Show simple item record

Files in this item


Item metadata

dc.contributor.authorPCAWG Consortium
dc.contributor.authorMC3 Working Group
dc.contributor.authorPCAWG novel somatic mutation calling methods working group
dc.contributor.authorBailey, Matthew H.
dc.contributor.authorMeyerson, William U.
dc.contributor.authorDursi, Lewis Jonathan
dc.contributor.authorWang, Liang-Bo
dc.contributor.authorDong, Guanlan
dc.contributor.authorLiang, Wen-Wei
dc.contributor.authorWeerasinghe, Amila
dc.contributor.authorLi, Shantao
dc.contributor.authorLi, Yize
dc.contributor.authorKelso, Sean
dc.contributor.authorSaksena, Gordon
dc.contributor.authorEllrott, Kyle
dc.contributor.authorWendl, Michael C.
dc.contributor.authorWheeler, David A.
dc.contributor.authorGetz, Gad
dc.contributor.authorSimpson, Jared T.
dc.contributor.authorGerstein, Mark B.
dc.contributor.authorDing, Li
dc.identifier.citationPCAWG Consortium , MC3 Working Group , PCAWG novel somatic mutation calling methods working group , Bailey , M H , Meyerson , W U , Dursi , L J , Wang , L-B , Dong , G , Liang , W-W , Weerasinghe , A , Li , S , Li , Y , Kelso , S , Saksena , G , Ellrott , K , Wendl , M C , Wheeler , D A , Getz , G , Simpson , J T , Gerstein , M B & Ding , L 2020 , ' Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples ' , Nature Communications , vol. 11 , 4748 .
dc.identifier.otherPURE: 271692684
dc.identifier.otherPURE UUID: 24414627-bd4d-4ecf-a6b9-db4bf8f2cea7
dc.identifier.otherRIS: urn:EED5606E37268DD04AF06D3CFADE8CD6
dc.identifier.otherRIS: Bailey2020
dc.identifier.otherScopus: 85079069163
dc.identifier.otherORCID: /0000-0002-7876-7338/work/85568435
dc.description.abstractThe 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.relation.ispartofNature Communicationsen
dc.rightsCopyright © The Author(s) 2020, corrected publication 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. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit
dc.subjectQH426 Geneticsen
dc.subjectRC0254 Neoplasms. Tumors. Oncology (including Cancer)en
dc.titleRetrospective evaluation of whole exome and genome mutation calls in 746 cancer samplesen
dc.typeJournal articleen
dc.description.versionPublisher PDFen
dc.contributor.institutionUniversity of St Andrews.Sir James Mackenzie Institute for Early Diagnosisen
dc.contributor.institutionUniversity of St Andrews.Cellular Medicine Divisionen
dc.contributor.institutionUniversity of St Andrews.Statisticsen
dc.contributor.institutionUniversity of St Andrews.School of Medicineen
dc.description.statusPeer revieweden

This item appears in the following Collection(s)

Show simple item record