Analysis of mutational signatures with yet another package for signature analysis.
BRCAness
YAPSA
biomarker
cancer genomics
mutational signatures
precision oncology
Journal
Genes, chromosomes & cancer
ISSN: 1098-2264
Titre abrégé: Genes Chromosomes Cancer
Pays: United States
ID NLM: 9007329
Informations de publication
Date de publication:
05 2021
05 2021
Historique:
revised:
06
11
2020
received:
01
08
2020
accepted:
06
11
2020
pubmed:
23
11
2020
medline:
16
2
2022
entrez:
22
11
2020
Statut:
ppublish
Résumé
Different mutational processes leave characteristic patterns of somatic mutations in the genome that can be identified as mutational signatures. Determining the contributions of mutational signatures to cancer genomes allows not only to reconstruct the etiology of somatic mutations, but can also be used for improved tumor classification and support therapeutic decisions. We here present the R package yet another package for signature analysis (YAPSA) to deconvolute the contributions of mutational signatures to tumor genomes. YAPSA provides in-built collections from the COSMIC and PCAWG SNV signature sets as well as the PCAWG Indel signatures and employs signature-specific cutoffs to increase sensitivity and specificity. Furthermore, YAPSA allows to determine 95% confidence intervals for signature exposures, to perform constrained stratified signature analyses to obtain enrichment and depletion patterns of the identified signatures and, when applied to whole exome sequencing data, to correct for the triplet content of individual target capture kits. With this functionality, YAPSA has proved to be a valuable tool for analysis of mutational signatures in molecular tumor boards in a precision oncology context. YAPSA is available at R/Bioconductor (http://bioconductor.org/packages/3.12/bioc/html/YAPSA.html).
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
314-331Informations de copyright
© 2020 The Authors. Genes, Chromosomes & Cancer published by Wiley Periodicals LLC.
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