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, Sean Kelso, Gordon Saksena, Kyle Ellrott, Michael C. Wendl, David A. Wheeler, Gad Getz, Jared T. Simpson, Mark B. Gerstein, Li Ding, Ake Borg (Contributor), Anna Ehinger (Contributor), Dominik Glodzik (Contributor)Dorthe Grabau (Contributor), Mi Ni Huang (Contributor), Chang Li (Contributor), Markus Ringnér (Contributor), Johan Staaf (Contributor), MC3 Working Group, PCAWG novel somatic mutation calling methods working group, PCAWG Consortium

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
Article number4748
JournalNature Communications
Issue number1
Publication statusPublished - 2020 Sept 21

Subject classification (UKÄ)

  • Cancer and Oncology
  • Medical Genetics


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