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

Author

Listed:
  • Matthew H. Bailey

    (The McDonnell Genome Institute at Washington University
    Washington University School of Medicine
    Washington University School of Medicine)

  • William U. Meyerson

    (Yale University
    Yale University)

  • Lewis Jonathan Dursi

    (Ontario Institute for Cancer Research
    The Hospital for Sick Children)

  • Liang-Bo Wang

    (The McDonnell Genome Institute at Washington University
    Washington University School of Medicine)

  • Guanlan Dong

    (Washington University School of Medicine)

  • Wen-Wei Liang

    (The McDonnell Genome Institute at Washington University
    Washington University School of Medicine)

  • Amila Weerasinghe

    (The McDonnell Genome Institute at Washington University
    Washington University School of Medicine)

  • 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
    Washington University in St. Louis
    Washington University School of Medicine)

  • David A. Wheeler

    (Baylor College of Medicine
    Baylor College of Medicine)

  • Gad Getz

    (Broad Institute of MIT and Harvard
    Harvard Medical School
    Massachusetts General Hospital
    Massachusetts General Hospital)

  • Jared T. Simpson

    (Ontario Institute for Cancer Research
    University of Toronto)

  • Mark B. Gerstein

    (Yale University
    Yale University
    Yale University)

  • Li Ding

    (The McDonnell Genome Institute at Washington University
    Washington University School of Medicine
    Washington University School of Medicine
    Washington University School of Medicine)

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

Suggested Citation

  • 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 & , 2020. "Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples," Nature Communications, Nature, vol. 11(1), pages 1-27, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-18151-y
    DOI: 10.1038/s41467-020-18151-y
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    Cited by:

    1. Michael Fraser & Julie Livingstone & Jeffrey L. Wrana & Antonio Finelli & Housheng Hansen He & Theodorus van der Kwast & Alexandre R. Zlotta & Robert G. Bristow & Paul C. Boutros, 2021. "Somatic driver mutation prevalence in 1844 prostate cancers identifies ZNRF3 loss as a predictor of metastatic relapse," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
    2. Ram Prakash Yadav & Pengwei Xing & Miao Zhao & Peter Hollander & Carina Strell & Minglu Xie & Maede Salehi & Emma Torell & Tobias Sjöblom & Gunilla Enblad & Rose-Marie Amini & Fredrik Johansson Swartl, 2025. "scFFPE-ATAC enables high-throughput single cell chromatin accessibility profiling in formalin-fixed paraffin-embedded samples," Nature Communications, Nature, vol. 16(1), pages 1-21, December.

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