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

TitleRetrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.
Publication TypeJournal Article
Year of Publication2020
AuthorsBailey, MH, Meyerson, WU, Dursi, LJonathan, Wang, L-B, Dong, G, Liang, W-W, Weerasinghe, A, Li, S, Li, Y, Kelso, S, Saksena, G, Ellrott, K, Wendl, MC, Wheeler, DA, Getz, G, Simpson, JT, Gerstein, MB, Ding, L
Corporate AuthorsMC3 Working Group, PCAWG novel somatic mutation calling methods working group, PCAWG Consortium
JournalNat Commun
Volume11
Issue1
Pagination4748
Date Published2020 09 21
ISSN2041-1723
KeywordsBase Composition, Databases, Genetic, DNA, Intergenic, Exome, Exons, Genome, Human, Humans, Mutation, Neoplasms, Retrospective Studies, Whole Exome Sequencing, Whole Genome Sequencing
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 

DOI10.1038/s41467-020-18151-y
Alternate JournalNat Commun
PubMed ID32958763
PubMed Central IDPMC7505971
Grant ListR01 CA235162 / CA / NCI NIH HHS / United States
/ HHMI / Howard Hughes Medical Institute / United States
T32 GM007205 / GM / NIGMS NIH HHS / United States
U24 CA210969 / CA / NCI NIH HHS / United States
MC_UU_12022/2 / MRC_ / Medical Research Council / United Kingdom
R35 GM127029 / GM / NIGMS NIH HHS / United States
P30 CA016672 / CA / NCI NIH HHS / United States
R01 CA183793 / CA / NCI NIH HHS / United States
P50 CA217694 / CA / NCI NIH HHS / United States