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Matthew H. Bailey, W. Meyerson, L. Dursi, Liang-Bo Wang, Guanlan Dong, Wen-Wei Liang, A. Weerasinghe, Shantao Li, Yize Li, Sean Kelso, Rehan Pavana Matthew H. Alex Kami Kyle Allison Li Kyle Y Akbani Anur Bailey Buchanan Chiotti Covington Crea, Rehan Akbani, Pavana Anur, Matthew H. Bailey, Alex Buchanan, Kami Chiotti, K. Covington, Allison L. Creason, Li-Hua Ding, Kyle Ellrott, Yu Fan, S. Foltz, G. Getz, W. Hale, D. Haussler, J. Hess, Carolyn M. Hutter, C. Kandoth, K. Kasaian, M. Kasapi, David B. Larson, I. Leshchiner, John H. Letaw, Singer Ma, M. McLellan, Yi-Fei Men, G. Mills, Beifang Niu, Myron Peto, Amie Radenbaugh, Sheila M. Reynolds, G. Saksena, Heidi Sofia, Chip Stewart, Adam Struck, Joshua M. Stuart, Wenyi Wang, J. Weinstein, David A. Wheeler, Christopher K. Wong, Liu Xi, Kai Ye, Matthew H. Beifang Matthias Paul C. Ivo Adam P. Ken Zechen Bailey Niu Bieg Boutros Buchhalter Butler Chen Cho, M. Bieg, P. Boutros, I. Buchhalter, A. Butler, Ken Chen, Zechen Chong, Oliver Drechsel, Lewis Jonathan Dursi, R. Eils, S. M. Espiritu, R. Fulton, Shengjie Gao, J. Gelpí, M. Gerstein, Santiago Gonzalez, I. Gut, Faraz Hach, Michael C. Heinold, Jonathan Hinton, Taobo Hu, Vincent Huang, Yi Huang, B. Hutter, David Jones, Jongsun Jung, N. Jäger, Hyung-Lae Kim, K. Kleinheinz, Sushant Kumar, Yogesh Kumar, Christopher M. Lalansingh, Ivica Letunic, D. Livitz, Eric Z. Ma, Y. Maruvka, R. J. Mashl, A. Menzies, A. Milovanović, M. Nielsen, S. Ossowski, N. Paramasivam, J. S. Pedersen, Marc D. Perry, Montserrat Puiggròs, K. Raine, Esther Rheinbay, R. Royo, S. Sahinalp, Iman Sarrafi, M. Schlesner, J. Simpson, L. Stebbings, Miranda D. Stobbe, J. Teague, G. Tiao, D. Torrents, J. Wala, Jia-Yin Wang, S. Waszak, J. Weischenfeldt, M. Wendl, J. Werner, Zhenggang Wu, Hong Xue, Sergei Yakneen, T. Yamaguchi, V. Yellapantula, Christina K. Yung, Junjun Zhang, G. Saksena, Kyle Ellrott, David A. Wheeler, G. Getz, M. Gerstein, Li-Hua Ding, Lauri A. Federico Adam Hiroyuki David J. Nishant Keun So Aaltonen Abascal Abeshouse Aburatani Adams Agrawal, L. Aaltonen, F. Abascal, Adam Abeshouse, H. Aburatani, D. J. Adams, N. Agrawal, K. Ahn, S. Ahn, H. Aikata, K. Akdemir, H. Al-Ahmadie, S. Al-Sedairy, F. Al-Shahrour, M. Alawi, Monique Albert, K. Aldape, L. Alexandrov, A. Ally, K. Alsop, Eva G. Álvarez, F. Amary, S. Amin, Brice Aminou, O. Ammerpohl, M. Anderson, Y. Ang, D. Antonello, S. Aparicio, Elizabeth L. Appelbaum, Y. Arai, Axel Aretz, K. Arihiro, S. Ariizumi, J. Armenia, L. Arnould, S. Asa, Y. Assenov, Gurnit Atwal, S. Aukema, J. Auman, M. R. Aure, P. Awadalla, M. Aymerich, Gary D Bader, Adrian Baez-Ortega, Peter J. Bailey, M. Balasundaram, S. Balu, P. Bandopadhayay, R. Banks, S. Barbi, A. Barbour, J. Barenboim, J. Barnholtz-Sloan, Hugh Barr, E. Barrera, John M. S. Bartlett, Javier Bartolome, C. Bassi, O. Bathe, D. Baumhoer, P. Bavi, S. Baylin, Wojciech Bazant, D. Beardsmore, Timothy A. Beck, S. Behjati, A. Behren, C. Bell, S. Beltrán, Christopher Benz, A. Berchuck, A. Bergmann, E. Bergstrom, B. Berman, D. Berney, S. Bernhart, R. Beroukhim, Mario Berrios, S. Bersani, Johanna Bertl, M. Betancourt, Vinayak Bhandari, S. Bhosle, A. Biankin, D. Bigner, H. Binder, E. Birney, M. Birrer, N. Biswas, B. Bjerkehagen, T. Bodenheimer, L. Boice, G. Bonizzato, J. D. de Bono, Arnoud Boot, M. Bootwalla, Å. Borg, A. Borkhardt, Keith A. Boroevich, I. Borozan, Christoph Borst, M. Bosenberg, Mattia Bosio, J. Boultwood, G. Bourque, G. Bova, D. Bowen, R. Bowlby, D. Bowtell, S. Boyault, R. Boyce, Jeffrey H. Boyd, A. Brazma, P. Brennan, D. Brewer, A. Brinkman, Rob Bristow, R. Broaddus, J. Brock, M. Brock, A. Broeks, Angela N. Brooks, Denise Brooks, B. Brors, S. Brunak, Timothy J. C. Bruxner, A. Bruzos, C. Buchholz, S. Bullman, H. Burke, B. Burkhardt, K. Burns, John P. Busanovich, C. D. Bustamante, A. Butte, Niall J. Byrne, A. Børresen-Dale, Samantha J. Caesar-Johnson, Andy Cafferkey, D. Cahill, C. Calabrese, Carlos Caldas, F. Calvo, Niedzica Camacho, P. Campbell, E. Campo, C. Cantù, S. Cao, T. Carey, Joana Carlevaro-Fita, R. Carlsen, I. Cataldo, M. Cazzola, J. Cebon, R. Cerfolio, D. Chadwick, D. Chakravarty, D. Chalmers, Calvin Wing Yiu Chan, Kin Chan, M. Chan-Seng-Yue, V. Chandan, David K. Chang, S. Chanock, L. Chantrill, A. Chateigner, N. Chatterjee, K. Chayama, Hsiao-wei Chen, Jie-Ming Chen, Yiwen Chen, Zhaohong Chen, A. Cherniack, Jeremy Chien, Y. Chiew, Suet-Feung Chin, Juok Cho, Sunghoon Cho, J. Choi, Wan Choi, C. Chomienne, S. Choo, A. Chou, Angelika N. Christ, E. Christie, E. Chuah, C. Cibulskis, K. Cibulskis, S. Cingarlini, P. Clapham, A. Claviez, S. Cleary, N. Cloonan, Marek Cmero, C. Collins, Ashton A. Connor, S. Cooke, C. Cooper, L. Cope, V. Corbo, M. Cordes, S. Cordner, I. Cortés-Ciriano, P. Cowin, B. Craft, David W Craft, C. Creighton, Yupeng Cun, Erin E. Curley, Ioana Cutcutache, Karolina M. Czajka, B. Czerniak, Rebecca A. Dagg, Ludmila V. Danilova, M. Davi', Natalie R. Davidson, H. Davies, Ian J. Davis, Brandi Davis-Dusenbery, K. Dawson, F. M. de la Vega, R. De Paoli-Iseppi, T. DeFreitas, A. D. Dei Tos, O. Delaneau, J. Demchok, J. Demeulemeester, German Demidov, Deniz Demircioğlu, Nening Dennis, R. Denroche, S. Dentro, Nikita Desai, V. Deshpande, A. Deshwar, C. Desmedt, J. Deu-Pons, Noreen Dhalla, N. Dhani, P. Dhingra, R. Dhir, Anthony Dibiase, Klev Diamanti, Shuai Ding, Huy Q. Dinh, L. Dirix, H. Doddapaneni, Nilgun Donmez, Michelle Dow, R. Drapkin, Ruben M. Drews, Serge Serge, T. Dudderidge, Ana Dueso-Barroso, Andrew J. Dunford, Michael Dunn, F. Duthie, K. Dutton-Regester, Jenna Eagles, D. Easton, Stuart D. Edmonds, Paul A. Edwards, S. Edwards, R. Eeles, A. Ehinger, Juergen Eils, A. El-Naggar, Matthew Eldridge, S. Erkek, G. Escaramís, X. Estivill, D. Etemadmoghadam, J. Eyfjord, B. Faltas, D. Fan, W. Faquin, Claudiu Farcas, M. Fassan, A. Fatima, Francesco Favero, Nodirjon Fayzullaev, Ina Felau, S. Fereday, M. Ferguson, Vincent Ferretti, L. Feuerbach, M. Field, J. L. Fink, G. Finocchiaro, C. Fisher, M. Fittall, A. Fitzgerald, R. Fitzgerald, A. Flanagan, N. Fleshner, P. Flicek, J. Foekens, K. Fong, Nuno A. Fonseca, Christopher S. Foster, Natalie S. Fox, M. Fraser, Scott R. Frazer, Milana Frenkel-Morgenstern, William Friedman, J. Frigola, Catrina C. Fronick, Akihiro Fujimoto, M. Fujita, M. Fukayama, L. Fulton, Mayuko Furuta, P. Futreal, Anja Füllgrabe, S. Gabriel, S. Gallinger, C. Gambacorti-Passerini, Jianjiong Gao, L. Garraway, Ø. Garred, Erik P. Garrison, D. Garsed, Nils Gehlenborg, J. George, D. Gerhard, C. Gerhauser, J. Gershenwald, M. Gerstung, Mohammed Ghori, R. Ghossein, N. Giama, R. Gibbs, A. Gill, P. Gill, D. Giri, D. Głodzik, V. Gnanapragasam, Maria Elisabeth Goebler, M. Goldman, Carmen Gómez, A. González-Pérez, D. Gordenin, J. Gossage, K. Gotoh, R. Govindan, D. Grabau, Janet S. Graham, R. Grant, A. Green, Eric D. Green, Liliana Greger, N. Grehan, Sonia Grimaldi, S. Grimmond, R. Grossman, A. Grundhoff, G. Gundem, Qianyun Guo, Manaswi Gupta, S. Gupta, M. Gut, Jonathan Göke, Gavin Ha, A. Haake, D. Haan, S. Haas, K. Haase, James E. Haber, Nina Habermann, S. Haider
49 21. 9. 2020.

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

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. With the generation of large pan-cancer whole-exome and whole-genome sequencing projects, a question remains about how comparable these datasets are. Here, using The Cancer Genome Atlas samples analysed as part of the Pan-Cancer Analysis of Whole Genomes project, the authors explore the concordance of mutations called by whole exome sequencing and whole genome sequencing techniques.


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