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  • Bailey, Matthew H.Washington University in St. Louis (author)

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

  • Article/chapterEnglish2020

Publisher, publication year, extent ...

  • 2020-09-21
  • Springer Science and Business Media LLC,2020

Numbers

  • LIBRIS-ID:oai:lup.lub.lu.se:70f79305-f522-4a74-b74b-4d7a566620c6
  • https://lup.lub.lu.se/record/70f79305-f522-4a74-b74b-4d7a566620c6URI
  • https://doi.org/10.1038/s41467-020-18151-yDOI
  • https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-431728URI
  • http://kipublications.ki.se/Default.aspx?queryparsed=id:145703659URI

Supplementary language notes

  • Language:English
  • Summary in:English

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  • Subject category:art swepub-publicationtype
  • Subject category:ref swepub-contenttype

Notes

  • Medlem i PCAWG Consortium. 
  • 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.

Subject headings and genre

Added entries (persons, corporate bodies, meetings, titles ...)

  • Meyerson, William U.Yale University (author)
  • Dursi, Lewis JonathanHospital for Sick Children, Toronto,Ontario Institute for Cancer Research (author)
  • Wang, Liang BoWashington University in St. Louis (author)
  • Dong, GuanlanWashington University in St. Louis (author)
  • Liang, Wen WeiWashington University in St. Louis (author)
  • Weerasinghe, AmilaWashington University in St. Louis (author)
  • Li, ShantaoYale University (author)
  • Kelso, SeanWashington University in St. Louis (author)
  • Saksena, GordonBroad Institute (author)
  • Ellrott, KyleOregon Health & Science University (author)
  • Wendl, Michael C.Washington University in St. Louis (author)
  • Wheeler, David A.Baylor College of Medicine (author)
  • Getz, GadMassachusetts General Hospital,Harvard Medical School,Broad Institute (author)
  • Simpson, Jared T.Ontario Institute for Cancer Research (author)
  • Gerstein, Mark B.Yale University (author)
  • Ding, LiWashington University in St. Louis (author)
  • Borg, AkeLund University,Lunds universitet,Bröstcancer-genetik,Sektion I,Institutionen för kliniska vetenskaper, Lund,Medicinska fakulteten,Familjär bröstcancer,Forskargrupper vid Lunds universitet,LUCC: Lunds universitets cancercentrum,Övriga starka forskningsmiljöer,Breastcancer-genetics,Section I,Department of Clinical Sciences, Lund,Faculty of Medicine,Familial Breast Cancer,Lund University Research Groups,LUCC: Lund University Cancer Centre,Other Strong Research Environments(Swepub:lu)onk-abo (creator_code:cre_t)
  • Ehinger, AnnaLund University,Lunds universitet,Avdelningen för translationell cancerforskning,Institutionen för laboratoriemedicin,Medicinska fakulteten,Division of Translational Cancer Research,Department of Laboratory Medicine,Faculty of Medicine(Swepub:lu)pat-amm (creator_code:cre_t)
  • Glodzik, DominikWellcome Trust Sanger Institute(Swepub:lu)do5123gl (creator_code:cre_t)
  • Grabau, DortheSkåne University Hospital(Swepub:lu)med-dgu (creator_code:cre_t)
  • Huang, Mi NiDuke–NUS Medical School(Swepub:lu)hu7785mi (creator_code:cre_t)
  • Li, ChangBeijing Genomics Institute,China National Genebank(Swepub:lu)ch6236li (creator_code:cre_t)
  • Ringnér, MarkusLund University,Lunds universitet,Molekylär cellbiologi,Biologiska institutionen,Naturvetenskapliga fakulteten,Molecular Cell Biology,Department of Biology,Faculty of Science(Swepub:lu)thep-mri (creator_code:cre_t)
  • Staaf, JohanLund University,Lunds universitet,Bröstcancer-genetik,Sektion I,Institutionen för kliniska vetenskaper, Lund,Medicinska fakulteten,LUCC: Lunds universitets cancercentrum,Övriga starka forskningsmiljöer,Bröst/lungcancer,Institutionen för kliniska vetenskaper, Lund,Breastcancer-genetics,Section I,Department of Clinical Sciences, Lund,Faculty of Medicine,LUCC: Lund University Cancer Centre,Other Strong Research Environments,Breast/lungcancer,Department of Clinical Sciences, Lund(Swepub:lu)onk-jst (creator_code:cre_t)
  • Li, Yize (author)
  • Washington University in St. LouisYale University (creator_code:org_t)
  • MC3 Working Group
  • PCAWG novel somatic mutation calling methods working group
  • PCAWG Consortium

Related titles

  • In:Nature Communications: Springer Science and Business Media LLC11:12041-1723

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