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

Matthew H. Bailey, William U. Meyerson, Lewis Jonathan Dursi, Liang-Bo Wang, Guanlan Dong, Wen-Wei Liang, Amila Weerasinghe, Shantao Li, Yize Li, Sean Kelso, Gordon Saksena, Kyle Ellrott, Michael C. Wendl, David A. Wheeler, Gad Getz, Jared T. Simpson, Mark B. Gerstein () and Li Ding ()
Additional contact information
Matthew H. Bailey: The McDonnell Genome Institute at Washington University
William U. Meyerson: Yale University
Lewis Jonathan Dursi: Ontario Institute for Cancer Research
Liang-Bo Wang: The McDonnell Genome Institute at Washington University
Guanlan Dong: Washington University School of Medicine
Wen-Wei Liang: The McDonnell Genome Institute at Washington University
Amila Weerasinghe: The McDonnell Genome Institute at Washington University
Shantao Li: Yale University
Yize Li: The McDonnell Genome Institute at Washington University
Sean Kelso: Washington University School of Medicine
Gordon Saksena: Broad Institute of MIT and Harvard
Kyle Ellrott: Oregon Health and Science University
Michael C. Wendl: The McDonnell Genome Institute at Washington University
David A. Wheeler: Baylor College of Medicine
Gad Getz: Broad Institute of MIT and Harvard
Jared T. Simpson: Ontario Institute for Cancer Research
Mark B. Gerstein: Yale University
Li Ding: The McDonnell Genome Institute at Washington University

Nature Communications, 2020, vol. 11, issue 1, 1-27

Abstract: 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

Date: 2020
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DOI: 10.1038/s41467-020-18151-y

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