Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples
dc.date.accessioned | 2021-04-22T19:44:26Z | |
dc.date.available | 2021-04-22T19:44:26Z | |
dc.date.created | 2021-02-22T14:32:01Z | |
dc.date.issued | 2020 | |
dc.identifier.citation | Bailey, Matthew H. Meyerson, William U. Dursi, L. Jonathan Wang, Liang-Bo Dong, Guanlan Liang, Wen-Wei Weerasinghe, Amila Li, Shantao Li, Yize Kelso, Sean Aure, Miriam Ragle Børresen-Dale, Anne-Lise Langerød, Anita Baumhoer, Daniel Bjerkehagen, Bodil Garred, Øystein Lingjærde, Ole Christian Sauer, Torill Zaikova, Olga Myklebost, Ola Knappskog, Stian Vazquez, Miguel Akbani, Rehan Anur, Pavana Buchanan, Alex Chiotti, Kami Covington, Kyle Creason, Allison Niu, Beifang Bieg, Matthias Boutros, Paul C. Buchhalter, Ivo Butler, Adam P. Chen, Ken Chong, Zechen Drechsel, Oliver Aaltonen, Lauri Abascal, Federico Abeshouse, Adam Aburatani, H Adams, David J. Van Loo, Peter Saksena, Gordon Ellrott, Kyle Wendl, Michael C. Wheeler, David A. Getz, Gad Simpson, Jared T. Gerstein, Mark B. Ding, Li . Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nature Communications. 2020, 11:4748, 1-27 | |
dc.identifier.uri | http://hdl.handle.net/10852/85470 | |
dc.description.abstract | 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. | |
dc.language | EN | |
dc.rights | Attribution 4.0 International | |
dc.rights.uri | https://creativecommons.org/licenses/by/4.0/ | |
dc.title | Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples | |
dc.type | Journal article | |
dc.creator.author | Bailey, Matthew H. | |
dc.creator.author | Meyerson, William U. | |
dc.creator.author | Dursi, L. Jonathan | |
dc.creator.author | Wang, Liang-Bo | |
dc.creator.author | Dong, Guanlan | |
dc.creator.author | Liang, Wen-Wei | |
dc.creator.author | Weerasinghe, Amila | |
dc.creator.author | Li, Shantao | |
dc.creator.author | Li, Yize | |
dc.creator.author | Kelso, Sean | |
dc.creator.author | Aure, Miriam Ragle | |
dc.creator.author | Børresen-Dale, Anne-Lise | |
dc.creator.author | Langerød, Anita | |
dc.creator.author | Baumhoer, Daniel | |
dc.creator.author | Bjerkehagen, Bodil | |
dc.creator.author | Garred, Øystein | |
dc.creator.author | Lingjærde, Ole Christian | |
dc.creator.author | Sauer, Torill | |
dc.creator.author | Zaikova, Olga | |
dc.creator.author | Myklebost, Ola | |
dc.creator.author | Knappskog, Stian | |
dc.creator.author | Vazquez, Miguel | |
dc.creator.author | Akbani, Rehan | |
dc.creator.author | Anur, Pavana | |
dc.creator.author | Buchanan, Alex | |
dc.creator.author | Chiotti, Kami | |
dc.creator.author | Covington, Kyle | |
dc.creator.author | Creason, Allison | |
dc.creator.author | Niu, Beifang | |
dc.creator.author | Bieg, Matthias | |
dc.creator.author | Boutros, Paul C. | |
dc.creator.author | Buchhalter, Ivo | |
dc.creator.author | Butler, Adam P. | |
dc.creator.author | Chen, Ken | |
dc.creator.author | Chong, Zechen | |
dc.creator.author | Drechsel, Oliver | |
dc.creator.author | Aaltonen, Lauri | |
dc.creator.author | Abascal, Federico | |
dc.creator.author | Abeshouse, Adam | |
dc.creator.author | Aburatani, H | |
dc.creator.author | Adams, David J. | |
dc.creator.author | Van Loo, Peter | |
dc.creator.author | Saksena, Gordon | |
dc.creator.author | Ellrott, Kyle | |
dc.creator.author | Wendl, Michael C. | |
dc.creator.author | Wheeler, David A. | |
dc.creator.author | Getz, Gad | |
dc.creator.author | Simpson, Jared T. | |
dc.creator.author | Gerstein, Mark B. | |
dc.creator.author | Ding, Li | |
cristin.unitcode | 185,53,49,12 | |
cristin.unitname | Institutt for kreftforskning | |
cristin.ispublished | true | |
cristin.fulltext | original | |
cristin.qualitycode | 2 | |
dc.identifier.cristin | 1892392 | |
dc.identifier.bibliographiccitation | info:ofi/fmt:kev:mtx:ctx&ctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Nature Communications&rft.volume=11:4748&rft.spage=1&rft.date=2020 | |
dc.identifier.jtitle | Nature Communications | |
dc.identifier.volume | 11 | |
dc.identifier.issue | 1 | |
dc.identifier.doi | https://doi.org/10.1038/s41467-020-18151-y | |
dc.identifier.urn | URN:NBN:no-88135 | |
dc.type.document | Tidsskriftartikkel | |
dc.type.peerreviewed | Peer reviewed | |
dc.source.issn | 2041-1723 | |
dc.identifier.fulltext | Fulltext https://www.duo.uio.no/bitstream/handle/10852/85470/1/Postnr%2B1892392_Bailey%2Bet%2Bal_Nat%2BCommun_s41467-020-18151-y.pdf | |
dc.type.version | PublishedVersion | |
cristin.articleid | 4748 |
Files in this item
Appears in the following Collection
-
Institutt for informatikk [4933]
-
Det odontologiske fakultet [1570]
-
Institutt for klinisk medisin [10751]
-
CRIStin høstingsarkiv [31257]