| Title | Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. |
| Publication Type | Journal Article |
| Year of Publication | 2020 |
| Authors | Bailey, 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 Authors | MC3 Working Group, PCAWG novel somatic mutation calling methods working group, PCAWG Consortium |
| Journal | Nat Commun |
| Volume | 11 |
| Issue | 1 |
| Pagination | 4748 |
| Date Published | 2020 Sep 21 |
| ISSN | 2041-1723 |
| Keywords | Base Composition, Databases, Genetic, DNA, Intergenic, Exome, Exome Sequencing, Exons, Genome, Human, Humans, Mutation, Neoplasms, Retrospective Studies, 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 |
| DOI | 10.1038/s41467-020-18151-y |
| Alternate Journal | Nat Commun |
| PubMed ID | 32958763 |
| PubMed Central ID | PMC7505971 |
| Grant List | R35 GM127029 / GM / NIGMS NIH HHS / United States T32 HG002295 / HG / NHGRI NIH HHS / United States P30 CA008748 / CA / NCI NIH HHS / United States MC_UU_12022/2 / MRC_ / Medical Research Council / United Kingdom U24 CA210969 / CA / NCI NIH HHS / United States R35 GM138212 / GM / NIGMS NIH HHS / United States R01 CA235162 / CA / NCI NIH HHS / United States / HHMI / Howard Hughes Medical Institute / United States R01 GM109031 / GM / NIGMS NIH HHS / United States T32 GM007205 / GM / NIGMS NIH HHS / United States U01 HG010971 / HG / NHGRI NIH HHS / United States R01 CA183793 / CA / NCI NIH HHS / United States P50 CA217694 / CA / NCI NIH HHS / United States |