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

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Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. / Bailey, Matthew H.; Meyerson, William U.; Dursi, Lewis Jonathan; Wang, Liang Bo; Dong, Guanlan; Liang, Wen Wei; Weerasinghe, Amila; Li, Shantao; Kelso, Sean; Akbani, Rehan; Anur, Pavana; Bailey, Matthew H.; Buchanan, Alex; Chiotti, Kami; Covington, Kyle; Creason, Allison; Ding, Li; Weischenfeldt, Joachim; Brunak, Søren; Ding, Li; Favero, Francesco; MC3 Working Group; PCAWG novel somatic mutation calling methods working group; PCAWG Consortium.

In: Nature Communications, Vol. 11, No. 1, 4748, 2020.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Bailey, MH, Meyerson, WU, Dursi, LJ, Wang, LB, Dong, G, Liang, WW, Weerasinghe, A, Li, S, Kelso, S, Akbani, R, Anur, P, Bailey, MH, Buchanan, A, Chiotti, K, Covington, K, Creason, A, Ding, L, Weischenfeldt, J, Brunak, S, Ding, L, Favero, F, MC3 Working Group, PCAWG novel somatic mutation calling methods working group & PCAWG Consortium 2020, 'Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples', Nature Communications, vol. 11, no. 1, 4748. https://doi.org/10.1038/s41467-020-18151-y

APA

Bailey, M. H., Meyerson, W. U., Dursi, L. J., Wang, L. B., Dong, G., Liang, W. W., Weerasinghe, A., Li, S., Kelso, S., Akbani, R., Anur, P., Bailey, M. H., Buchanan, A., Chiotti, K., Covington, K., Creason, A., Ding, L., Weischenfeldt, J., Brunak, S., ... PCAWG Consortium (2020). Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nature Communications, 11(1), [4748]. https://doi.org/10.1038/s41467-020-18151-y

Vancouver

Bailey MH, Meyerson WU, Dursi LJ, Wang LB, Dong G, Liang WW et al. Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nature Communications. 2020;11(1). 4748. https://doi.org/10.1038/s41467-020-18151-y

Author

Bailey, Matthew H. ; Meyerson, William U. ; Dursi, Lewis Jonathan ; Wang, Liang Bo ; Dong, Guanlan ; Liang, Wen Wei ; Weerasinghe, Amila ; Li, Shantao ; Kelso, Sean ; Akbani, Rehan ; Anur, Pavana ; Bailey, Matthew H. ; Buchanan, Alex ; Chiotti, Kami ; Covington, Kyle ; Creason, Allison ; Ding, Li ; Weischenfeldt, Joachim ; Brunak, Søren ; Ding, Li ; Favero, Francesco ; MC3 Working Group ; PCAWG novel somatic mutation calling methods working group ; PCAWG Consortium. / Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. In: Nature Communications. 2020 ; Vol. 11, No. 1.

Bibtex

@article{813857d72bb74183a7cbe6451136efa3,
title = "Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples",
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.",
author = "Bailey, {Matthew H.} and Meyerson, {William U.} and Dursi, {Lewis Jonathan} and Wang, {Liang Bo} and Guanlan Dong and Liang, {Wen Wei} and Amila Weerasinghe and Shantao Li and Sean Kelso and Rehan Akbani and Pavana Anur and Bailey, {Matthew H.} and Alex Buchanan and Kami Chiotti and Kyle Covington and Allison Creason and Li Ding and Joachim Weischenfeldt and S{\o}ren Brunak and Li Ding and Francesco Favero and {MC3 Working Group} and {PCAWG novel somatic mutation calling methods working group} and {PCAWG Consortium}",
note = "Publisher Copyright: {\textcopyright} 2020, The Author(s).",
year = "2020",
doi = "10.1038/s41467-020-18151-y",
language = "English",
volume = "11",
journal = "Nature Communications",
issn = "2041-1723",
publisher = "nature publishing group",
number = "1",

}

RIS

TY - JOUR

T1 - Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

AU - Bailey, Matthew H.

AU - Meyerson, William U.

AU - Dursi, Lewis Jonathan

AU - Wang, Liang Bo

AU - Dong, Guanlan

AU - Liang, Wen Wei

AU - Weerasinghe, Amila

AU - Li, Shantao

AU - Kelso, Sean

AU - Akbani, Rehan

AU - Anur, Pavana

AU - Bailey, Matthew H.

AU - Buchanan, Alex

AU - Chiotti, Kami

AU - Covington, Kyle

AU - Creason, Allison

AU - Ding, Li

AU - Weischenfeldt, Joachim

AU - Brunak, Søren

AU - Ding, Li

AU - Favero, Francesco

AU - MC3 Working Group

AU - PCAWG novel somatic mutation calling methods working group

AU - PCAWG Consortium

N1 - Publisher Copyright: © 2020, The Author(s).

PY - 2020

Y1 - 2020

N2 - 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.

AB - 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.

U2 - 10.1038/s41467-020-18151-y

DO - 10.1038/s41467-020-18151-y

M3 - Journal article

C2 - 32958763

AN - SCOPUS:85079069163

VL - 11

JO - Nature Communications

JF - Nature Communications

SN - 2041-1723

IS - 1

M1 - 4748

ER -

ID: 284293850