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

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Bailey, Matthew H., Meyerson, William U., Dursi, Lewis Jonathan, Wang, Liang-Bo, Dong, Guanlan, Liang, Wen-Wei, Weerasinghe, Amila, Li, Shantao, Li, Yize, Kelso, Sean, Saksena, Gordon, Ellrott, Kyle, Wendl, Michael C., Wheeler, David A., Getz, Gad, Simpson, Jared T., Gerstein, Mark B. and Ding, Li and MC3 Working Group, PCAWG novel somatic mutation calling methods working group, PCAWG Consortium (2020) Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nature Communications, 11. ISSN 2041-1723

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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.

Item Type:	Article
Additional Information:	Author correction: The original version of this Article omitted from the author list the 9th author Yize Li, who is from the ‘The McDonnell Genome Institute at Washington University, St. Louis, MO 63108, USA and Department of Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO 63108, USA’. This has been corrected in both the PDF and HTML versions of the Article.
Uncontrolled Keywords:	chemistry(all),biochemistry, genetics and molecular biology(all),general,physics and astronomy(all),sdg 3 - good health and well-being ,/dk/atira/pure/subjectarea/asjc/1600
Faculty \ School:	Faculty of Medicine and Health Sciences > Norwich Medical School
UEA Research Groups:	Faculty of Medicine and Health Sciences > Research Centres > Metabolic Health
Related URLs:	http://www.scopus.com/inward/record.url?...
Depositing User:	LivePure Connector
Date Deposited:	18 Jul 2022 09:30
Last Modified:	07 Jun 2024 14:30
URI:	https://ueaeprints.uea.ac.uk/id/eprint/86449
DOI:	10.1038/s41467-020-18151-y

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