Mutographs HNC

Scripts used for Mutographs HNC downstream analysis.

 

Whole genome sequencing data and patient metadata are deposited in the European Genome-phenome Archive (EGA) associated with study [EGAS00001005450](https://ega-archive.org/studies/EGAS00001005450). Aligned BAM files for all HNC cases included in the final analysis are deposited in dataset [EGAD00001015386](https://ega-archive.org/datasets/EGAD00001015386), consensus SNV and indel variant calling files are in dataset [EGAD00001015388](https://ega-archive.org/datasets/EGAD00001015388), patient metadata are in dataset [EGAD00001015387](https://ega-archive.org/datasets/EGAD00001015387), structural rearrangement variant calling files are in dataset [EGAD00001015389](https://ega-archive.org/datasets/EGAD00001015389) and copy number variant calling are in dataset [EGAD00001015390](https://ega-archive.org/datasets/EGAD00001015390). Mutational catalogs for the PCAWG dataset can be accessed at https://dcc.icgc.org/releases/PCAWG. Data regarding mutation profiles and signature attributions are provided in [Input](Input). All other data is provided in the accompanying Supplementary Tables and Supplementary Notes.

Input matrices used for mutational signature analysis are available in [Input_mutation_matrices/](Input/Input_mutation_matrices/) subfolder. These were generated from consensus calls from CaVEMan and Strelka2 (SNVs) or Pindel and Strelka2 (Indels). These matrices can be used to extract and attribute signatures using [SigProfilerExtractor](https://github.com/AlexandrovLab/SigProfilerExtractor) and [MSA](https://gitlab.com/s.senkin/MSA/) tools. Attributed signatures and metadata available on [EGA](https://ega-archive.org/studies/EGAS00001005450) can then be used to reproduce the downstream analysis. Mutational catalogs for the PCAWG dataset can be accessed at https://dcc.icgc.org/releases/PCAWG. All other data is provided in the accompanying Supplementary Tables of the HNC manuscript.

 

The plotting scripts for figures and tables are implemented in R version 4.1.2, in the corresponding subfolders: [Figures/](Figures/), [Extended_Data_Figures/](Extended_Data_Figures/), [Supplementary_Tables/](Supplementary_Tables/), and [Supplementary_Note_Tables](Supplementary_Note_Tables).

 

The main script with epidemiological regression can be found in the following R script: [risk_factor_regressions.R](risk_factor_regressions.R).