3280,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "9256", + "display": "Colorectal Cancer" } ] } @@ -3827,19 +3319,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "B (Clinical evidence)" } }, { @@ -3847,41 +3333,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "318341", + "display": "Cetuximab" } ] } @@ -3890,33 +3352,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Does Not Support Resistance" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "816" } ] } @@ -3925,7 +3379,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d73", + "id": "dv-63287c9ff7c8d34d272a3d68", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -3973,8 +3427,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "1909", - "display": "Melanoma" + "code": "3969", + "display": "Thyroid Gland Papillary Carcinoma" } ] } @@ -4035,19 +3489,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "3757" + "value": "1591" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a3d76", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -4064,40 +3518,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "9256", + "display": "Colorectal Cancer" } ] } @@ -4107,19 +3557,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "C (Case study)" } }, { @@ -4127,41 +3571,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "263034", + "display": "Panitumumab" } ] } @@ -4170,33 +3590,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Resistance" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "3827" } ] } @@ -4205,7 +3617,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d77", + "id": "dv-63287c9ff7c8d34d272a3d79", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -4253,8 +3665,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "9256", - "display": "Colorectal Cancer" + "code": "162", + "display": "Cancer" } ] } @@ -4270,7 +3682,7 @@ ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "text": "D (Preclinical evidence)" } }, { @@ -4287,8 +3699,8 @@ "coding": [ { "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "263034", - "display": "Panitumumab" + "code": "1722365", + "display": "Cobimetinib" } ] } @@ -4304,7 +3716,7 @@ ] }, "valueCodeableConcept": { - "text": "Does Not Support Resistance" + "text": "Supports Sensitivity/Response" } } ], @@ -4315,19 +3727,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "816" + "value": "1141" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a3d70", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -4344,40 +3756,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "1909", + "display": "Melanoma" } ] } @@ -4387,19 +3795,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "B (Clinical evidence)" } }, { @@ -4407,41 +3809,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1425099", + "display": "Trametinib" } ] } @@ -4450,33 +3828,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "2135" } ] } @@ -4485,7 +3855,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d6f", + "id": "dv-63287c9ff7c8d34d272a3d7c", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -4567,8 +3937,8 @@ "coding": [ { "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "51499", - "display": "Irinotecan" + "code": "1424911", + "display": "Dabrafenib" } ] } @@ -4584,7 +3954,7 @@ ] }, "valueCodeableConcept": { - "text": "Supports Resistance" + "text": "Does Not Support Sensitivity/Response" } } ], @@ -4595,19 +3965,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "2118" + "value": "1406" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a3d7e", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -4624,40 +3994,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "9256", + "display": "Colorectal Cancer" } ] } @@ -4667,19 +4033,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "C (Case study)" } }, { @@ -4687,41 +4047,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1147220", + "display": "Vemurafenib" } ] } @@ -4730,33 +4066,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "5960" } ] } @@ -4765,7 +4093,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d7b", + "id": "dv-63287c9ff7c8d34d272a3d84", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -4813,8 +4141,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "8923", - "display": "Skin Melanoma" + "code": "3969", + "display": "Thyroid Gland Papillary Carcinoma" } ] } @@ -4830,7 +4158,7 @@ ] }, "valueCodeableConcept": { - "text": "A (Validated association)" + "text": "B (Clinical evidence)" } }, { @@ -4875,19 +4203,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "1409" + "value": "9018" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a3d63", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -4904,40 +4232,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "1909", + "display": "Melanoma" } ] } @@ -4947,19 +4271,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "C (Case study)" } }, { @@ -4967,41 +4285,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "", + "display": "Pictilisib" } ] } @@ -5010,33 +4304,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "757" } ] } @@ -5045,7 +4331,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d7a", + "id": "dv-63287c9ff7c8d34d272a3d66", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -5093,8 +4379,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "3908", - "display": "Lung Non-small Cell Carcinoma" + "code": "3969", + "display": "Thyroid Gland Papillary Carcinoma" } ] } @@ -5110,7 +4396,7 @@ ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "text": "C (Case study)" } }, { @@ -5155,19 +4441,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "5958" + "value": "1414" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a3d67", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -5184,40 +4470,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "285", + "display": "Hairy Cell Leukemia" } ] } @@ -5227,19 +4509,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "B (Clinical evidence)" } }, { @@ -5247,41 +4523,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1147220", + "display": "Vemurafenib" } ] } @@ -5290,33 +4542,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "1579" } ] } @@ -5325,7 +4569,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d81", + "id": "dv-63287c9ff7c8d34d272a3d72", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -5373,8 +4617,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "2394", - "display": "Ovarian Cancer" + "code": "1909", + "display": "Melanoma" } ] } @@ -5435,19 +4679,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "5959" + "value": "3755" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a3d75", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -5464,40 +4708,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "50933", + "display": "Ovarian Serous Carcinoma" } ] } @@ -5507,19 +4747,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "C (Case study)" } }, { @@ -5527,76 +4761,44 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "51963-7", + "display": "medication-assessed" } ] }, - "valueString": "A" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1147220", + "display": "Vemurafenib" } ] - }, - "valueString": "T" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] + "text": "Supports Sensitivity/Response" } - }, + } + ], + "identifier": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "3787" } ] } @@ -5605,7 +4807,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d5d", + "id": "dv-63287c9ff7c8d34d272a3d86", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -5653,8 +4855,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "1909", - "display": "Melanoma" + "code": "7146", + "display": "Langerhans Cell Sarcoma" } ] } @@ -5670,7 +4872,7 @@ ] }, "valueCodeableConcept": { - "text": "D (Preclinical evidence)" + "text": "B (Clinical evidence)" } }, { @@ -5687,8 +4889,8 @@ "coding": [ { "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1425099", - "display": "Trametinib" + "code": "1147220", + "display": "Vemurafenib" } ] } @@ -5704,7 +4906,7 @@ ] }, "valueCodeableConcept": { - "text": "Does Not Support Resistance" + "text": "Supports Sensitivity/Response" } } ], @@ -5715,19 +4917,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "86" + "value": "7583" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a40a8", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -5744,40 +4946,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "50626", + "display": "Gastrointestinal Neuroendocrine Tumor" } ] } @@ -5787,19 +4985,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "C (Case study)" } }, { @@ -5807,41 +4999,37 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "51963-7", + "display": "medication-assessed" } ] }, - "valueString": "A" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1424911", + "display": "Dabrafenib" } ] - }, - "valueString": "T" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1147220", + "display": "Vemurafenib" } ] } @@ -5851,33 +5039,45 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "51963-7", + "display": "medication-assessed" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "coding": [ + { + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1425099", + "display": "Trametinib" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" + }, + { + "system": "https://civicdb.org/evidence", + "value": "1430" + } ] } }, @@ -5885,7 +5085,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d5e", + "id": "dv-63287c9ff7c8d34d272a40ab", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -5933,8 +5133,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "1909", - "display": "Melanoma" + "code": "8923", + "display": "Skin Melanoma" } ] } @@ -5950,7 +5150,7 @@ ] }, "valueCodeableConcept": { - "text": "D (Preclinical evidence)" + "text": "B (Clinical evidence)" } }, { @@ -5967,8 +5167,28 @@ "coding": [ { "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" + "code": "1424911", + "display": "Dabrafenib" + } + ] + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "51963-7", + "display": "medication-assessed" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1425099", + "display": "Trametinib" } ] } @@ -5984,7 +5204,7 @@ ] }, "valueCodeableConcept": { - "text": "Supports Resistance" + "text": "Supports Sensitivity/Response" } } ], @@ -5995,19 +5215,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "90" + "value": "3758" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a40ad", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -6024,40 +5244,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "4928", + "display": "Intrahepatic Cholangiocarcinoma" } ] } @@ -6067,19 +5283,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "C (Case study)" } }, { @@ -6087,41 +5297,37 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "51963-7", + "display": "medication-assessed" } ] }, - "valueString": "A" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1424911", + "display": "Dabrafenib" } ] - }, - "valueString": "T" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1425099", + "display": "Trametinib" } ] } @@ -6130,33 +5336,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "5903" } ] } @@ -6165,7 +5363,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d71", + "id": "dv-63287c9ff7c8d34d272a40ae", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -6247,8 +5445,28 @@ "coding": [ { "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" + "code": "1424911", + "display": "Dabrafenib" + } + ] + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "51963-7", + "display": "medication-assessed" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1425099", + "display": "Trametinib" } ] } @@ -6275,19 +5493,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "3750" + "value": "6178" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a40b9", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -6304,40 +5522,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "9256", + "display": "Colorectal Cancer" } ] } @@ -6347,19 +5561,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "D (Preclinical evidence)" } }, { @@ -6367,41 +5575,37 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "51963-7", + "display": "medication-assessed" } ] }, - "valueString": "A" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "", + "display": "Dactolisib" } ] - }, - "valueString": "T" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "", + "display": "GDC-0879" } ] } @@ -6410,33 +5614,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "1428" } ] } @@ -6445,7 +5641,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d74", + "id": "dv-63287c9ff7c8d34d272a40bc", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -6493,8 +5689,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "6812", - "display": "Childhood Pilocytic Astrocytoma" + "code": "9256", + "display": "Colorectal Cancer" } ] } @@ -6510,7 +5706,7 @@ ] }, "valueCodeableConcept": { - "text": "C (Case study)" + "text": "B (Clinical evidence)" } }, { @@ -6527,8 +5723,8 @@ "coding": [ { "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" + "code": "2049106", + "display": "Encorafenib" } ] } @@ -6537,10709 +5733,20 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "system": "http://loinc.org", + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "3777" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d78", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "1909", - "display": "Melanoma" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "B (Clinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "", - "display": "MEK Inhibitor RO4987655" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Does Not Support Resistance" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "994" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d61", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "3908", - "display": "Lung Non-small Cell Carcinoma" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "C (Case study)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1424911", - "display": "Dabrafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Resistance" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "91" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d64", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "9256", - "display": "Colorectal Cancer" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "B (Clinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "318341", - "display": "Cetuximab" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Does Not Support Resistance" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "816" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d68", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "3969", - "display": "Thyroid Gland Papillary Carcinoma" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "B (Clinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "1591" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d76", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "9256", - "display": "Colorectal Cancer" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "C (Case study)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "263034", - "display": "Panitumumab" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Resistance" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "3827" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d79", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "162", - "display": "Cancer" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "D (Preclinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1722365", - "display": "Cobimetinib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "1141" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d70", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "1909", - "display": "Melanoma" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "B (Clinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1425099", - "display": "Trametinib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "2135" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d7c", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "9256", - "display": "Colorectal Cancer" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "B (Clinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1424911", - "display": "Dabrafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Does Not Support Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "1406" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d7e", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "9256", - "display": "Colorectal Cancer" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "C (Case study)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "5960" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d84", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "3969", - "display": "Thyroid Gland Papillary Carcinoma" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "B (Clinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "9018" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d63", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "1909", - "display": "Melanoma" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "C (Case study)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "", - "display": "Pictilisib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "757" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d66", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "3969", - "display": "Thyroid Gland Papillary Carcinoma" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "C (Case study)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "1414" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d67", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "285", - "display": "Hairy Cell Leukemia" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "B (Clinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "1579" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d72", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "1909", - "display": "Melanoma" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "B (Clinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "3755" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d75", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "50933", - "display": "Ovarian Serous Carcinoma" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "C (Case study)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "3787" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a3d86", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "7146", - "display": "Langerhans Cell Sarcoma" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "B (Clinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "7583" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a40a8", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "50626", - "display": "Gastrointestinal Neuroendocrine Tumor" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "C (Case study)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1424911", - "display": "Dabrafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1425099", - "display": "Trametinib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "1430" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a40ab", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "8923", - "display": "Skin Melanoma" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "B (Clinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1424911", - "display": "Dabrafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1425099", - "display": "Trametinib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "3758" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a40ad", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "4928", - "display": "Intrahepatic Cholangiocarcinoma" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "C (Case study)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1424911", - "display": "Dabrafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1425099", - "display": "Trametinib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "5903" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a40ae", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "1909", - "display": "Melanoma" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "B (Clinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1424911", - "display": "Dabrafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1425099", - "display": "Trametinib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "6178" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a40b9", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "9256", - "display": "Colorectal Cancer" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "D (Preclinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "", - "display": "Dactolisib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "", - "display": "GDC-0879" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "1428" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a40bc", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "9256", - "display": "Colorectal Cancer" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "B (Clinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "2049106", - "display": "Encorafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "2049122", - "display": "Binimetinib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "318341", - "display": "Cetuximab" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "7260" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a40d3", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "9256", - "display": "Colorectal Cancer" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "B (Clinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "32592", - "display": "Oxaliplatin" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "194000", - "display": "Capecitabine" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "253337", - "display": "Bevacizumab" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Resistance" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "2121" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a40d4", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "9256", - "display": "Colorectal Cancer" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "C (Case study)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "263034", - "display": "Panitumumab" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "1589" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a40d8", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "9256", - "display": "Colorectal Cancer" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "D (Preclinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "", - "display": "Pictilisib Bismesylate" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "", - "display": "PLX4720" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "96" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a4085", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "9256", - "display": "Colorectal Cancer" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "B (Clinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "2049122", - "display": "Binimetinib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "318341", - "display": "Cetuximab" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "2049106", - "display": "Encorafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "7612" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a40b0", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "1909", - "display": "Melanoma" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "B (Clinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1424911", - "display": "Dabrafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1425099", - "display": "Trametinib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "6940" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a40ed", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "9256", - "display": "Colorectal Cancer" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "B (Clinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "263034", - "display": "Panitumumab" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Does Not Support Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "1413" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a4086", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "9256", - "display": "Colorectal Cancer" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "D (Preclinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "194000", - "display": "Capecitabine" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "253337", - "display": "Bevacizumab" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "98" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a40b1", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "4607", - "display": "Biliary Tract Cancer" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "B (Clinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1424911", - "display": "Dabrafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1425099", - "display": "Trametinib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "7264" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a40c8", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "9256", - "display": "Colorectal Cancer" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "B (Clinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "51499", - "display": "Irinotecan" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "318341", - "display": "Cetuximab" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "1902" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a40c9", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "4947", - "display": "Cholangiocarcinoma" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "C (Case study)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "51499", - "display": "Irinotecan" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "263034", - "display": "Panitumumab" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "5906" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a40dd", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "9256", - "display": "Colorectal Cancer" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "D (Preclinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "", - "display": "Nutlin-3" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "", - "display": "PLX4720" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "97" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a40e4", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "9256", - "display": "Colorectal Cancer" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "D (Preclinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "495881", - "display": "Sorafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "263034", - "display": "Panitumumab" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "89" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a40ee", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "1909", - "display": "Melanoma" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "B (Clinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1722365", - "display": "Cobimetinib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "1421" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a40af", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "4928", - "display": "Intrahepatic Cholangiocarcinoma" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "C (Case study)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1424911", - "display": "Dabrafenib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1425099", - "display": "Trametinib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" - } - ] - }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" - } - } - ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "5904" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] + "coding": [ + { + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "2049122", + "display": "Binimetinib" + } + ] } }, { @@ -17247,17 +5754,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "318341", + "display": "Cetuximab" } ] } @@ -17266,77 +5773,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] + "text": "Supports Sensitivity/Response" } - }, + } + ], + "identifier": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 140753335 - } - } + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "7260" } ] } @@ -17345,7 +5800,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a40b2", + "id": "dv-63287c9ff7c8d34d272a40d3", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -17393,8 +5848,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "1909", - "display": "Melanoma" + "code": "9256", + "display": "Colorectal Cancer" } ] } @@ -17427,8 +5882,8 @@ "coding": [ { "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1424911", - "display": "Dabrafenib" + "code": "32592", + "display": "Oxaliplatin" } ] } @@ -17447,8 +5902,28 @@ "coding": [ { "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1425099", - "display": "Trametinib" + "code": "194000", + "display": "Capecitabine" + } + ] + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "51963-7", + "display": "medication-assessed" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "253337", + "display": "Bevacizumab" } ] } @@ -17464,7 +5939,7 @@ ] }, "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" + "text": "Supports Resistance" } } ], @@ -17475,19 +5950,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "95" + "value": "2121" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a40d4", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -17504,40 +5979,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "9256", + "display": "Colorectal Cancer" } ] } @@ -17547,19 +6018,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "C (Case study)" } }, { @@ -17567,41 +6032,17 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "263034", + "display": "Panitumumab" } ] } @@ -17611,33 +6052,45 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "51963-7", + "display": "medication-assessed" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "coding": [ + { + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1147220", + "display": "Vemurafenib" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" + }, + { + "system": "https://civicdb.org/evidence", + "value": "1589" + } ] } }, @@ -17645,7 +6098,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a40e7", + "id": "dv-63287c9ff7c8d34d272a40d8", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -17693,8 +6146,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "80522", - "display": "Thyroid Gland Anaplastic Carcinoma" + "code": "9256", + "display": "Colorectal Cancer" } ] } @@ -17710,7 +6163,7 @@ ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "text": "D (Preclinical evidence)" } }, { @@ -17727,8 +6180,8 @@ "coding": [ { "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1425099", - "display": "Trametinib" + "code": "", + "display": "Pictilisib Bismesylate" } ] } @@ -17747,8 +6200,8 @@ "coding": [ { "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1424911", - "display": "Dabrafenib" + "code": "", + "display": "PLX4720" } ] } @@ -17775,19 +6228,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "6975" + "value": "96" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a4085", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -17804,40 +6257,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "9256", + "display": "Colorectal Cancer" } ] } @@ -17847,19 +6296,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "B (Clinical evidence)" } }, { @@ -17867,41 +6310,37 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "51963-7", + "display": "medication-assessed" } ] }, - "valueString": "A" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "2049122", + "display": "Binimetinib" } ] - }, - "valueString": "T" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "318341", + "display": "Cetuximab" } ] } @@ -17911,33 +6350,45 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "51963-7", + "display": "medication-assessed" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "coding": [ + { + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "2049106", + "display": "Encorafenib" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" + }, + { + "system": "https://civicdb.org/evidence", + "value": "7612" + } ] } }, @@ -17945,7 +6396,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a40ef", + "id": "dv-63287c9ff7c8d34d272a40b0", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -17993,8 +6444,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "80522", - "display": "Thyroid Gland Anaplastic Carcinoma" + "code": "1909", + "display": "Melanoma" } ] } @@ -18010,7 +6461,7 @@ ] }, "valueCodeableConcept": { - "text": "C (Case study)" + "text": "B (Clinical evidence)" } }, { @@ -18027,8 +6478,8 @@ "coding": [ { "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" + "code": "1424911", + "display": "Dabrafenib" } ] } @@ -18047,8 +6498,8 @@ "coding": [ { "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1298944", - "display": "Pertuzumab" + "code": "1425099", + "display": "Trametinib" } ] } @@ -18075,19 +6526,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "5961" + "value": "6940" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a40ed", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -18104,60 +6555,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ + "derivedFrom": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" + "system": "https://disease-ontology.org", + "code": "9256", + "display": "Colorectal Cancer" } ] } @@ -18167,41 +6594,31 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueString": "T" + "valueCodeableConcept": { + "text": "B (Clinical evidence)" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1147220", + "display": "Vemurafenib" } ] } @@ -18211,33 +6628,45 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "51963-7", + "display": "medication-assessed" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "coding": [ + { + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "263034", + "display": "Panitumumab" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "text": "Does Not Support Sensitivity/Response" } } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" + }, + { + "system": "https://civicdb.org/evidence", + "value": "1413" + } ] } }, @@ -18245,7 +6674,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a40bd", + "id": "dv-63287c9ff7c8d34d272a4086", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -18310,7 +6739,7 @@ ] }, "valueCodeableConcept": { - "text": "A (Validated association)" + "text": "D (Preclinical evidence)" } }, { @@ -18327,8 +6756,8 @@ "coding": [ { "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "2049106", - "display": "Encorafenib" + "code": "194000", + "display": "Capecitabine" } ] } @@ -18347,8 +6776,28 @@ "coding": [ { "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "318341", - "display": "Cetuximab" + "code": "253337", + "display": "Bevacizumab" + } + ] + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "51963-7", + "display": "medication-assessed" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1147220", + "display": "Vemurafenib" } ] } @@ -18375,19 +6824,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "9851" + "value": "98" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a40b1", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -18404,40 +6853,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "4607", + "display": "Biliary Tract Cancer" } ] } @@ -18447,19 +6892,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "B (Clinical evidence)" } }, { @@ -18467,41 +6906,37 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "51963-7", + "display": "medication-assessed" } ] }, - "valueString": "A" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1424911", + "display": "Dabrafenib" } ] - }, - "valueString": "T" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1425099", + "display": "Trametinib" } ] } @@ -18510,33 +6945,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "7264" } ] } @@ -18545,7 +6972,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a4090", + "id": "dv-63287c9ff7c8d34d272a40c8", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -18610,7 +7037,7 @@ ] }, "valueCodeableConcept": { - "text": "D (Preclinical evidence)" + "text": "B (Clinical evidence)" } }, { @@ -18627,8 +7054,8 @@ "coding": [ { "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "318341", - "display": "Cetuximab" + "code": "51499", + "display": "Irinotecan" } ] } @@ -18647,8 +7074,8 @@ "coding": [ { "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "328134", - "display": "Gefitinib" + "code": "318341", + "display": "Cetuximab" } ] } @@ -18695,19 +7122,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "1408" + "value": "1902" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a40c9", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -18724,40 +7151,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "4947", + "display": "Cholangiocarcinoma" } ] } @@ -18767,19 +7190,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "C (Case study)" } }, { @@ -18787,41 +7204,37 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "51963-7", + "display": "medication-assessed" } ] }, - "valueString": "A" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "51499", + "display": "Irinotecan" } ] - }, - "valueString": "T" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1147220", + "display": "Vemurafenib" } ] } @@ -18831,33 +7244,45 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "51963-7", + "display": "medication-assessed" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "coding": [ + { + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "263034", + "display": "Panitumumab" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" + }, + { + "system": "https://civicdb.org/evidence", + "value": "5906" + } ] } }, @@ -18865,7 +7290,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a40a9", + "id": "dv-63287c9ff7c8d34d272a40dd", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -18913,8 +7338,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "3908", - "display": "Lung Non-small Cell Carcinoma" + "code": "9256", + "display": "Colorectal Cancer" } ] } @@ -18930,7 +7355,7 @@ ] }, "valueCodeableConcept": { - "text": "A (Validated association)" + "text": "D (Preclinical evidence)" } }, { @@ -18947,8 +7372,8 @@ "coding": [ { "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1424911", - "display": "Dabrafenib" + "code": "", + "display": "Nutlin-3" } ] } @@ -18967,8 +7392,8 @@ "coding": [ { "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1425099", - "display": "Trametinib" + "code": "", + "display": "PLX4720" } ] } @@ -18995,19 +7420,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "3017" + "value": "97" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a40e4", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -19024,40 +7449,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "9256", + "display": "Colorectal Cancer" } ] } @@ -19067,19 +7488,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "D (Preclinical evidence)" } }, { @@ -19087,41 +7502,37 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "51963-7", + "display": "medication-assessed" } ] }, - "valueString": "A" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "495881", + "display": "Sorafenib" } ] - }, - "valueString": "T" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "263034", + "display": "Panitumumab" } ] } @@ -19130,33 +7541,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "89" } ] } @@ -19165,7 +7568,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a40aa", + "id": "dv-63287c9ff7c8d34d272a40ee", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -19213,8 +7616,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "4947", - "display": "Cholangiocarcinoma" + "code": "1909", + "display": "Melanoma" } ] } @@ -19230,7 +7633,7 @@ ] }, "valueCodeableConcept": { - "text": "C (Case study)" + "text": "B (Clinical evidence)" } }, { @@ -19247,8 +7650,8 @@ "coding": [ { "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1424911", - "display": "Dabrafenib" + "code": "1147220", + "display": "Vemurafenib" } ] } @@ -19267,8 +7670,8 @@ "coding": [ { "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1425099", - "display": "Trametinib" + "code": "1722365", + "display": "Cobimetinib" } ] } @@ -19295,19 +7698,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "5902" + "value": "1421" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a40af", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -19324,60 +7727,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ + "derivedFrom": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } - }, + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" + "system": "https://disease-ontology.org", + "code": "4928", + "display": "Intrahepatic Cholangiocarcinoma" } ] } @@ -19387,41 +7766,51 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "93044-6", + "display": "Level of evidence" } ] }, - "valueString": "A" + "valueCodeableConcept": { + "text": "C (Case study)" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "51963-7", + "display": "medication-assessed" } ] }, - "valueString": "T" + "valueCodeableConcept": { + "coding": [ + { + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1424911", + "display": "Dabrafenib" + } + ] + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1425099", + "display": "Trametinib" } ] } @@ -19430,33 +7819,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "5904" } ] } @@ -19465,7 +7846,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a40ca", + "id": "dv-63287c9ff7c8d34d272a40b2", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -19513,8 +7894,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "9256", - "display": "Colorectal Cancer" + "code": "1909", + "display": "Melanoma" } ] } @@ -19530,27 +7911,7 @@ ] }, "valueCodeableConcept": { - "text": "D (Preclinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "51499", - "display": "Irinotecan" - } - ] + "text": "B (Clinical evidence)" } }, { @@ -19567,8 +7928,8 @@ "coding": [ { "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" + "code": "1424911", + "display": "Dabrafenib" } ] } @@ -19587,8 +7948,8 @@ "coding": [ { "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "318341", - "display": "Cetuximab" + "code": "1425099", + "display": "Trametinib" } ] } @@ -19615,19 +7976,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "8506" + "value": "95" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a40e7", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -19644,40 +8005,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "80522", + "display": "Thyroid Gland Anaplastic Carcinoma" } ] } @@ -19687,19 +8044,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "B (Clinical evidence)" } }, { @@ -19707,41 +8058,37 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "51963-7", + "display": "medication-assessed" } ] }, - "valueString": "A" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1425099", + "display": "Trametinib" } ] - }, - "valueString": "T" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1424911", + "display": "Dabrafenib" } ] } @@ -19750,33 +8097,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "6975" } ] } @@ -19785,7 +8124,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a40f1", + "id": "dv-63287c9ff7c8d34d272a40ef", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -19833,8 +8172,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "9256", - "display": "Colorectal Cancer" + "code": "80522", + "display": "Thyroid Gland Anaplastic Carcinoma" } ] } @@ -19850,7 +8189,7 @@ ] }, "valueCodeableConcept": { - "text": "D (Preclinical evidence)" + "text": "C (Case study)" } }, { @@ -19887,8 +8226,8 @@ "coding": [ { "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "337525", - "display": "Erlotinib" + "code": "1298944", + "display": "Pertuzumab" } ] } @@ -19915,19 +8254,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "8507" + "value": "5961" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a40bd", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -19943,41 +8282,37 @@ ], "code": { "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, + "subject": { + "reference": "Patient/CA12345" + }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "9256", + "display": "Colorectal Cancer" } ] } @@ -19987,19 +8322,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "A (Validated association)" } }, { @@ -20007,41 +8336,37 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "51963-7", + "display": "medication-assessed" } ] }, - "valueString": "A" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "2049106", + "display": "Encorafenib" } ] - }, - "valueString": "T" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "318341", + "display": "Cetuximab" } ] } @@ -20050,33 +8375,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "9851" } ] } @@ -20085,7 +8402,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a40b6", + "id": "dv-63287c9ff7c8d34d272a4090", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -20133,8 +8450,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "1909", - "display": "Melanoma" + "code": "9256", + "display": "Colorectal Cancer" } ] } @@ -20167,8 +8484,8 @@ "coding": [ { "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "", - "display": "Dactolisib" + "code": "318341", + "display": "Cetuximab" } ] } @@ -20187,8 +8504,28 @@ "coding": [ { "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "2289380", - "display": "Selumetinib" + "code": "328134", + "display": "Gefitinib" + } + ] + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "51963-7", + "display": "medication-assessed" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1147220", + "display": "Vemurafenib" } ] } @@ -20215,19 +8552,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "1005" + "value": "1408" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a40a9", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -20244,40 +8581,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "3908", + "display": "Lung Non-small Cell Carcinoma" } ] } @@ -20287,19 +8620,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "A (Validated association)" } }, { @@ -20307,41 +8634,37 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "51963-7", + "display": "medication-assessed" } ] }, - "valueString": "A" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1424911", + "display": "Dabrafenib" } ] - }, - "valueString": "T" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1425099", + "display": "Trametinib" } ] } @@ -20350,33 +8673,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "3017" } ] } @@ -20385,7 +8700,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a40c2", + "id": "dv-63287c9ff7c8d34d272a40aa", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -20433,8 +8748,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "9256", - "display": "Colorectal Cancer" + "code": "4947", + "display": "Cholangiocarcinoma" } ] } @@ -20450,7 +8765,7 @@ ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "text": "C (Case study)" } }, { @@ -20467,8 +8782,8 @@ "coding": [ { "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "", - "display": "FOLFOX-4 Regimen" + "code": "1424911", + "display": "Dabrafenib" } ] } @@ -20487,8 +8802,8 @@ "coding": [ { "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "318341", - "display": "Cetuximab" + "code": "1425099", + "display": "Trametinib" } ] } @@ -20504,7 +8819,7 @@ ] }, "valueCodeableConcept": { - "text": "Supports Resistance" + "text": "Supports Sensitivity/Response" } } ], @@ -20515,19 +8830,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "3739" + "value": "5902" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a40ca", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -20544,40 +8859,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "9256", + "display": "Colorectal Cancer" } ] } @@ -20587,19 +8898,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "D (Preclinical evidence)" } }, { @@ -20607,41 +8912,37 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "51963-7", + "display": "medication-assessed" } ] }, - "valueString": "A" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "51499", + "display": "Irinotecan" } ] - }, - "valueString": "T" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1147220", + "display": "Vemurafenib" } ] } @@ -20651,33 +8952,45 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "51963-7", + "display": "medication-assessed" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "coding": [ + { + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "318341", + "display": "Cetuximab" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" + }, + { + "system": "https://civicdb.org/evidence", + "value": "8506" + } ] } }, @@ -20685,7 +8998,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a40d5", + "id": "dv-63287c9ff7c8d34d272a40f1", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -20750,27 +9063,7 @@ ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "263034", - "display": "Panitumumab" - } - ] + "text": "D (Preclinical evidence)" } }, { @@ -20787,8 +9080,8 @@ "coding": [ { "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1425099", - "display": "Trametinib" + "code": "1147220", + "display": "Vemurafenib" } ] } @@ -20807,8 +9100,8 @@ "coding": [ { "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1424911", - "display": "Dabrafenib" + "code": "337525", + "display": "Erlotinib" } ] } @@ -20835,19 +9128,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "6123" + "value": "8507" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a40b6", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -20864,40 +9157,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "1909", + "display": "Melanoma" } ] } @@ -20907,19 +9196,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "D (Preclinical evidence)" } }, { @@ -20927,41 +9210,37 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "51963-7", + "display": "medication-assessed" } ] }, - "valueString": "A" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "", + "display": "Dactolisib" } ] - }, - "valueString": "T" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "2289380", + "display": "Selumetinib" } ] } @@ -20970,33 +9249,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "1005" } ] } @@ -21005,7 +9276,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a40d6", + "id": "dv-63287c9ff7c8d34d272a40c2", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -21053,8 +9324,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "50861", - "display": "Colorectal Adenocarcinoma" + "code": "9256", + "display": "Colorectal Cancer" } ] } @@ -21087,8 +9358,8 @@ "coding": [ { "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "263034", - "display": "Panitumumab" + "code": "", + "display": "FOLFOX-4 Regimen" } ] } @@ -21107,8 +9378,8 @@ "coding": [ { "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1425099", - "display": "Trametinib" + "code": "318341", + "display": "Cetuximab" } ] } @@ -21124,7 +9395,7 @@ ] }, "valueCodeableConcept": { - "text": "Does Not Support Sensitivity/Response" + "text": "Supports Resistance" } } ], @@ -21135,19 +9406,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "6124" + "value": "3739" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a40d5", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -21164,40 +9435,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "9256", + "display": "Colorectal Cancer" } ] } @@ -21207,19 +9474,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "B (Clinical evidence)" } }, { @@ -21227,41 +9488,37 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "51963-7", + "display": "medication-assessed" } ] }, - "valueString": "A" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "263034", + "display": "Panitumumab" } ] - }, - "valueString": "T" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1425099", + "display": "Trametinib" } ] } @@ -21271,33 +9528,45 @@ "coding": [ { "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "51963-7", + "display": "medication-assessed" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "coding": [ + { + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1424911", + "display": "Dabrafenib" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" + }, + { + "system": "https://civicdb.org/evidence", + "value": "6123" + } ] } }, @@ -21305,7 +9574,7 @@ "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-63287c9ff7c8d34d272a40e6", + "id": "dv-63287c9ff7c8d34d272a40d6", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" @@ -21353,8 +9622,8 @@ "coding": [ { "system": "https://disease-ontology.org", - "code": "1909", - "display": "Melanoma" + "code": "50861", + "display": "Colorectal Adenocarcinoma" } ] } @@ -21387,8 +9656,8 @@ "coding": [ { "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1425099", - "display": "Trametinib" + "code": "263034", + "display": "Panitumumab" } ] } @@ -21407,8 +9676,8 @@ "coding": [ { "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1424911", - "display": "Dabrafenib" + "code": "1425099", + "display": "Trametinib" } ] } @@ -21424,7 +9693,7 @@ ] }, "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" + "text": "Does Not Support Sensitivity/Response" } } ], @@ -21435,19 +9704,19 @@ }, { "system": "https://civicdb.org/evidence", - "value": "6938" + "value": "6124" } ] } }, { - "name": "variant", + "name": "implication", "resource": { "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "id": "dv-63287c9ff7c8d34d272a40e6", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, "status": "final", @@ -21464,40 +9733,36 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" } ] }, "subject": { "reference": "Patient/CA12345" }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], "component": [ { "code": { "coding": [ { "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "phenotypic treatment context" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "system": "https://disease-ontology.org", + "code": "1909", + "display": "Melanoma" } ] } @@ -21507,19 +9772,13 @@ "coding": [ { "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" - } - ] + "text": "B (Clinical evidence)" } }, { @@ -21527,41 +9786,37 @@ "coding": [ { "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "51963-7", + "display": "medication-assessed" } ] }, - "valueString": "A" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1425099", + "display": "Trametinib" } ] - }, - "valueString": "T" + } }, { "code": { "coding": [ { "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "51963-7", + "display": "medication-assessed" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "system": "http://www.nlm.nih.gov/research/umls/rxnorm", + "code": "1424911", + "display": "Dabrafenib" } ] } @@ -21570,33 +9825,25 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } + } + ], + "identifier": [ + { + "system": "https://civicdb.org/variant", + "value": "12" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/evidence", + "value": "6938" } ] } diff --git a/tests/utilities.py b/tests/utilities.py index 247124dbb..e2ef02c58 100644 --- a/tests/utilities.py +++ b/tests/utilities.py @@ -140,7 +140,7 @@ def find_the_gene_query(query): def compare_actual_and_expected_output(filename, actual_json): with open(filename) as expected_output_file: expected_json = json.load(expected_output_file) - diff = DeepDiff(actual_json, expected_json, ignore_order=True) + diff = DeepDiff(actual_json, expected_json, ignore_order=True,report_repetition=True) if diff != {}: if 'OVERWRITE_TEST_EXPECTED_DATA' in os.environ: From 8f34104cf686678edd4a1625b64cf3a29faee500 Mon Sep 17 00:00:00 2001 From: Akash Date: Fri, 11 Oct 2024 18:41:20 -0400 Subject: [PATCH 2/2] fixed linting issue --- tests/utilities.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/utilities.py b/tests/utilities.py index e2ef02c58..f327e58f6 100644 --- a/tests/utilities.py +++ b/tests/utilities.py @@ -140,7 +140,7 @@ def find_the_gene_query(query): def compare_actual_and_expected_output(filename, actual_json): with open(filename) as expected_output_file: expected_json = json.load(expected_output_file) - diff = DeepDiff(actual_json, expected_json, ignore_order=True,report_repetition=True) + diff = DeepDiff(actual_json, expected_json, ignore_order=True, report_repetition=True) if diff != {}: if 'OVERWRITE_TEST_EXPECTED_DATA' in os.environ: