MutationalPatterns: comprehensive genome-wide analysis of mutational processes

TLDR

Base substitution catalogues record historical mutational processes, which can be distinguished by mutation type, sequence context, strand bias, genomic distribution, and epigenomic associations. We developed MutationalPatterns, an R/Bioconductor package that enables researchers to characterize base substitution patterns to dissect underlying molecular mechanisms, supporting fundamental research and potentially improving cancer diagnosis and treatment. The package efficiently quantifies contributions of known mutational signatures in single samples, allowing assessment of perturbed DNA repair mechanisms and further characterization of signature processes. MutationalPatterns facilitates easy characterization and visualization of mutational patterns and is freely available at http://bioconductor.org/packages/MutationalPatterns.

Abstract

Base substitution catalogues represent historical records of mutational processes that have been active in a cell. Such processes can be distinguished by various characteristics, like mutation type, sequence context, transcriptional and replicative strand bias, genomic distribution and association with (epi)-genomic features. We have created MutationalPatterns, an R/Bioconductor package that allows researchers to characterize a broad range of patterns in base substitution catalogues to dissect the underlying molecular mechanisms. Furthermore, it offers an efficient method to quantify the contribution of known mutational signatures within single samples. This analysis can be used to determine whether certain DNA repair mechanisms are perturbed and to further characterize the processes underlying known mutational signatures. MutationalPatterns allows for easy characterization and visualization of mutational patterns. These analyses willsupport fundamental research into mutational mechanisms and may ultimately improve cancer diagnosis and treatment strategies. MutationalPatterns is freely available at http://bioconductor.org/packages/MutationalPatterns .