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

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Bailey_2020_NatComm_Retrospective_CC.pdf (2.416Mb)
Date
21/09/2020
Author
PCAWG Consortium
MC3 Working Group
PCAWG novel somatic mutation calling methods working group
Bailey, Matthew H.
Meyerson, William U.
Dursi, Lewis Jonathan
Wang, Liang-Bo
Dong, Guanlan
Liang, Wen-Wei
Weerasinghe, Amila
Li, Shantao
Li, Yize
Kelso, Sean
Saksena, Gordon
Ellrott, Kyle
Wendl, Michael C.
Wheeler, David A.
Getz, Gad
Simpson, Jared T.
Gerstein, Mark B.
Ding, Li
Lynch, Andy
Keywords
QH426 Genetics
RC0254 Neoplasms. Tumors. Oncology (including Cancer)
DAS
Metadata
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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 < 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.
Citation
PCAWG Consortium , MC3 Working Group , PCAWG novel somatic mutation calling methods working group , Bailey , M H , Meyerson , W U , Dursi , L J , Wang , L-B , Dong , G , Liang , W-W , Weerasinghe , A , Li , S , Li , Y , Kelso , S , Saksena , G , Ellrott , K , Wendl , M C , Wheeler , D A , Getz , G , Simpson , J T , Gerstein , M B , Ding , L & Lynch , A 2020 , ' Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples ' , Nature Communications , vol. 11 , 4748 . https://doi.org/10.1038/s41467-020-18151-y
Publication
Nature Communications
Status
Peer reviewed
DOI
https://doi.org/10.1038/s41467-020-18151-y
ISSN
2041-1723
Type
Journal article
Rights
Copyright © The Author(s) 2020, corrected publication 2020. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
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  • University of St Andrews Research
URL
https://www.nature.com/articles/s41467-020-20128-w
URI
http://hdl.handle.net/10023/21162

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