This is the GitHub repository for the paper "Pan-cancer association of DNA repair deficiencies with whole genome mutational patterns"
It is possible to run the analysis and all figures of the paper based on somatic variants of the publicly available PCAWG samples (https://dcc.icgc.org/releases/PCAWG/). We have necessary annotations included CADD (v1.6), ClinVar annotations and gnomAD (v2.1.1) populatioon frequencies in the data folder.
Signature contributions of single base substitutions are obtained from the supplementary information of the article "A practical framework and online tool for mutational signature analyses show inter-tissue variation and driver dependencies" by Degaspari et al. [1]. The number of indels and SVs are counted using a local installation of the Sig.tols.lib (https://github.com/Nik-Zainal-Group/signature.tools.lib). The combined set of features is made available in the Data folder (To be uploaded) and in th supplementary tables S3 and S4 of the paper.
We will here provide all code needed for running an example of the analysis, shown in the paper "Pan-cancer association of DNA repair deficiencies with whole genome mutational patterns". The code is designed to run in R4.0.2. Package versions are specified in the scripts.
[1] Degasperi A, Amarante TD, Czarnecki J, Shooter S, Zou X, Glodzik D, Morganella S, Nanda AS, Badja C, Koh G, Momen SE, Georgakopoulos-Soares I, Dias JML, Young J, Memari Y, Davies H, Nik-Zainal S. A practical framework and online tool for mutational signature analyses show inter-tissue variation and driver dependencies. Nat Cancer. 2020 Feb;1(2):249-263. doi: 10.1038/s43018-020-0027-5. Epub 2020 Feb 17. PMID: 32118208; PMCID: PMC7048622.