作者
William U Meyerson, Lewis Jonathan Dursi, Liang-Bo Wang, Guanlan Dong, Wen-Wei Liang, Amila Weerasinghe, Yize Li, Sean Kelso, Michael C Wendl, Jared T Simpson, Rehan Akbani, Pavana Anur, Matthew H Bailey, Alex Buchanan, Kami Chiotti, Kyle Covington, Allison Creason, Li Ding, Kyle Ellrott, Yu Fan, Steven Foltz, Gad Getz, Walker Hale, David Haussler, Julian M Hess, Carolyn M Hutter, Cyriac Kandoth, Katayoon Kasaian, Melpomeni Kasapi, Dave Larson, Ignaty Leshchiner, John Letaw, Singer Ma, Michael D McLellan, Yifei Men, Gordon B Mills, Beifang Niu, Myron Peto, Amie Radenbaugh, Sheila M Reynolds, Gordon Saksena, Heidi Sofia, Chip Stewart, Adam J Struck, Joshua M Stuart, Wenyi Wang, John N Weinstein, David A Wheeler, Christopher K Wong, Liu Xi, Kai Ye, Matthias Bieg, Paul C Boutros, Ivo Buchhalter, Adam P Butler, Ken Chen, Zechen Chong, Oliver Drechsel, Lewis Jonathan Dursi, Roland Eils, Shadrielle MG Espiritu, Robert S Fulton, Shengjie Gao, Mark B Gerstein, Santiago Gonzalez, Ivo G Gut, Faraz Hach, Michael C Heinold, Jonathan Hinton, Taobo Hu, Vincent Huang, Yi Huang, Barbara Hutter, David R Jones, Jongsun Jung, Natalie Jäger, Hyung-Lae Kim, Kortine Kleinheinz, Sushant Kumar, Yogesh Kumar, Christopher M Lalansingh, Ivica Letunic, Dimitri Livitz, Eric Z Ma, Yosef E Maruvka, R Jay Mashl, Andrew Menzies, Ana Milovanovic, Morten Muhlig Nielsen, Stephan Ossowski, Nagarajan Paramasivam, Jakob Skou Pedersen, Marc D Perry, Montserrat Puiggròs, Keiran M Raine, Esther Rheinbay, Romina Royo, S Cenk Sahinalp, Iman Sarrafi, Matthias Schlesner, Lucy Stebbings, Miranda D Stobbe, Jon W Teague, Grace Tiao, David Torrents, Jeremiah A Wala, Jiayin Wang, Sebastian M Waszak, Joachim Weischenfeldt, Johannes Werner, Zhenggang Wu, Hong Xue, Sergei Yakneen, Takafumi N Yamaguchi, Venkata D Yellapantula, Christina K Yung, Junjun Zhang, Lauri A Aaltonen, Federico Abascal, Adam Abeshouse, Hiroyuki Aburatani, David J Adams, Nishant Agrawal, Keun Soo Ahn, Sung-Min Ahn, Hiroshi Aikata, Kadir C Akdemir, Hikmat Al-Ahmadie, Sultan T Al-Sedairy, Fatima Al-Shahrour, Malik Alawi, Monique Albert, Kenneth Aldape, Ludmil B Alexandrov, Adrian Ally, Kathryn Alsop, Eva G Alvarez, Fernanda Amary, Samirkumar B Amin, Brice Aminou, Ole Ammerpohl, Matthew J Anderson, Yeng Ang, Davide Antonello, Samuel Aparicio, Elizabeth L Appelbaum, Yasuhito Arai, Axel Aretz, Koji Arihiro, Shun-ichi Ariizumi
发表日期
2020/9/21
出版商
Nature Publishing Group UK
简介
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.
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