Update permissible value list for Clinical Tier 1 Diagnosis: 'Precancerous Condition Type'

[kristenanton]

Data element 'Precancerous Condition Type' permissible values required updating. Several values are to be removed, three values are to be added.

Proposed change:

Omit 9 existing permissible values: Carcinoma NOS, Invasive melanoma - superficial spreading, Invasive melanoma - nodular type, Invasive melanoma - lentigo maligna, Invasive melanoma - acral lentiginous, Invasive melanoma - desmoplastic, Invasive melanoma - nevoid, Invasive melanoma, Normal WDA

Add 3 permissible values: Normal, Squamous carcinoma in situ, Neuroendocrine cell hyperplasia

Attached Excel spreadsheet also contains the requested changes.

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How important is this feature?

• 🌗 Medium - can do work without it; but it's important (e.g. to save time or for convenience)

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When will use cases depending on this become relevant?

Next sprint

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Additional context

There are only two records in the current dataset that contain data in the 'Precancerous Condition Type' field. They are HTAPP participants, and the value for both is 'Ductal Carcinoma In Situ' (these records have been moved from Tier 2 into Tier 1 by Clarisse and Kristen). Therefore this change has no impact on data already submitted.

PrecancerousConditionType_PVs.xlsx

[adamjtaylor]

Confirming @kristenanton's assessment of previously submitted values

SELECT 
  Precancerous_Condition_Type, 
  COUNT(*) as n 
FROM `htan-dcc.combined_assays.Diagnosis` 
GROUP BY Precancerous_Condition_Type

Precancerous_Condition_Type	n
null	2207
Not Applicable	110
Ductal Carcinoma In Situ	2

note that this field is not required

[aclayton555]

Can be done in a single PR with #306
Please ensure both issues are linked to the PR, when ready.

[aclayton555]

Expect to include in release in early 24-6 sprint