期刊
NATURE COMMUNICATIONS
卷 11, 期 1, 页码 -出版社
NATURE RESEARCH
DOI: 10.1038/s41467-020-18151-y
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资金
- MRC [MC_UU_12022/2] Funding Source: UKRI
- Howard Hughes Medical Institute Funding Source: Medline
- Medical Research Council [MC_UU_12022/2] Funding Source: Medline
- NCI NIH HHS [P50 CA217694, R01 CA183793, R01 CA235162, P30 CA008748, U24 CA210969] Funding Source: Medline
- NHGRI NIH HHS [T32 HG002295, U01 HG010971] Funding Source: Medline
- NIGMS NIH HHS [R35 GM138212, R35 GM127029, T32 GM007205, R01 GM109031] Funding Source: Medline
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 similar to 30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both similar to 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.
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