SMuRF: a novel tool to identify genomic regions enriched for somatic point mutations

Abstract

MotivationSingle Nucleotide Variants (SNVs), including somatic point mutations and Single Nucleotide Polymorphisms (SNPs), in noncoding cis-regulatory elements (CREs) can affect gene regulation and lead to disease development (Zhou et al., 2016; Zhang et al., 2014). Others have previously developed methods to identify important clusters of somatic point mutations based on proximity (Weinhold et al., 2014) or the enrichment of inherited risk-SNPs at CREs (Ahmed et al., 2017). Here, we present SMuRF (Significantly Mutated Region Finder), a user-friendly command-line tool to identify these significantly mutated regions from user-defined genomic intervals and SNVs.\n\nResultsSMuRF identified 72 significantly mutated CREs in liver cancer, including known mutated gene promoters as well as previously unreported regions.\n\nAvailabilityThe source code for SMuRF is open-source and freely available on GitHub (https://github.com/LupienLabOrganization/SMuRF) under the GNU GPLv3 license. SMuRF is implemented in Bash and R; it runs on any platform with Bash ([≥]4.1.2), R ([≥]3.3.0) and BEDTools ([≥]2.26.0). It requires the following R packages: GenomicRanges, gtools, gplots, ggplot2, data.table, psych, and dplyr.\n\nSupplementary InformationSupplementary information available at Bioinformatics online.\n\nContactpaul.guilhamon@uhnresearch.ca; mlupien@uhnres.utoronto.ca