CANCERSIGN: a user-friendly and robust tool for identification and classification of mutational signatures and patterns in cancer genomes

Abstract

Analyses of large somatic mutation datasets, using advanced computational algorithms, have revealed at least 30 independent mutational signatures in tumor samples. These studies have been instrumental in identification and quantification of responsible endogenous and exogenous molecular processes in cancer. The quantitative approach used to deconvolute mutational signatures is becoming an integral part of cancer research. Therefore, development of a stand-alone tool with a user-friendly graphical interface for analysis of cancer mutational signatures is necessary. In this manuscript, we introduce CANCERSIGN as an open access bioinformatics tool that uses raw mutation data (BED files) as input, and identifies 3-mer and 5-mer mutational signatures. CANCERSIGN enables users to identify signatures within whole genome, whole exome or pooled samples. It can also identify signatures in specific regions of the genome (defined by user). Additionally, this tool enables users to perform clustering on tumor samples based on the raw mutation counts as well as using the proportion of mutational signatures in each sample. Using this tool, we analysed all the whole genome somatic mutation datasets profiled by the International Cancer Genome Consortium (ICGC) and identified a number of novel signatures. By examining signatures found in exonic and non-exonic regions of the genome using WGS and comparing this to signatures found in WES data we observe that WGS can identify additional non-exonic signatures that are enriched in the non-coding regions of the genome while the deeper sequencing of WES may help identify weak signatures that are otherwise missed in shallower WGS data.