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Åke Borg

Åke Borg

Principal investigator

Åke Borg

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

Author

  • 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
Show all

Other contributions

  • Ake Borg
  • Anna Ehinger
  • Dominik Glodzik
  • Dorthe Grabau
  • Mi Ni Huang
  • Chang Li
  • Markus Ringnér
  • Johan Staaf

Summary, in English

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.

Department/s

  • LUCC: Lund University Cancer Centre
  • Familial Breast Cancer
  • Breastcancer-genetics
  • Division of Translational Cancer Research
  • Molecular Cell Biology
  • Breast/lungcancer

Publishing year

2020-09-21

Language

English

Publication/Series

Nature Communications

Volume

11

Issue

1

Document type

Journal article

Publisher

Nature Publishing Group

Topic

  • Cancer and Oncology
  • Medical Genetics

Status

Published

Research group

  • Familial Breast Cancer

ISBN/ISSN/Other

  • ISSN: 2041-1723