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

Bailey, Matthew H; Hirano, Satoshi; Yang, Lixing; Juul, Malene; Purdie, Colin A; O'Neill, Brian Patrick; Kabbe, Rolf; Papaemmanuil, Elli; Fan, Yu; Hayes, D Neil; Raeder, Benjamin; Juul, Sissel; group, PCAWG novel somatic mutation calling methods working; Stretch, Jonathan R; Nielsen, Morten Muhlig; He, Yao; Ringel, Matthew; Lou, Shaoke; Eeles, Rosalind A; Sperandio, Nicola; Rätsch, Gunnar; Zou, Lihua; Bustamante, Carlos D; Jung, Jongsun; Knappskog, Stian; Bassi, Claudio; Schumacher, Steven E; Li, Xiaotong; Ye, Kai; Simon, Ronald; Ahn, Keun Soo; Thorne, Heather; Bailey, Matthew H; Mirabello, Lisa; Mikkelsen, Tom; Sidiropoulos, Nikos; Beltran, Sergi; Alexandrov, Ludmil B; Van Den Berg, David J; Brooks, Angela N; Demchok, John A; Noble, Michael S; Lopez-Guillermo, Armando; Nones, Katia; Wong, Bernice H; Dei Tos, Angelo P; Schilhabel, Markus B; Atwal, Gurnit; Stenhouse, Alasdair; Gordenin, Dmitry A; Donmez, Nilgun; Williams, Ashley; Song, Lei; Favero, Francesco; Roehrl, Michael H A; Taylor-Weiner, Amaro; Faquin, William C; Roach, Jeffrey; Dentro, Stefan; Men, Yifei; Anur, Pavana; Gupta, Shailja; Tam, Angela; Gao, Jianjiong; Helmy, Mohamed; Wiznerowicz, Maciej; Imbusch, Charles David; Rino, Yasushi; Landgraf, Pablo; Boot, Arnoud; Haider, Syed; Barbour, Andrew P; Nakagama, Hitoshi; Rodríguez-González, F Germán; Christ, Angelika N; Kovacevic, Milena; Milella, Michele; Baumhoer, Daniel; Kumar, Kiran; Bigner, Darell; Schultz, Nikolaus; Hua, Xing; Behjati, Sam; Schramm, Sarah-Jane; Borkhardt, Arndt; Hosoda, Fumie; Nicol, David; Salvia, Roberto; Berney, Daniel M; Stuart, Joshua M; Fukayama, Masashi; Turner, Daniel J; Zhang, Jing; Raine, Keiran M; Camacho, Niedzica; Leshchiner, Ignaty; Arihiro, Koji; Teh, Bin Tean; Yugawa, Takashi; Matthews, Lucy; Torrents, David; Shin, Seung Jun; Wang, Jiayin; Nastic, Mia; Shackleton, Mark; Veluvolu, Umadevi; Salichos, Leonidas; Staib, Peter; Wilson, Richard K; Johnson, Todd A; Sanchez-Vega, Francisco; Nettekoven, Gerd; Biankin, Andrew V; Butler, Adam P; Chan, Calvin Wing Yiu; Appelbaum, Elizabeth L; Voet, Douglas; Moore, Malcolm J; Marchal, Kathleen; Merrett, Neil D; Chan, Kin; Rodriguez-Martin, Bernardo; Hasegawa, Takanori; Parsons, Simon L; Tortora, Giampaolo; Gerhard, Daniela S; Betancourt, Miguel; Kay, Jonathan D; Lee, Jeong-Yeon; Mungall, Karen; Skelly, Tara J; Heath, Allison P; Aminou, Brice; Grant, Robert C; Berman, Benjamin P; Rausch, Tobias; Xue, Hong; Wu, Yang; Cazzola, Mario; Chiew, Yoke-Eng; Baylin, Stephen B; Yau, Christina; Hersey, Peter; Kazanov, Marat D; Tojo, Marta; Lee, Darlene; Gonzalez-Perez, Abel; Yu, Kaixian; Jamieson, Nigel B; Letourneau, Louis; Van Meir, Erwin G; Van Laere, Steven; Miller, David K; Isaacs, William B; Newhouse, Steven J; Sungalee, Stephanie; Ueno, Naoto T; Jayasinghe, Reyka; Valencia, Alfonso; Cingarlini, Sara; Peto, Myron; Mills, Gordon B; Malcovati, Luca; Wu, Dai-Ying; van de Vijver, Marc J; Lynch, Andy G; Lu, Yong-Jie; Lanzós, Andrés; Grimmond, Sean M; Liu, Fenglin; Viksna, Juris; Waddell, Nicola; Lee, Juhee; Huang, Yi; Beardsmore, Duncan; Boultwood, Jacqueline; Cloonan, Nicole; Dunford, Andrew J; Chen, Hsiao-Wei; Gut, Ivo G; Lamaze, Fabien C; Deshwar, Amit G; Trotta, Jean-Rémi; Cerfolio, Robert; Bhandari, Vinayak; Matthew, Thomas J; Kefford, Richard F; Tarabichi, Maxime; Ferguson, Martin L; Habermann, Nina; Martin, Sancha; Feuerbach, Lars; Carey, Thomas E; Morganella, Sandro; Robertson, Alan J; Ittmann, Michael; Burke, Hazel; Tavaré, Simon; Caldas, Carlos; Hess, Julian M; Bristow, Robert G; Xi, Liu; Jäger, Natalie; Mularoni, Loris; Provenzano, Elena; Trümper, Lorenz H P; Wang, Qi; Akdemir, Kadir C; Lau, Loretta M S; Kasapi, Melpomeni; Scully, Ralph; Serra, Stefano; Lichter, Peter; Perry, Marc D; Salgado, Roberto; Sahinalp, S Cenk; Weinstein, John N; Fonseca, Nuno A; Dhani, Neesha C; Chou, Angela; Xing, Rui; Hazell, Steven; Kumar, Yogesh; Langerød, Anita; Simpson, Peter T; Bailey, Peter J; Mayo, Michael; Bergstrom, Erik N; Wang, Zhining; Newton, Yulia; Shi, Yan; Wu, Guanming; Hornshøj, Henrik; Karsch, Dennis; Katai, Hitoshi; Thai, Kevin; van As, Nicholas; Wigle, Dennis; Smith-McCune, Karen; Bosio, Mattia; Jonathan Dursi, Lewis; Molnár-Gábor, Fruzsina; Long, Georgina V; Fronick, Catrina C; Moore, Richard A; Buchhalter, Ivo; Lee, Jake June-Koo; Kumar, Pardeep; Reuter, Victor; P'ng, Christine; Anderson, Matthew J; Huber, Wolfgang; Beck, Timothy A; Bernhart, Stephan H; Lalonde, Emilie; Stobbe, Miranda D; Hudson, Thomas J; Demeulemeester, Jonas; Ha, Gavin; Ocana, David; Hong, Eun Pyo; Yamaguchi, Takafumi N; Thompson, R Houston; MacRae, Shona; Joly, Yann; Ramakrishnan, Kamna; Salcedo, Adriana; Xiang, Qian; Dutton-Regester, Ken; von Kalle, Christof; Semple, Colin A; Staaf, Johan; Collins, Colin C; Shang, Catherine A; Perou, Charles M; Senbabaoglu, Yasin; Birney, Ewan; De Bono, Johann S; Richardson, Andrea L; Hepperla, Austin J; Biswas, Nidhan K; Hegde, Apurva M; Chakravarty, Dimple; Paczkowska, Marta; Eils, Roland; Armenia, Joshua; Wilson, Gavin W; Kellis, Manolis; Mijalkovic, Sanja; Planko, Laura; 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Waring, Paul M; Jegalian, Karine; deFazio, Anna; Vilain, Ricardo E; Iskar, Murat; Jonasson, Jon G; Patch, Ann-Marie; Green, Anthony R; Bartlett, John; Ohi, Kazuhiro; Campo, Elias; Ivkovic, Sinisa; Rohde, Marius; Chomienne, Christine; Brooks, Denise; Chan-Seng-Yue, Michelle; Peifer, Martin; Chateigner, Aurélien; Sasaki-Oku, Aya; Mitchell, Chris; Myers, Jerome; Ma, Singer; Underwood, Timothy J; Uusküla-Reimand, Liis; Buchholz, Christiane; Fayzullaev, Nodirjon; Bhosle, Shriram G; Liu, Eric Minwei; Zeps, Nikolajs; von Mering, Christian; Jayaseelan, Joy C; Bova, G Steven; Reifenberger, Guido; Pihl, Todd D; Nakano, Kaoru; Gibbs, Richard A; Warnatz, Hans-Jörg; Navarro, Fabio C P; Vyas, Paresh; Lawrence, Michael S; O'Meara, Sarah; Fisher, Cyril; Davi, Maria Vittoria; Stewart, Chip; Rodriguez, Javier Bartolomé; Johns, Amber L; Garsed, Dale W; Al-Shahrour, Fatima; Letaw, John; Chen, Ken; Grimaldi, Sonia; Covington, Kyle; Tarpey, Patrick; Koscher, Michael; Akbani, Rehan; Hayashi, Shuto; Livingstone, Julie; Wang, Wenyi; Abascal, Federico; Zhang, Fan; Zhou, Wanding; Ma, Yussanne; Burns, Kathleen H; Whitaker, Hayley C; Stratton, Michael R; Luo, Xuemei; Sadeghi, Sara; Papatheodorou, Irene; Harrington, Eoghan; Brazma, Alvis; Borg, Ake; Rosenwald, Andreas; Agrawal, Nishant; Garrison, Erik; Chantrill, Lorraine A; Toprak, Umut H; Butte, Atul J; Samra, Jaswinder S; Busanovich, John; Mardis, Elaine R; Khurana, Ekta; Wilkerson, Matthew D; Boutros, Paul C; Eyfjord, Jorunn E; Cooke, Susanna L; Chen, Yiwen; Hayami, Shinya; Schwarz, Roland F; Hanna, George B; Reyna, Matthew A; Karaszi, Katalin; Cherniack, Andrew D; Shah, Nimish C; Jones, David R; Simbolo, Michele; López-Otín, Carlos; Kreuz, Markus; Reyes-Salazar, Iker; Prinz, Manuel; Alvarez, Eva G; Pickett, Hilda A; Serge, Serge; Sipahimalani, Payal; Vedururu, Ravikiran; Hovestadt, Volker; Hu, Jianhong; Signoretti, Sabina; Küppers, Ralf; Segre, Ayellet V; Huang, Mi Ni; Fereday, Sian; Hamilton, Mark P; Shen, Ciyue; Chiotti, Kami; Kim, Jaegil; Ellrott, Kyle; Knoppers, Bartha M; Jakrot, Valerie; Van der Kwast, Theodorus; Dawson, Kevin J; Scolyer, Richard A; Visakorpi, Tapio; Espiritu, Shadrielle M G; Grundhoff, Adam; Larson, Dave; Felau, Ina; Umer, Husen M; Schlesner, Matthias; Xu, Qinying; Wilmott, James S; Lee, Hee Jin; Su, Xiaoping; Jones, David T W; Zhang, Hongwei; Vazquez, Miguel; Simpson, Jared T; Ghori, Mohammed; Hübschmann, Daniel; Giama, Nasra H; Nie, Yongzhan; Finocchiaro, Gaetano; Möller, Peter; Yousif, Fouad; Korchina, Viktoriya; Lungu, Ilinca; Hinton, Jonathan; Khoo, David; Livitz, Dimitri; Boyault, Sandrine; Guo, Qianyun; Al-Ahmadie, Hikmat; Scardoni, Maria; Lenze, Dido; Boice, Lori; Hale, Walker; Calabrese, Claudia; Leongamornlert, Daniel A; Aaltonen, Lauri A; Schmidt, Heather K; MacGrogan, Gaetan; Potapova, Olga; Schreiber, Stefan; Mayer, Erik; Craft, Brian; Jerman, Lara; Ji, Yuan; Okusaka, Takuji; Vermeulen, Peter; Smith, Jaclyn; Lu, Yiling; Tommasi, Stefania; Dursi, Lewis Jonathan; Hong, Chen; Grabau, Dorthe; Kilpinen, Helena; Gerstein, Mark B; Warrell, Jonathan; Grehan, Nicola; Spellman, Paul T; Park, Keunchil; Hilmarsdottir, Holmfridur; Yachida, Shinichi; Connor, Ashton A; Tiao, Grace; Cibulskis, Kristian; Yang, Jean Y; Popescu, Irinel; Ng, Anthony; Dunn, Michael; Consortium, PCAWG; Wadelius, Claes; Dudderidge, Tim; Sander, Chris; Hutter, Carolyn M; Jolly, Clemency; Wong, Tina; Foekens, John A; Woo, Youngchoon; Ott, German; Mieczkowski, Piotr A; Kleinheinz, Kortine; Chatterjee, Nilanjan; Mitchell, Thomas J; Le, Xuan; Zhang, Xiuqing; Göke, Jonathan; Kang, Koo Jeong; Barnholtz-Sloan, Jill; Kakavand, Hojabr; Teague, Jon W; Aikata, Hiroshi; Ally, Adrian; Ochoa, Angelica; Bourque, Guillaume; Alsop, Kathryn; Prokopec, Stephenie D; Fitzgerald, Anna; Saito-Adachi, Mihoko; Hiraoka, Nobuyoshi; Haas, Siegfried; Park, Kiejung; Mijalkovic-Lazic, Ana Mijalkovic; Lalansingh, Christopher M; Scott, David; Hobolth, Asger; Kong, Gu; Füllgrabe, Anja; Hoadley, Katherine A; Stunnenberg, Henk G; Amary, Fernanda; Wu, Zhenggang; Ehinger, Anna; Vázquez-García, Ignacio; Cho, Juok; Paiella, Salvatore; Rosenstiel, Philip C; Fatima, Aquila; Huska, Matthew R; Kandoth, Cyriac; Liu, Xingmin; Green, Eric; Bonizzato, Giada; Musgrove, Elizabeth A; Villasante, Izar; Eagles, Jenna; Sabarinathan, Radhakrishnan; Gomez, Carmen; Spring, Jonathan; Jones, Corbin D; Karlić, Rosa; Pajic, Marina; Tirabosco, Roberto; Edwards, Paul A; Wadi, Lina; Fong, Kwun M; De La Vega, Francisco M; Pivot, Xavier; Baez-Ortega, Adrian; Heins, Zachary; Lin, Pei; Lazar, Alexander J; Al-Sedairy, Sultan T; Susak, Hana; Martin-Subero, Jose I; Zhang, Zemin; Johns, Jeremy; Lawlor, Rita T; Friedman, William; Fink, J Lynn; Chen, Zhaohong; Jang, Se Jin; Kazakoff, Stephen H; Hou, Yong; Vasudev, Naveen; Christie, Elizabeth L; Cope, Leslie; Yao, Xiaotong; Turkington, Richard; Pasternack, Danielle; Nicholson, Jonathan; Delaneau, Olivier; Group, MC3 Working; Larsson, Erik; Jennings, Jennifer L; Pupo, Gulietta M; Shi, Ruian; Bertl, Johanna; Creason, Allison; Marra, Marco A; Broeks, Annegien; Shimizu, Eigo; Holik, Aliaksei Z; Ju, Young Seok; Rabionet, Raquel; Futreal, P Andrew; Davis-Dusenbery, Brandi N; Rubin, Mark A; Vincent-Salomon, Anne; Wala, Jeremiah A; Sinnott-Armstrong, Nasa; Ohno-Machado, Lucila; Balasundaram, Miruna; Tembe, Varsha; Garred, Øystein; McLellan, Michael D; Preston, Shaun R; Auman, J Todd; Yuen, Denis; Dinh, Huy Q; Suzuki, Akihiro; Sieverling, Lina; Rokutan, Hirofumi; King, Tari A; McPherson, Treasa A; Koures, Antonios; Zheng, Xiuqing; Waddell, Nick M; Sun, Ren X; Wang, Yumeng; Siebert, Reiner; Fujimoto, Akihiro; Kumar, Sushant; Kim, Hyung-Yong; Choi, Wan; Van't Veer, L.; Borozan, Ivan; Thayer, Sarah P; Luchini, Claudio; Gehlenborg, Nils; Rusev, Borislav C; Gershenwald, Jeffrey E; Zhu, Hongtu; Boyd, Jeffrey; Marin, Maximillian G; Govindan, Ramaswamy; Karlan, Beth; Bell, Cindy; Menzies, Andrew; Scarlett, Christopher J; Hodzic, Ermin; Luxton, Hayley J; Zamora, Jorge; López, Cristina; Choo, Su Pin; Zenz, Thorsten; Shen, Hui; Bersani, Samantha; Chayama, Kazuaki; Herrmann, Carl; Hummel, Michael; Radenbaugh, Amie; Dhir, Rajiv; Robertson, A Gordon; Byrne, Niall J; Kim, Jong K; Notta, Faiyaz; Sereni, Elisabetta; Lathrop, Mark; Johansson, Peter A; van Deurzen, Carolien H M; Ramalingam, Suresh; Calvo, Fabien; Park, Peter J; Shrestha, Raunak; Weerasinghe, Amila; Bowen, David T; Pedersen, Jakob Skou; Muzny, Donna M; Rheinbay, Esther; Tarnuzzer, Roy; Kneba, Michael; Spiro, Oliver; Yuan, Yuan; Davidson, Natalie R; Saini, Natalie; Rowe, Edward W; Tucker, Olga; Heisler, Lawrence E; Tutt, Andrew; Gut, Marta; Totoki, Yasushi; Haradhvala, Nicholas J; Khoo, Vincent; Aymerich, Marta; Heath, Simon C; Arnau, Gisela Mir; Gonzalez, Santiago; Omberg, Larsson; Schein, Jacqueline E; Haussler, David; Broaddus, Russell R; Davies, Helen; Glodzik, Dominik; Buchanan, Alex; Hoffmann, Steve; Thiessen, Nina; Livni, Naomi; Kennedy, Catherine J; Fraser, Michael; Lehrach, Hans; Zhu, Shida; Pea, Antonio; Hooijer, Gerrit K; Ogden, Christopher; Goldman, Mary J; Ojima, Hidenori; Kelso, Sean; Rippe, Karsten; Van Loo, Peter; Jonkers, Jos; Erkek, Serap; Hayes, Stephen J; Lawerenz, Chris; Davis, Ian J; Traficante, Nadia; Yakneen, Sergei; O'Neill, J Robert; Pich, Oriol; Li, Yilong; Furuta, Mayuko; Asa, Sylvia; Korshunov, Andrey; Maruvka, Yosef E; Holt, Robert A; Szczepanowski, Monika; Berchuck, Andrew; Puente, Xose S; Yamamoto, Masakazu; Greger, Liliana; Townend, David; Urushidate, Tomoko; Yu, Yingyan; Ghossein, Ronald; Soloway, Matthew G; Zapatka, Marc; Deu-Pons, Jordi; Maejima, Kazuhiro; Hama, Natsuko; Span, Paul N; Oesper, Layla; Klapper, Wolfram; Fassan, Matteo; Drapkin, Ronny; Yung, Christina K; Shmulevich, Ilya; Pulido-Tamayo, Sergio; Estivill, Xavier; Shimizu, Kiyo; Fulton, Robert S; Banks, Rosamonde E; Rosebrock, Daniel; Ammerpohl, Ole; Cmero, Marek; Shang, Ping; Saw, Robyn P M; Miyoshi, Naoki; Flanagan, Adrienne M; Levine, Douglas A; Miotto, Marco; O'Donnell, Peter; Barenboim, Jonathan; Izarzugaza, Jose M G; Weischenfeldt, Joachim; Hu, Taobo; Lakhani, Sunil R; Chuah, Eric; Rozen, Steven G; Madsen, Tobias; Gill, Pelvender; Verrill, Clare; Fujita, Masashi; Stark, Stefan G; Heiman, David I; Nahal-Bose, Hardeep K; Goebler, Maria Elisabeth; Foster, Christopher S; Dennis, Nening M; Barbi, Stefano; Li, Xinyue; Taschuk, Morgan L; Gambacorti-Passerini, Carlo; Dhingra, Priyanka; Su, Hong; Gabriel, Stacey B; Meyerson, William U; Denroche, Robert E; Thorne, Leigh B; McDermott, Ultan; Zou, Xueqing; Kim, Hyung-Lae; Viari, Alain; Wu, Jianmin; Albert, Monique; Wong, Winghing; Paramasivam, Nagarajan; Ng, Alvin Wei Tian; Laird, Peter W; Spillane, Andrew J; Hofmann, Oliver; Aukema, Sietse; Pritchard, Antonia L; Cao, Shaolong; Brewer, Daniel S; Nagrial, Adnan M; Rathmell, W Kimryn; Isaev, Keren; Zhang, Junjun; Lee-Six, Henry; Hedley, David; Liu, Fei-Fei; Mutch, David; Hupp, Ted R; Zhou, Yong; Ueno, Masaki; Bootwalla, Moiz S; Puiggròs, Montserrat; Reimand, Jüri; Chen, Jieming; Phillips, Mark; Arai, Yasuhito; Li, Jun; Wintersinger, Jeffrey A; Harmanci, Arif O; Wouters, Bradly G; Ferretti, Vincent; Muiños, Ferran; Louis, David N; Gnanapragasam, Vincent J; Holmes, Oliver; Kim, Hyunghwan; Dong, Guanlan; Nielsen, G Petur; Saksena, Gordon; Ruzzenente, Andrea; Burkhardt, Birgit; Winterhoff, Boris; Yu, Jun; Piñeiro-Yáñez, Elena; Faltas, Bishoy M; Frenkel-Morgenstern, Milana; Ossowski, Stephan; Yates, Lucy; Ong, Choon Kiat; Pauporté, Iris; Martinez-Fundichely, Alexander; Shahabi, Sagedeh; Ahn, Sung-Min; Lee, Donghoon; Shelton, Troy; Sabelnykova, Veronica Y; Cordner, Stephen M; Assenov, Yassen; Zheng, Liangtao; Struck, Adam J; Pinder, Sarah; Taylor, Darrin F; Sotiriou, Christos; Brors, Benedikt; Kato, Mamoru; Milovanovic, Ana; Yellapantula, Venkata D; Caesar-Johnson, Samantha J; Lander, Eric; Larsimont, Denis; Beroukhim, Rameen; Shriver, Craig; Nakamura, Toru; Roberts, Lewis R; Cun, Yupeng; Nandi, Tannistha; Park, Joong-Won; Hollingsworth, Michael A; Hong, Jongwhi H; Johnson, Rory; Heo, Seong Gu; Yaspo, Marie-Laure; Tijanic, Nebojsa; Tan, Benita Kiat Tee; Raphael, Benjamin J; Lewis, Lora; Hruban, Ralph H; Sauer, Torill; Petryszak, Robert; Fitzgerald, Rebecca C; Binder, Hans; Gossage, James; Pedamallu, Chandra Sekhar; Bergmann, Anke K; Xu, Yanxun; Moser, Catherine D; Oien, Karin A; Shiah, Yu-Jia; Etemadmoghadam, Dariush; Wilson, Julie M; Petrelli, Nicholas; Yang, Liming; Navarro, Arcadi; Juul, Randi Istrup; Socci, Nicholas D; Balu, Saianand; Abeshouse, Adam; Choi, Jung Kyoon; Prasad, Aparna; Singer, Samuel; Zaikova, Olga; Aretz, Axel; De Paoli-Iseppi, Ricardo; Garraway, Levi; Morrison, Carl; Wong, Christopher K; Hung, Jillian A; Xiao, Xiao; Minner, Sarah; Kundra, Ritika; Hoyle, Alan P; Liang, Wen-Wei; Tamborero, David; Yoon, Sung-Soo; Yoon, Christopher J; Imielinski, Marcin; Yang, Shanlin; Grossman, Robert L; Edwards, Sandra E; Li, Chang; Komorowski, Jan; Kube, Dieter; Soulette, Cameron M; Landoni, Luca; Liang, Sheng-Ben; Frigola, Joan; Wang, Linghua; Huang, Vincent; Bruzos, Alicia L; Danilova, Ludmila; Quinn, Michael C; Ushiku, Tetsuo; Escaramis, Georgia; Amin, Samirkumar B; 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doi:10.1038/s41467-020-18151-y

000165904 001__ 165904
000165904 005__ 20240229123215.0
000165904 0247_ $$2doi$$a10.1038/s41467-020-18151-y
000165904 0247_ $$2pmid$$apmid:32958763
000165904 0247_ $$2pmc$$apmc:PMC7505971
000165904 0247_ $$2altmetric$$aaltmetric:90890294
000165904 037__ $$aDKFZ-2020-02461
000165904 041__ $$aeng
000165904 082__ $$a500
000165904 1001_ $$00000-0003-4526-9727$$aBailey, Matthew H$$b0
000165904 245__ $$aRetrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.
000165904 260__ $$a[London]$$bNature Publishing Group UK$$c2020
000165904 3367_ $$2DRIVER$$aarticle
000165904 3367_ $$2DataCite$$aOutput Types/Journal article
000165904 3367_ $$0PUB:(DE-HGF)16$$2PUB:(DE-HGF)$$aJournal Article$$bjournal$$mjournal$$s1659101616_23226
000165904 3367_ $$2BibTeX$$aARTICLE
000165904 3367_ $$2ORCID$$aJOURNAL_ARTICLE
000165904 3367_ $$00$$2EndNote$$aJournal Article
000165904 520__ $$aThe 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.
000165904 536__ $$0G:(DE-HGF)POF3-312$$a312 - Functional and structural genomics (POF3-312)$$cPOF3-312$$fPOF III$$x0
000165904 588__ $$aDataset connected to CrossRef, PubMed,
000165904 650_7 $$2NLM Chemicals$$aDNA, Intergenic
000165904 650_2 $$2MeSH$$aBase Composition
000165904 650_2 $$2MeSH$$aDNA, Intergenic
000165904 650_2 $$2MeSH$$aDatabases, Genetic
000165904 650_2 $$2MeSH$$aExome: genetics
000165904 650_2 $$2MeSH$$aExons
000165904 650_2 $$2MeSH$$aGenome, Human: genetics
000165904 650_2 $$2MeSH$$aHumans
000165904 650_2 $$2MeSH$$aMutation
000165904 650_2 $$2MeSH$$aNeoplasms: genetics
000165904 650_2 $$2MeSH$$aRetrospective Studies
000165904 650_2 $$2MeSH$$aWhole Exome Sequencing
000165904 650_2 $$2MeSH$$aWhole Genome Sequencing
000165904 7001_ $$aMeyerson, William U$$b1
000165904 7001_ $$00000-0002-4697-798X$$aDursi, Lewis Jonathan$$b2
000165904 7001_ $$00000-0001-6977-9348$$aWang, Liang-Bo$$b3
000165904 7001_ $$00000-0002-4747-6036$$aDong, Guanlan$$b4
000165904 7001_ $$aLiang, Wen-Wei$$b5
000165904 7001_ $$00000-0003-3568-5823$$aWeerasinghe, Amila$$b6
000165904 7001_ $$00000-0002-5440-2780$$aLi, Shantao$$b7
000165904 7001_ $$aKelso, Sean$$b8
000165904 7001_ $$aGroup, MC3 Working$$b9$$eCollaboration Author
000165904 7001_ $$agroup, PCAWG novel somatic mutation calling methods working$$b10$$eCollaboration Author
000165904 7001_ $$00000-0001-6630-7935$$aSaksena, Gordon$$b11
000165904 7001_ $$00000-0002-6573-5900$$aEllrott, Kyle$$b12
000165904 7001_ $$aWendl, Michael C$$b13
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000165904 7001_ $$00000-0002-9746-3719$$aGerstein, Mark B$$b17
000165904 7001_ $$aDing, Li$$b18
000165904 7001_ $$aConsortium, PCAWG$$b19$$eCollaboration Author
000165904 7001_ $$aAkbani, Rehan$$b20
000165904 7001_ $$aAnur, Pavana$$b21
000165904 7001_ $$aBailey, Matthew H$$b22
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