← Back to cohort
Pathway and network analysis of more than 2500 whole cancer genomes
Matthew A. Reyna, David Haan, Marta Paczkowska, Lieven P. C. Verbeke, Miguél Vázquez, Abdullah Kahraman, Sergio Pulido-Tamayo, Jonathan Barenboim, Lina Wadi, Priyanka Dhingra, Raunak Shrestha, Gad Getz, Michael S. Lawrence, Jakob Skou Pedersen, Mark A. Rubin, David A. Wheeler, Søren Brunak, José M. G. Izarzugaza, Ekta Khurana, Kathleen Marchal, Christian von Mering, S. Cenk Şahinalp, Alfonso Valencia, Federico Abascal, Samirkumar B. Amin, Pratiti Bandopadhayay, Rameen Beroukhim, Johanna Bertl, Keith A. Boroevich, John Busanovich, Joana Carlevaro-Fita, Dimple Chakravarty, Calvin Wing Yiu Chan, Ken Chen, Jung Kyoon Choi, Jordi Deu-Pons, Klev Diamanti, J. Lynn Fink, Nuno A. Fonseca, Carlo Gambacorti‐Passerini, Dale W. Garsed, Mark Gerstein, Marta Gut, Mark P. Hamilton, Nicholas J. Haradhvala, Arif Harmanci, Carl Herrmann, Ermin Hodzic, Chen Hong, Henrik Hornshøj, Keren Isaev, Rory Johnson, Todd A. Johnson, Malene Juul, Randi Istrup Juul, André Kahles, Jong K. Kim, Jan Komorowski, Jan O. Korbel, Sushant Kumar, Andrés Lanzós, Erik Larsson, Kjong-Van Lehmann, Shantao Li, Xiaotong Li, Ziao Lin, Eric Minwei Liu, Lucas Lochovsky, Shaoke Lou, Tobias Madsen, Iñigo Martincorena, Alexander Martinez‐Fundichely, Yosef E. Maruvka, Patrick D. McGillivray, William Meyerson, Ferran Muiños, Loris Mularoni, Hidewaki Nakagawa, Morten Muhlig Nielsen, Keunchil Park, Kiejung Park, Iker Reyes-Salazar, Esther Rheinbay, Carlota Rubio-Pérez, Leonidas Salichos, Chris Sander, Steven E. Schumacher, Mark Shackleton, Ciyue Shen, Shimin Shuai, Lina Sieverling, Lincoln Stein, Grace Tiao, Tatsuhiko Tsunoda, Claes Wadelius, Jiayin Wang, Jonathan Warrell, Sebastian M. Waszak, Joachim Weischenfeldt, Guanming Wu, Jing Zhang, Xuanping Zhang, Yan Zhang, Zhongming Zhao, Lihua Zou, Jüri Reimand, Benjamin J. Raphael, Lauri A. Aaltonen, Adam Abeshouse, Hiroyuki Aburatani, David J. Adams, Nishant Agrawal, Keun Soo Ahn, Sung-Min Ahn, Hiroshi Aikata, Rehan Akbani, Kadir C. Akdemir, Hikmat Al‐Ahmadie, Sultan T. Al‐Sedairy, Fátima Al‐Shahrour, Malik Alawi, Monique Albert, Kenneth Aldape, Ludmil B. Alexandrov, Adrian Ally, Kathryn Alsop, Eva G. Álvarez, Fernanda Amary, Brice Aminou, Ole Ammerpohl, Matthew J. Anderson, Yeng Ang, Davide Antonello, Pavana Anur, Samuel Aparício, Elizabeth L. Appelbaum, Yasuhito Arai, Axel Aretz, Koji Arihiro, Shun‐ichi Ariizumi, Joshua Armenia, Laurent Arnould, L. Sylvia, Yassen Assenov, Gurnit Atwal, Sietse Aukema, J. Todd Auman, Miriam R. R. Aure, Philip Awadalla, Marta Aymerich, Adrian Baez‐Ortega, Matthew H. Bailey, Peter J. Bailey, Miruna Balasundaram, Saianand Balu, Rosamonde E. Banks, Stefano Barbi, Andrew P. Barbour, Jill S. Barnholtz‐Sloan, Hugh Barr, Elisabet Barrera, John Bartlett, Javier Bartolomé, Claudio Bassi, Oliver F. Bathe, Daniel Baumhoer, Prashant Bavi, Stephen B. Baylin, Wojciech Bażant, Duncan Beardsmore, Tim Beck, Sam Behjati, Andreas Behren, Beifang Niu, Cindy Bell, Sergi Beltrán, Christopher C. Benz, Andrew Berchuck, Anke K. Bergmann, Erik N. Bergstrom, Benjamin P. Berman, Daniel M. Berney, Mario Berríos, Samantha Bersani, Miguel Betancourt, Vinayak Bhandari, Shriram G. Bhosle, Andrew V. Biankin, Matthias Bieg, Darell D. Bigner, Hans Binder, Ewan Birney, Michael Birrer, Nidhan K. Biswas, Bodil Bjerkehagen, Tom Bodenheimer, Lori Boice, Giada Bonizzato, Johann S. de Bono, Arnoud Boot, Åke Borg, Arndt Borkhardt, Ivan Borozan, Christoph W. Borst, Marcus Bosenberg, Mattia Bosio, Jacqueline Boultwood, Guillaume Bourque, Paul C. Boutros, G. Steven Bova, David Bowen, Reanne Bowlby, David D.L. Bowtell, Sandrine Boyault, Rich Boyce, Jeffrey M. Boyd, Alvis Brāzma, Paul Brennan, Daniel S. Brewer, Arie B. Brinkman, Robert G. Bristow, Russell R. Broaddus, Jane E. Brock, Malcolm V. Brock, Annegien Broeks, Angela N. Brooks, Denise Brooks, Benedikt Brors, Timothy J. C. Bruxner, Alicia L. Bruzos, Alex Buchanan, Ivo Buchhalter, Christiane Buchholz, Susan Bullman, Hazel Burke, Birgit Burkhardt, Kathleen H. Burns, Carlos D. Bustamante, Adam P. Butler, Atul J. Butte, Niall J. Byrne, Anne‐Lise Børresen‐Dale, Andy Cafferkey, Declan Cahill, Claudia Calabrese, Carlos Caldas, Fabien Calvo, Niedzica Camacho, Elı́as Campo, Cinzia Cantù, Shaolong Cao, Thomas E. Carey, Rebecca Carlsen, Ivana Cataldo, Mario Cazzola, Jonathan Cebon, Robert Cerfolio, Dianne Chadwick, Drc Chalmers, Kin Chan, Michelle Chan‐Seng‐Yue, Vishal S. Chandan, David K. Chang, Stephen J. Chanock, Aurélien Chateigner, Nilanjan Chatterjee, Kazuaki Chayama, Hsiao-Wei Chen, Jieming Chen, Yiwen Chen, Zhaohong Chen, Andrew D. Cherniack, Jeremy Chien, Yoke-Eng Chiew, Suet‐Feung Chin, Juok Cho, Sunghoon Cho, Wan Choi, Christine Chomienne, Zechen Chong, Su Pin Choo, Angela Chou, Angelika N. Christ, Elizabeth L. Christie, Eric Chuah, Carrie Cibulskis, Kristian Cibulskis, Sara Cingarlini, Peter Clapham, Alexander Claviez, Sean P. Cleary, Nicole Cloonan, Marek Cmero, Colin C. Collins, Ashton A. Connor, Susanna L. Cooke, Colin S. Cooper, Leslie Cope, Vincenzo Corbo, Matthew G. Cordes, Stephen Cordner, Isidro Cortés‐Ciriano, Kyle R. Covington, Prue A. Cowin, Brian Craft, David Craft, Chad J. Creighton, Yupeng Cun, Erin Curley, Ioana Cutcutache, Karolina Czajka, Bogdan Czerniak, Rebecca A. Dagg, Ludmila Danilova, Maria Vittoria Davì, Natalie R. Davidson, Helen Davies, Ian J. Davis, Brandi N. Davis‐Dusenbery, Kevin J. Dawson, Francisco M. De La Vega, Ricardo De Paoli‐Iseppi, Timothy Defreitas, Angelo Paolo Dei Tos, Olivier Delaneau, John A. Demchok, Jonas Demeulemeester, German Demidov, Deniz Demircioğlu, Nening M. Dennis, Robert E. Denroche, Stefan C. Dentro, Nikita Desai, Vikram Deshpande, Amit G. Deshwar, Christine Desmedt, Noreen Dhalla, Neesha C. Dhani, Rajiv Dhir, Anthony DiBiase, Li Ding, Huy Q. Dinh, Luc Dirix, HarshaVardhan Doddapaneni, Nilgun Donmez, Michelle T. Dow, Ronny Drapkin, Oliver Drechsel, Ruben M. Drews, Serge Serge, Tim Dudderidge, Ana Dueso-Barroso, Andrew Dunford, Michael J. Dünn, Lewis Jonathan Dursi, Fraser R. Duthie, Ken Dutton‐Regester, Jenna Eagles, Douglas F. Easton, Stuart Edmonds, Paul A. Edwards, Sandra E. Edwards, Rosalind A. Eeles, Anna Ehinger, Roland Eils, Adel K. El‐Naggar, Matthew Eldridge, Kyle Ellrott, Serap Erkek, Geòrgia Escaramís, Shadrielle M. G. Espiritu, Xavier Estivill, Dariush Etemadmoghadam, Jórunn E. Eyfjörd, Bishoy M. Faltas, Daiming Fan, Yu Fan, William C. Faquin, Claudiu Farcas, Matteo Fassan, Aquila Fatima, Francesco Favero, Nodirjon Fayzullaev, Ina Felau, Sián Fereday, Martin L. Ferguson, Vincent Ferretti, Matthew A. Field, Gaetano Finocchiaro, Cyril Fisher, Matthew W. Fittall, Anna Fitzgerald, Rebecca C. Fitzgerald, Adrienne M. Flanagan, Neil Fleshner, Paul Flicek, John A. Foekens, Kwun M. Fong, Christopher S. Foster, Natalie S. Fox, Michael Fraser, Scott Frazer, Milana Frenkel‐Morgenstern, William A. Friedman, Catrina C. Fronick, Akihiro Fujimoto, Masashi Fujita, Masashi Fukayama, Lucinda A. Fulton, Robert S. Fulton, Mayuko Furuta, P. Andrew Futreal, Anja Füllgrabe, Stacey Gabriel, Steven Gallinger, Jianjiong Gao, Shengjie Gao, Levi A. Garraway, Øystein Garred, Erik Garrison, Nils Gehlenborg, Josep L. L. Gelpi, Joshy George, Daniela S. Gerhard, Clarissa Gerhäuser, Moritz Gerstung, Mohammed Ghori, Ronald Ghossein, Nasra H. Giama, Richard A. Gibbs, Bob Gibson, Anthony J. Gill, Pelvender Gill, Dilip D. Giri, Dominik Głodzik, Vincent J. Gnanapragasam, Maria Elisabeth Goebler, Mary J. Goldman, Carmen Gómez, Santiago Gonzalez, Abel González-Pérez, Dmitry A. Gordenin, James Gossage, Kunihito Gotoh, Ramaswamy Govindan, Dorthe Grabau, Janet S. Graham, Robert C. Grant, Anthony R. Green, Eric Green, Liliana Greger, Nicola Grehan, Sonia Grimaldi, Sean M. Grimmond, Robert L. Grossman, Adam Grundhoff, Gunes Gundem, Manaswi Gupta, Shailja Gupta, Jonathan Göke, Gavin Ha, Andrea Haake, Siegfried Haas, Kerstin Haase, James E. Haber, Faraz Hach, Syed Haider, Natsuko Hama, Freddie C. Hamdy, Anne Hamilton, Leng Han, George B. Hanna, Martin Hansmann, Olivier Harismendy, Ivon Harliwong, Arif O. Harmanci, Eoghan Harrington, Takanori Hasegawa, David Haussler, Steve Hawkins, Shinya Hayami, Shuto Hayashi, D. Neil Hayes, Stephen J. Hayes, Nicholas K. Hayward, Steven Hazell, Xiaotong Yao, Allison P. Heath, Simon Heath, David W. Hedley, Apurva M. Hegde, David I. Heiman, Michael C. Heinold, Zachary Heins, Lawrence E. Heisler, Eva Hellstrom-Lindberg, Seong Gu Heo, Austin J. Hepperla, José María Heredia‐Genestar, Peter Hersey, Hólmfríður Hilmarsdóttir, Jonathan Hinton, Satoshi Hirano, Nobuyoshi Hiraoka, Katherine A. Hoadley, Jessica I. Hoell, Steve Hoffmann, Oliver Hofmann, Andrea Holbrook, Aliaksei Z. Holik, Michael A. Hollingsworth, Oliver Holmes, Robert A. Holt, Eun Pyo Hong, Jongwhi H. Hong, Gerrit K. Hooijer, Fumie Hosoda, Yong Hou, Volker Hovestadt, William Howat, Alan P. Hoyle, Ralph H. Hruban, Taobo Hu, Xing Hua, Kuan-lin Huang, Mei Huang, Mi Ni Huang, Vincent Huang, Yi Huang, Wolfgang Huber, Thomas J. Hudson, Michael Hummel, Jillian A. Hung, David G. Huntsman, Ted R. Hupp, Jason T. Huse, Matthew R. Huska, Barbara Hutter, Carolyn M. Hutter, Daniel Hübschmann, Christine A. Iacobuzio–Donahue, Charles D. Imbusch, Marcin Imieliński, Seiya Imoto, William B. Isaacs, Shumpei Ishikawa, Murat Iskar, S. M. Ashiqul Islam, Michael Ittmann, Sinisa Ivkovic, Jocelyne Jacquemier, Valerie Jakrot, Nigel B. Jamieson, Gun Ho Jang, Se Jin Jang, Joy C. Jayaseelan, Reyka G. Jayasinghe, Karine Jegalian, Jennifer L. Jennings, Seung-Hyup Jeon, Lara Jerman, Yuan Ji, Wei Jiao, Peter A. Johansson, Amber L. Johns, Jeremy Johns, Clemency Jolly, Yann Joly, Jón G. Jónasson, Corbin D. Jones, David R. Jones, David Jones, Nic Jones, Steven J.M. Jones, Jos Jonkers, Young Seok Ju, Hartmut Juhl, Jongsun Jung, Natalie Jäger, Rolf Kabbe, Vera B. Kaiser, Hojabr Kakavand, Sangeetha Kalimuthu, Christof von Kalle, Koo Jeong Kang, Katalin Karászi, Beth Y. Karlan, Rosa Karlić, Dennis Karsch, Karin S. Kassahn, Hitoshi Katai, Mamoru Kato, Hiroto Katoh, Yoshiiku Kawakami, Jonathan D. Kay, Stephen H. Kazakoff, Marat D. Kazanov, Maria Keays, Electron Kebebew, Richard Kefford, James G. Kench, Catherine J. Kennedy, Jules N. A. Kerssemakers, David Khoo, Vincent Khoo, Narong Khuntikeo, Helena Kilpinen, Hark Kyun Kim, Hyung‐Lae Kim, Hyung-Yong Kim, Hyunghwan Kim, Jihoon Kim, Tari A. King, Wolfgang Hiddemann, Kortine Kleinheinz, Leszek J. Klimczak, Stian Knappskog, Michael Kneba, Bartha Maria Knoppers, Youngil Koh, Daisuke Komura, Mitsuhiro Komura, Gu Kong, Marcel Kool, Viktoriya Korchina, Andrey Korshunov, Michael Koscher, Roelof Koster, Zsofia Kote‐Jarai, Antonios Koures, Milena Kovačević, Bárbara Kremeyer, Helene Kretzmer, Markus Kreuz, Savitri Krishnamurthy, Dieter Kube, Kiran Kumar, Yogesh Kumar, Ritika Kundra, Kirsten Kübler, Ralf Küppers, Jesper Lagergren, Phillip H. Lai, Peter W. Laird, Sunil R. Lakhani, Christopher M. Lalansingh, Emilie Lalonde, Fabien C. Lamaze, Adam Lambert, Eric Lander, Pablo Landgraf, Luca Landoni, Anita Langerød, Denis Larsimont, Mark Lathrop, Loretta M. S. Lau, Chris Lawerenz, Rita T. Lawlor, Alexander J. Lazar, Ana Mijalkovic Lazic, Xuan Le, Darlene Lee, Eunjung Alice Lee, Hee Jin Lee, Jake June-Koo Lee, Jeong‐Yeon Lee, Juhee Lee, Ming Ta Michael Lee, Henry Lee-Six, Hans Lehrach, Dido Lenze, Conrad Leonard, Daniel Leongamornlert, Ignaty Leshchiner, Louis Létourneau, Ivica Letunić, Douglas A. Levine, Lora Lewis, Tim Ley, Constance H. Li, Haiyan Irene Li, Jun Li, Lin Li, Siliang Li, Xiaobo Li, Xinyue Li, Yilong Li, Han Liang, Sheng‐Ben Liang, Peter Lichter, Pei Lin, W. Marston Linehan, Ole Christian Lingjærde, Dongbing Liu, Fei-Fei Fei Liu, Fenglin Liu, Jia Liu, Xingmin Liu, Julie Livingstone, Dimitri Livitz, Naomi Livni, Markus Loeffler, Georgina V. Long, Armando López‐Guillermo, David N. Louis, Laurence Lovat, Yue Lu, Yong‐Jie Lu, Youyong Lu, Claudio Luchini, Ilinca M. Lungu, Xuemei Luo, Hayley J. Luxton, Andy G. Lynch, Lisa Lype, Cristina López, Carlos López-Otı́n, Z. Eric, Yussanne Ma, Gaëtan MacGrogan, Shona MacRae, Geoff Macintyre, Kazuhiro Maejima, Andrea Mafficini, Dennis T. Maglinte, Arindam Maitra, Partha P. Majumder, Luca Malcovati, Salem Malikić, Giuseppe Malleo, Graham J. Mann, Luisa Mantovani‐Löffler, Giovanni Marchegiani, Elaine R. Mardis, Adam A. Margolin, Maximillian G. Marin, Florian Markowetz, Julia Markowski, Jeffrey R. Marks, Tomàs Marquès‐Bonet, Marco A. Marra, Luke Marsden, John W.M. Martens, Sancha Martin, José I. Martín‐Subero, R. Jay Mashl, Charlie E. Massie, Thomas J. Matthew, Lucy Matthews, Erik Mayer, Simon Mayes, Michael Mayo, Faridah Mbabaali, Karen McCune, Ultan McDermott, Michael D. McLellan, John D. McPherson, John R. McPherson, Treasa A. McPherson, Samuel R. Meier, Alice Meng, Shaowu Meng, Andrew Menzies, Neil D. Merrett, Sue Merson, Matthew Meyerson, Piotr A. Mieczkowski, George L. Mihaiescu, Sanja Mijalković, Tom Mikkelsen, Michèle Milella, Linda Mileshkin, Christopher A. Miller, David K. Miller, Jessica K. Miller, Gordon B. Mills, Ana Milovanovic, Sarah Minner, Marco Miotto, Gisela Mir Arnau, Thomas J. Mitchell, Satoru Miyano, Naoki Miyoshi, Shinichi Mizuno, Fruzsina Molnár‐Gábor, Malcolm J. Moore, Richard A. Moore, Sandro Morganella, Quaid Morris, Lisle E. Mose, Catherine D. Moser, Andrew J. Mungall, Karen Mungall, Elizabeth A. Musgrove, Ville Mustonen, David G. Mutch, Francesc Muyas, Donna M. Muzny, Alfonso Muñoz, Jerome Myers, Ola Myklebost, Peter Möller, Genta Nagae, Adnan Nagrial, Hardeep K. Nahal-Bose, Hitoshi Nakagama, Hiromi Nakamura, Tõru Nakamura, Kaoru Nakano, Tannistha Nandi, Jyoti Nangalia, Mia Nastic, Arcadi Navarro, Fábio C. P. Navarro, David E. Neal, Gerd Nettekoven, Felicity Newell, Steven Newhouse, Yulia Newton, Alvin Wei Tian Ng, Anthony Ng, Jonathan Nicholson, David Nicol, Yongzhan Nie, G. Petur Nielsen, Serena Nik‐Zainal, Michael S. Noble, Kátia Nones, Paul A. Northcott, Faiyaz Notta, Brian D. O’Connor, Peter O’Donnell, Maria O’Donovan, Sarah O’Meara, Brian Patrick O’Neill, J. Robert O’Neill, David Ocaña, Angelica Ochoa, Layla Oesper, Christopher Ogden, Hideki Ohdan, Kazuhiro Ohi, Lucila Ohno‐Machado, Karin A. Oien, Akinyemi I. Ojesina, Hidenori Ojima, Takuji Okusaka, Larsson Omberg, Choon Kiat Ong, Stephan Ossowski, German Ott, B. F. Francis Ouellette, Christine P’ng, Salvatore Paiella, Chawalit Pairojkul, Marina Pajic, Qiang Pan‐Hammarström, Elli Papaemmanuil, Irene Papatheodorou, Nagarajan Paramasivam, Ji Wan Park, Joong‐Won Park, Peter J. Park, Joel S. Parker, Simon L. Parsons, Harvey I. Pass, Danielle Pasternack, Alessandro Pastore, Ann‐Marie Patch, Iris Pauporté, Antonio Pea, John V. Pearson, Chandra Sekhar Pedamallu, Paolo Pederzoli, Martin Peifer, Nathan A. Pennell, Charles M. Perou, Marc D. Perry, Gloria M. Petersen, Myron Peto, Nicholas Petrelli, Robert Petryszak, Stefan M. Pfister, Mark Phillips, Oriol Pich, Hilda A. Pickett, Todd Pihl, Nischalan Pillay, Sarah E. Pinder, Mark Pinese, Andreia V. Pinho, Esa Pitkänen, Xavier Pivot, Elena Piñeiro-Yáñez, Laura Planko, Christoph Plass, Paz Polak, Irinel Popescu, Olga Potapova, Aparna Prasad, Shaun R. Preston, Manuel Prinz, Antonia L. Pritchard, Stephenie D. Prokopec, Elena Provenzano, Xosé S. Puente, Montserrat Puiggròs, Gulietta M. Pupo, Colin A. Purdie, Michael C. Quinn, Raquel Rabionet, Janet S. Rader, Bernhard Radlwimmer, Petar Radovic, Benjamin Raeder, Keiran Raine, Manasa Ramakrishna, Kamna Ramakrishnan, Suresh Ramalingam, W. Kimryn Rathmell, Tobias Rausch, Guido Reifenberger, Jorge S. Reis‐Filho, Victor E. Reuter, Sheila M. Reynolds, Yasser Riazalhosseini, Andrea L. Richardson, Julia Richter, Matthew D. Ringel, Markus Ringnér, Yasushi Rino, Karsten Rippe, Jeffrey Roach, Lewis R. Roberts, Nicola D. Roberts, Steven A. Roberts, A. Gordon Robertson, Alan J. Robertson, Javier Bartolomé Rodriguez, Bernardo Rodríguez–Martín, F. Germán Rodríguez-González, Michael H. A. Roehrl, Marius Rohde, Hirofumi Rokutan, Gilles Romieu, Ilse Rooman, Tom Roques, Daniel Rosebrock, Mara Rosenberg, Philip Rosenstiel, Andreas Rosenwald, Edward Rowe, Romina Royo, Steve Rozen, Yulia Rubanova, Vasilisa A. Rudneva, Borislav C. Rusev, Andrea Ruzzenente, Gunnar Rätsch, Radhakrishnan Sabarinathan, Veronica Y. Sabelnykova, Sara Sadeghi, Natalie Saini, Mihoko Saito-Adachi, Adriana Salcedo, Roberto Salgado, Richard Sallari, Charles Saller, Roberto Salvia, Michelle Sam, Jaswinder S. Samra, Francisco Sánchez-Vega, Grant Sanders, Rajiv Sarin, Iman Sarrafi, Aya Sasaki-Oku, Torill Sauer, Guido Sauter, Robyn P.M. Saw, Maria Scardoni, Christopher J. Scarlett, Aldo Scarpa, Ghislaine Scélo, Dirk Schadendorf, Jacqueline E. Schein, Markus B. Schilhabel, Matthias Schlesner, Thorsten Schlomm, Heather K. Schmidt, Sarah‐Jane Schramm, Stefan Schreiber, Nikolaus Schultz, Roland F. Schwarz, Richard A. Scolyer, David L. Scott, Ralph Scully, Raja S. Seethala, Ayellet V. Segrè, Iris Selander, Colin A. Semple, Yasin Şenbabaoğlu, Subhajit Sengupta, Elisabetta Sereni, Stefano Serra, Dennis C. Sgroi, Nimish Shah, Sagedeh Shahabi, Catherine A. Shang, Ping Shang, Troy Shelton, Hui Shen, Rebecca Shepherd, Ruian Shi, Yan Shi, Yu-Jia Shiah, Tatsuhiro Shibata, Juliann Shih, Eigo Shimizu, Kiyo Shimizu, Seung Jun Shin, Yuichi Shiraishi, Tal Shmaya, Ilya Shmulevich, Solomon I. Shorser, Charles Short, Suyash Shringarpure, Craig D. Shriver, Reiner Siebert, Anieta M. Sieuwerts, Sabina Signoretti, Katarzyna Sikora, Michele Simbolo, Ronald Simon, Janae V. Simons, Jared T. Simpson, Peter T. Simpson, Samuel Singer, Payal Sipahimalani, Tara Skelly, Marcel Smid, John A. Smith, Karen Smith‐McCune, Nicholas D. Socci, Heidi J. Sofia, Matthew G. Soloway, Lei Song, Anil K. Sood, Sharmila Sothi, Christos Sotiriou, Cameron M. Soulette, Paul N. Span, Paul T. Spellman, Nicola Sperandio, Andrew J. Spillane, Oliver Spiro, Jonathan Spring, Johan Staaf, Peter F. Stadler, Peter Staib, Stefan G. Stark, Lucy Stebbings, Ólafur Andri Stefánsson, Oliver Stegle, Alasdair Stenhouse, Chip Stewart, Stephan Stilgenbauer, Miranda D. Stobbe, Michael R. Stratton, Jonathan R. Stretch, Adam J. Struck, Henk G. Stunnenberg, Hong Su, Xiaoping Su, Ren Sun, Stéphanie Sungalee, Hana Sušak, Akihiro Suzuki, Fred C.G.J. Sweep, Monika Szczepanowski, Holger Sültmann, Takashi Yugawa, Angela Tam, Benita Kiat Tee Tan, Donghui Tan, Patrick Tan, Hiroko Tanaka, Hirokazu Taniguchi, Tomas Tanskanen, Maxime Tarabichi, Roy Tarnuzzer, Patrick Tarpey, Morgan L. Taschuk, Kenji Tatsuno, Simon Tavaré, Darrin F. Taylor, Amaro Taylor‐Weiner, Jon W. Teague, Bin Tean Teh, Varsha Tembe, Javier Temes, Kevin Thai, Sarah P. Thayer, Nina Thiessen, Gilles Thomas, Sarah Thomas, Alan Thompson, Alastair M. Thompson, John F. Thompson, R. Houston Thompson, Heather Thorne, Leigh B. Thorne, Adrian Thorogood, Nebojša Tijanić, Lee E. Timms, Roberto Tirabosco, Marta Tojo, Stefania Tommasi, Christopher W. Toon, Umut H. Toprak, David Torrents, Giampaolo Tortora, Jörg Tost, Yasushi Totoki, David Townend, Nadia Traficante, Isabelle Treilleux, Jean-Rémi Trotta, Lorenz Trümper, Ming‐Sound Tsao, José M. C. Tubío, Olga Tucker, Richard Turkington, Daniel J. Turner, Andrew Tutt, Masaki Ueno, Naoto T. Ueno, Christopher B. Umbricht, Tim Underwood, Lara Urban, Tomoko Urushidate, Tetsuo Ushiku, David Van Den Berg, Steven Van Laere, Peter Van Loo, Erwin G. Van Meir, Gert G. Van den Eynden, Theodorus van der Kwast, Naveen Vasudev, Ravikiran Vedururu, Umadevi Veluvolu, Shankar Vembu, Peter Vermeulen, Clare Verrill, Alain Viari, David Vicente, Caterina Vicentini, K. VijayRaghavan, Juris Vīksna, Ricardo E. Vilain, Izar Villasante, Anne Vincent‐Salomon, Tapio Visakorpi, Douglas Voet, Paresh Vyas, Ignacio Vázquez-Garćıa, Nick M. Waddell, Nicola Waddell, Rabea Wagener, Jeremiah A. Wala, Jian Wang, Linghua Wang, Qi Wang, Wenyi Wang, Yumeng Wang, Zhining Wang, Paul Waring, Hans-Jörg Warnatz, Anne Y. Warren, David C. Wedge, Dieter Weichenhan, Paul Weinberger, John N. Weinstein, Daniel J. Weisenberger, Ian Welch, Michael C. Wendl, Johannes Werner, Justin P. Whalley, Hayley C. Whitaker, Dennis A. Wigle, Matthew D. Wilkerson, Ashley Williams, James S. Wilmott, Gavin W. Wilson, Julie M. Wilson, Richard K. Wilson, Boris Winterhoff, Jeffrey A. Wintersinger, Maciej Wiznerowicz, Stephan Wolf, Bernice H. Wong, Tina Wong, Winghing Wong, Youngchoon Woo, Scott Wood, Bradly G. Wouters, A. Jordan Wright, Derek Wright, Mark H. Wright, Chin‐Lee Wu, Dai‐Ying Wu, Jianmin Wu, Kui Wu, Yang Wu, Zhenggang Wu, Xi Liu, Tian Xia, Qian Xiang, Xiao Xiao, Rui Xing, Heng Xiong, Qinying Xu, Yanxun Xu, Hong Xue, Shinichi Yachida, Sergei Yakneen, Takafumi N. Yamaguchi, Masakazu Yamamoto, Shogo Yamamoto, Hiroki Yamaue, Fan Yang, Huanming Yang, Jean Yang, Liming Yang, Lixing Yang, Shanlin Yang, Tsun-Po Yang, Yang Yang, Xiaotong Yao, Marie‐Laure Yaspo, Lucy Yates, Christina Yau, Chen Ye, Kai Ye, Venkata Yellapantula, Christopher J. Yoon, Sung-Soo Yoon, Fouad Yousif, Kaixian Yu, Willie Yu, Yingyan Yu, Ke Yuan, Yuan Yuan, Denis Yuen, Christina K. Yung, Olga Zaikova, Jorge Zamora, Marc Zapatka, Jean C. Zenklusen, Thorsten Zenz, Nikolajs Zeps, Cheng‐Zhong Zhang, Fan Zhang, Hailei Zhang, Hongwei Zhang, Hongxin Zhang, Jiashan Zhang, Junjun Zhang, Xiuqing Zhang, Zemin Zhang, Liangtao Zheng, Xiuqing Zheng, Wanding Zhou, Yong Zhou, Bin Zhu, Hongtu Zhu, Jingchun Zhu, Shida Zhu, Xueqing Zou, Anna DeFazio, Nicholas van As, Carolien H. M. van Deurzen, Marc J. van de Vijver, L. van’t Veer
Bibliographic record
VenueNature Communications · 2020
Typearticle
Languageen
FieldBiochemistry, Genetics and Molecular Biology
TopicCancer Genomics and Diagnostics
Canadian institutionsUniversity of British ColumbiaProstate Cancer CanadaUniversité de MontréalHospital for Sick ChildrenLunenfeld-Tanenbaum Research InstituteMount Sinai HospitalPrincess Margaret Cancer CentreUniversity of CalgaryVector InstituteMcGill University and Génome Québec Innovation CentreToronto General HospitalUniversity Health NetworkUniversity of TorontoBC Cancer AgencySickKids FoundationGenome CanadaCanada's Michael Smith Genome Sciences CentreUniversity of OttawaMcGill UniversitySimon Fraser UniversityInstitute of Cancer ResearchOntario Institute for Cancer Research
FundersNational Cancer InstituteNatural Sciences and Engineering Research Council of CanadaCancer Research UKNovo Nordisk FondenNovo NordiskFonds Wetenschappelijk OnderzoekInnovationsfondenNational Institutes of HealthNational Human Genome Research InstituteOntario Institute for Cancer ResearchFrancis Crick InstituteGovernment of OntarioCanadian Institutes of Health ResearchCancer Research Society
KeywordsBiologyGeneGeneticsComputational biologyGenomeCoding regionRNA splicingRNA
Abstract
The catalog of cancer driver mutations in protein-coding genes has greatly expanded in the past decade. However, non-coding cancer driver mutations are less well-characterized and only a handful of recurrent non-coding mutations, most notably TERT promoter mutations, have been reported. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancer across 38 tumor types, we perform multi-faceted pathway and network analyses of non-coding mutations across 2583 whole cancer genomes from 27 tumor types compiled by the ICGC/TCGA PCAWG project that was motivated by the success of pathway and network analyses in prioritizing rare mutations in protein-coding genes. While few non-coding genomic elements are recurrently mutated in this cohort, we identify 93 genes harboring non-coding mutations that cluster into several modules of interacting proteins. Among these are promoter mutations associated with reduced mRNA expression in TP53, TLE4, and TCF4. We find that biological processes had variable proportions of coding and non-coding mutations, with chromatin remodeling and proliferation pathways altered primarily by coding mutations, while developmental pathways, including Wnt and Notch, altered by both coding and non-coding mutations. RNA splicing is primarily altered by non-coding mutations in this cohort, and samples containing non-coding mutations in well-known RNA splicing factors exhibit similar gene expression signatures as samples with coding mutations in these genes. These analyses contribute a new repertoire of possible cancer genes and mechanisms that are altered by non-coding mutations and offer insights into additional cancer vulnerabilities that can be investigated for potential therapeutic treatments.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
metaresearch head score (Codex)0.000
metaresearch head score (Gemma)0.000
Version: codex-gemma-dda1882f352aValidation status: machine_predicted_unvalidated
Candidate categoriesnone
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Not applicable · Consensus signal: none
GenreCandidate signal: Empirical · Consensus signal: Empirical
Teacher disagreement score0.794
Threshold uncertainty score0.292
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
Opus teacher head0.014
GPT teacher head0.284
Teacher spread0.271 · how far apart the two teachers sit on this one work
Validation status
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
The models applied no category: nothing in the taxonomy fit this work.
Study designNot applicable
Domainnot available
GenreEmpirical
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".
Quick stats
Citations115
Published2020
Admission routes2
Has abstractyes