Alpha 2.0
Login Register
» Articles » PMID: 26163694

SomaticSignatures: Inferring Mutational Signatures from Single-nucleotide Variants

Overview
Journal Bioinformatics
Publisher Oxford University Press
Specialty Biology
Date 2015 Jul 12
PMID 26163694
Citations 189
Authors
Julian S Gehring
Bernd Fischer
Michael Lawrence
Wolfgang Huber
Affiliations
Soon will be listed here.
Abstract

Unlabelled: 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.

Citing Articles

UVA-light-induced mutagenesis in the exome of human nucleotide excision repair-deficient cells.

Quintero-Ruiz N, Corradi C, Moreno N, de Souza T, Menck C Photochem Photobiol Sci. 2025; .

PMID: 40063310 DOI: 10.1007/s43630-025-00697-9.

Prognosis conferred by molecular features of appendix-derived Pseudomyxoma Peritonei.

Ma R, Li G, Ye Y, Liang L, Wang C, Zhou H Transl Oncol. 2025; 53:102279.

PMID: 39929063 PMC: 11867523. DOI: 10.1016/j.tranon.2025.102279.

Proteogenomic analysis of air-pollution-associated lung cancer reveals prevention and therapeutic opportunities.

Zhang H, Liu C, Wang S, Wang Q, Feng X, Jiang H Elife. 2024; 13.

PMID: 39432560 PMC: 11493407. DOI: 10.7554/eLife.95453.

Functional landscape of genome-wide postzygotic somatic mutations between monozygotic twins.

Yamamoto K, Lee Y, Masuda T, Ozono K, Iwatani Y, Watanabe M DNA Res. 2024; 31(5).

PMID: 39306676 PMC: 11472055. DOI: 10.1093/dnares/dsae028.

Somatic CpG hypermutation is associated with mismatch repair deficiency in cancer.

Flynn A, Waszak S, Weischenfeldt J Mol Syst Biol. 2024; 20(9):1006-1024.

PMID: 39026103 PMC: 11369196. DOI: 10.1038/s44320-024-00054-5.

References
1.
Durinck S, Stawiski E, Pavia-Jimenez A, Modrusan Z, Kapur P, Jaiswal B . Spectrum of diverse genomic alterations define non-clear cell renal carcinoma subtypes. Nat Genet. 2014; 47(1):13-21. PMC: 4489427. DOI: 10.1038/ng.3146. View
2.
Fischer A, Illingworth C, Campbell P, Mustonen V . EMu: probabilistic inference of mutational processes and their localization in the cancer genome. Genome Biol. 2013; 14(4):R39. PMC: 3663107. DOI: 10.1186/gb-2013-14-4-r39. View
3.
Obenchain V, Lawrence M, Carey V, Gogarten S, Shannon P, Morgan M . VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants. Bioinformatics. 2014; 30(14):2076-8. PMC: 4080743. DOI: 10.1093/bioinformatics/btu168. View
4.
Alexandrov L, Nik-Zainal S, Wedge D, Aparicio S, Behjati S, Biankin A . Signatures of mutational processes in human cancer. Nature. 2013; 500(7463):415-21. PMC: 3776390. DOI: 10.1038/nature12477. View
5.
Alexandrov L, Nik-Zainal S, Wedge D, Campbell P, Stratton M . Deciphering signatures of mutational processes operative in human cancer. Cell Rep. 2013; 3(1):246-59. PMC: 3588146. DOI: 10.1016/j.celrep.2012.12.008. View