Genetic Determinants of the Somatic Selection of Mutational Processes in 3566 Human Cancers

Introduction

• This repository contains the necessary data and code to replicate the analysis and figures of
  JT Guo et al,Genetic Determinants of the Somatic Selection of Mutational Processes in 3566 Human Cancers. Cancer Res. 2021 Aug 15;81(16):4205-4217. doi: 10.1158/0008-5472.CAN-21-0086. Epub 2021 Jul 2. PMID: 34215622. https://aacrjournals.org/cancerres/article/81/16/4205/670294/Genetic-Determinants-of-Somatic-Selection-of

• Scripts in this repository are written in R, Python, and Julia.

• The results here are based upon data generated by the TCGA Research Network: https://www.cancer.gov/tcga.

• All the multiomics data can be download from UCSC Xena TCGA hub https://tcga.xenahubs.net, Cancer Cell Line Encyclopedia project (CCLE, https://portals.broadinstitute.org/ccle), The Cancer Dependency Map Project at Broad Institute (DepMap, v19q2; https://depmap.org/portal/) and Genomics of Drug Sensitivity in Cancer V8 (GDSC, https://www.cancerrxgene.org/).

• The other data supporting the findings of this study are available from the corresponding author upon reasonable request.

• Please don't hesitate to address comments, questions or suggestions regarding this study.

  • Co-first author:
    • Jintao Guo: [email protected]
    • Ying Zhou: [email protected]
  • Corresponding author:
    • Qiyuan Li: [email protected]
  • Institute
    • National Institute for Data Science in Health and Medicine, Xiamen University
    • School of Medicine Xiamen University, China

Data collection and preAnalysis

1. Genotypes of common SNPs

2. Statuses of gene functional variants

3. Somatic signature

4. Genes' expression

5. Clinical information

Association anslysis

1. Intergrated regressioin for genes

2. Quantitative trait loci of the mutational propensities

Causality inference

Figures and Tables