SomaticSignatures: inferring mutational signatures from single-nucleotide variants

Abstract

Mutational signatures are patterns in the occurrence of somatic single-nucleotide variants that can reflect underlying mutational processes. The SomaticSignatures package provides flexible, interoperable and easy-to-use tools that identify such signatures in cancer sequencing data. It facilitates large-scale, cross-dataset estimation of mutational signatures, implements existing methods for pattern decomposition, supports extension through user-defined approaches and integrates with existing Bioconductor workflows.

Availability and implementation: The R package SomaticSignatures is available as part of the Bioconductor project. Its documentation provides additional details on the methods and demonstrates applications to biological datasets.

Contact: julian.gehring@embl.de, whuber@embl.de

Supplementary information: Supplementary data are available at Bioinformatics online.

Fig. 1.

Analysis of mutational signatures for eight TCGA studies (Gehring, 2014). The observed mutational spectrum of each study (panel a) was decomposed into five distinct mutational signatures S1–S5 (panel b) with NMF. The presence of these signatures in the studies (panel c), as shown by hierarchical clustering, underlines the similarities in mutational processes of biologically related cancer types. An annotated high-resolution version of this figure is available as Supplementary Figure S1