Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

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• dc.contributor.author Bailey, Matthew H.
• dc.contributor.author Drechsel, Oliver
• dc.contributor.author Gut, Ivo Glynne
• dc.contributor.author Ossowski, Stephan
• dc.contributor.author Stobbe, Miranda D.
• dc.contributor.author Gonzalez-Perez, Abel
• dc.contributor.author PCAWG Consortium
• dc.date.accessioned 2022-06-07T09:05:53Z
• dc.date.available 2022-06-07T09:05:53Z
• dc.date.issued 2020
• dc.description.abstract The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts.
• dc.format.mimetype application/pdf
• dc.identifier.citation Bailey MH, Meyerson WU, Dursi LJ, Wang LB, Dong G, Liang WW et al. Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nat Commun. 2020 Sep 21;11(1):4748. DOI:10.1038/s41467-020-18151-y
• dc.identifier.doi http://dx.doi.org/10.1038/s41467-020-18151-y
• dc.identifier.issn 2041-1723
• dc.identifier.uri http://hdl.handle.net/10230/53396
• dc.language.iso eng
• dc.publisher Nature Research
• dc.rights © Matthew H. Bailey et al. 2020. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri https://creativecommons.org/licenses/by/4.0/
• dc.subject.other Genòmica
• dc.subject.other Genètica
• dc.subject.other Càncer
• dc.title Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion