Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.
Bailey MH., Meyerson WU., Dursi LJ., Wang L-B., Dong G., Liang W-W., Weerasinghe A., Li S., Li Y., Kelso S., MC3 Working Group None., PCAWG novel somatic mutation calling methods working group None., Saksena G., Ellrott K., Wendl MC., Wheeler DA., Getz G., Simpson JT., Gerstein MB., Ding L., PCAWG Consortium None.
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