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Retrospective evalu...
Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples
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- Bailey, Matthew H. (author)
- Washington University in St. Louis
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- Meyerson, William U. (author)
- Yale University
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- Dursi, Lewis Jonathan (author)
- Hospital for Sick Children, Toronto,Ontario Institute for Cancer Research
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- Wang, Liang Bo (author)
- Washington University in St. Louis
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- Dong, Guanlan (author)
- Washington University in St. Louis
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- Liang, Wen Wei (author)
- Washington University in St. Louis
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- Weerasinghe, Amila (author)
- Washington University in St. Louis
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- Li, Shantao (author)
- Yale University
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- Kelso, Sean (author)
- Washington University in St. Louis
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- Saksena, Gordon (author)
- Broad Institute
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- Ellrott, Kyle (author)
- Oregon Health & Science University
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- Wendl, Michael C. (author)
- Washington University in St. Louis
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- Wheeler, David A. (author)
- Baylor College of Medicine
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- Getz, Gad (author)
- Massachusetts General Hospital,Harvard Medical School,Broad Institute
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- Simpson, Jared T. (author)
- Ontario Institute for Cancer Research
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- Gerstein, Mark B. (author)
- Yale University
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- Ding, Li (author)
- Washington University in St. Louis
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- Borg, Ake (creator_code:cre_t)
- Lund University,Lunds universitet,Bröstcancer-genetik,Sektion I,Institutionen för kliniska vetenskaper, Lund,Medicinska fakulteten,Familjär bröstcancer,Forskargrupper vid Lunds universitet,LUCC: Lunds universitets cancercentrum,Övriga starka forskningsmiljöer,Breastcancer-genetics,Section I,Department of Clinical Sciences, Lund,Faculty of Medicine,Familial Breast Cancer,Lund University Research Groups,LUCC: Lund University Cancer Centre,Other Strong Research Environments
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- Ehinger, Anna (creator_code:cre_t)
- Lund University,Lunds universitet,Avdelningen för translationell cancerforskning,Institutionen för laboratoriemedicin,Medicinska fakulteten,Division of Translational Cancer Research,Department of Laboratory Medicine,Faculty of Medicine
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- Glodzik, Dominik (creator_code:cre_t)
- Wellcome Trust Sanger Institute
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- Grabau, Dorthe (creator_code:cre_t)
- Skåne University Hospital
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- Huang, Mi Ni (creator_code:cre_t)
- Duke–NUS Medical School
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- Li, Chang (creator_code:cre_t)
- Beijing Genomics Institute,China National Genebank
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- Ringnér, Markus (creator_code:cre_t)
- Lund University,Lunds universitet,Molekylär cellbiologi,Biologiska institutionen,Naturvetenskapliga fakulteten,Molecular Cell Biology,Department of Biology,Faculty of Science
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- Staaf, Johan (creator_code:cre_t)
- Lund University,Lunds universitet,Bröstcancer-genetik,Sektion I,Institutionen för kliniska vetenskaper, Lund,Medicinska fakulteten,LUCC: Lunds universitets cancercentrum,Övriga starka forskningsmiljöer,Bröst/lungcancer,Institutionen för kliniska vetenskaper, Lund,Breastcancer-genetics,Section I,Department of Clinical Sciences, Lund,Faculty of Medicine,LUCC: Lund University Cancer Centre,Other Strong Research Environments,Breast/lungcancer,Department of Clinical Sciences, Lund
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Li, Yize (author)
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Washington University in St Louis Yale University (creator_code:org_t)
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- 2020-09-21
- 2020
- English.
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11:1
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http://dx.doi.org/10... (free)
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https://www.nature.c...
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https://doi.org/10.1...
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https://uu.diva-port... (primary) (Raw object)
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https://lup.lub.lu.s...
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https://doi.org/10.1...
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Abstract
Subject headings
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- 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.
Subject headings
- MEDICIN OCH HÄLSOVETENSKAP -- Klinisk medicin -- Cancer och onkologi (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Clinical Medicine -- Cancer and Oncology (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Medicinsk genetik (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Medical Genetics (hsv//eng)
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- By the author/editor
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Bailey, Matthew ...
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Meyerson, Willia ...
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Dursi, Lewis Jon ...
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Wang, Liang Bo
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Dong, Guanlan
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Liang, Wen Wei
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show more...
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Weerasinghe, Ami ...
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Li, Shantao
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Kelso, Sean
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Saksena, Gordon
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Ellrott, Kyle
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Wendl, Michael C ...
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Wheeler, David A ...
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Getz, Gad
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Simpson, Jared T ...
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Gerstein, Mark B ...
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Ding, Li
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Borg, Ake
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Ehinger, Anna
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Glodzik, Dominik
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Grabau, Dorthe
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Huang, Mi Ni
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Li, Chang
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Ringnér, Markus
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Staaf, Johan
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Li, Yize
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- About the subject
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- MEDICAL AND HEALTH SCIENCES
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MEDICAL AND HEAL ...
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and Clinical Medicin ...
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and Cancer and Oncol ...
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- MEDICAL AND HEALTH SCIENCES
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MEDICAL AND HEAL ...
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and Basic Medicine
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and Medical Genetics
- Articles in the publication
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Nature Communica ...
- By the university
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Lund University
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Uppsala University
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Karolinska Institutet