MAD1L1_syndrome_aneuploidy

Description

This github repository contains the analysis code used in "Bilallelic germline mutations in MAD1L1 induce a syndrome of aneuploidy with high tumor susceptibility" published in Science Advances:

Link: https://www.science.org/doi/10.1126/sciadv.abq5914

Table of contents

• Data
• Scripts

Data

scRNA-seq data are available at the GEO repository under the accession code: GSE197267. Proteomics data are available at ProteomeXchange (Project accession: PXD035765). R and Python notebooks used in this work are accessible at Zenodo and malumbreslab Github. All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials.

Scripts

• Preprocessing.ipynb: Using as input files CellRanger outputs, it is done a preprocessing in python code of single cell data from patient, father, mother control1 and control2.
• scRNAseq.ipynb: contains the python code to reproduce all single cell analysis (statistics, visualization, differential expression, functional analysis, aneuploidy)
• inferCNV.ipynb: contains the python code to infer copy number variations from single cell data.
• Interaction.ipynb: contains the python code to manage interaction data from cellphoneDB.