Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition
Bernardo Rodríguez–Martín(Universidade de Santiago de Compostela), Eva G. Alvarez(Universidade de Santiago de Compostela), Adrian Baez‐Ortega(University of Cambridge), Jorge Zamora(Universidade de Santiago de Compostela), Fran Supek(Institució Catalana de Recerca i Estudis Avançats), Jonas Demeulemeester(The Francis Crick Institute), Martín Santamarina(Universidade de Santiago de Compostela), Young Seok Ju(Korea Advanced Institute of Science and Technology), Javier Temes(Universidade de Santiago de Compostela), Daniel García‐Souto(Universidade de Santiago de Compostela), Harald Detering(Galicia Sur Biomedical Foundation), Yilong Li(Wellcome Sanger Institute), Jorge Rodríguez‐Castro(Universidade de Santiago de Compostela), Ana Dueso-Barroso(Universitat de Vic - Universitat Central de Catalunya), Alicia L. Bruzos(Universidade de Santiago de Compostela), Stefan C. Dentro(The Francis Crick Institute), Miguel G. Blanco(Universidade de Santiago de Compostela), Gianmarco Contino(University of Cambridge), Daniel Ardeljan(Johns Hopkins University), Marta Tojo(Universidade de Vigo), Nicola D. Roberts(Wellcome Sanger Institute), Sonia Zumalave(Universidade de Santiago de Compostela), Paul A. Edwards(University of Cambridge), Joachim Weischenfeldt(University of Copenhagen), Montserrat Puiggròs(Barcelona Supercomputing Center), Zechen Chong(The University of Texas MD Anderson Cancer Center), Ken Chen(The University of Texas MD Anderson Cancer Center), Eunjung Alice Lee(Boston Children's Hospital), Jeremiah A. Wala(Broad Institute), Keiran M. Raine(Wellcome Sanger Institute), Adam P. Butler(Wellcome Sanger Institute), Sebastian M. Waszak(European Molecular Biology Laboratory), Fábio C. P. Navarro(Yale University), Steven E. Schumacher(Broad Institute), Jean Monlong(McGill University), Francesco Maura(University of Milan), Niccolò Bolli(University of Milan), Guillaume Bourque(McGill University), Mark Gerstein(Yale University), Peter J. Park(Harvard University), David C. Wedge(Wellcome Sanger Institute), Rameen Beroukhim(Broad Institute), David Torrents(Institució Catalana de Recerca i Estudis Avançats), Jan O. Korbel(European Bioinformatics Institute), Iñigo Martincorena(University of Cambridge), Rebecca C. Fitzgerald(University of Cambridge), Peter Van Loo(Johns Hopkins University), Haig H. Kazazian(Johns Hopkins University), Kathleen H. Burns(The University of Texas MD Anderson Cancer Center), PCAWG Structural Variation Working Group(Universidade de Santiago de Compostela), Kadir C. Akdemir(The University of Texas MD Anderson Cancer Center), Eva G. Alvarez(Broad Institute), Adrian Baez‐Ortega(Ontario Institute for Cancer Research), Rameen Beroukhim(Broad Institute), Paul C. Boutros(Ontario Institute for Cancer Research), David D.L. Bowtell(Johns Hopkins University), Benedikt Brors(German Cancer Research Center), Kathleen H. Burns(Johns Hopkins University), Peter J. Campbell(The University of Texas MD Anderson Cancer Center), Kin Chan(Harvard University), Ken Chen(Universitat de Vic - Universitat Central de Catalunya), Isidro Cortés-Ciriano(Broad Institute), Ana Dueso-Barroso(Universitat de Vic - Universitat Central de Catalunya), Andrew Dunford(Broad Institute), Paul A. Edwards(University of Cambridge), Xavier Estivill(German Cancer Research Center), Dariush Etemadmoghadam(The University of Melbourne), Lars Feuerbach(Bar-Ilan University), J. Lynn Fink(The University of Queensland), Milana Frenkel‐Morgenstern(Bar-Ilan University), Dale W. Garsed(The University of Melbourne), Mark Gerstein(University of California, Santa Cruz), Dmitry A. Gordenin(National Institute of Environmental Health Sciences), David Haan(Broad Institute), James E. Haber(National Center for Tumor Diseases), Julian M. Hess(Broad Institute), Barbara Hutter(German Cancer Research Center), Marcin Imielinski(Cornell University), David Jones(Skolkovo Institute of Science and Technology), Young Seok Ju(Korea Advanced Institute of Science and Technology), Marat D. Kazanov(Skolkovo Institute of Science and Technology), Leszek J. Klimczak(National Institute of Environmental Health Sciences), Youngil Koh(Broad Institute), Jan O. Korbel(Broad Institute), Kiran Kumar(Broad Institute), Eunjung Alice Lee(Boston Children's Hospital), Jake June-Koo Lee(Harvard University), Yilong Li(University of Cambridge), Andy G. Lynch(University of St Andrews), Geoff Macintyre(University of Cambridge), Florian Markowetz(Cornell University), Iñigo Martincorena(Broad Institute), Alexander Martinez‐Fundichely(Cornell University), Matthew Meyerson(Broad Institute), Satoru Miyano(Yale University), Hidewaki Nakagawa(Universitat Pompeu Fabra), Fábio C. P. Navarro(Harvard University), Stephan Ossowski(The University of Queensland), Peter J. Park(Harvard University), John V. Pearson(The University of Queensland), Montserrat Puiggròs(Barcelona Supercomputing Center), Karsten Rippe(German Cancer Research Center), Nicola D. Roberts(Universidade de Santiago de Compostela), Steven A. Roberts(Broad Institute), Bernardo Rodriguez-Martin(Beth Israel Deaconess Medical Center), Steven E. Schumacher(Broad Institute), Ralph Scully(University of Copenhagen), Mark Shackleton(The University of Melbourne), Nikos Sidiropoulos(Broad Institute), Lina Sieverling(German Cancer Research Center), Chip Stewart(Broad Institute), David Torrents(Institució Catalana de Recerca i Estudis Avançats), José M. C. Tubío(The University of Queensland), Izar Villasante(Broad Institute), Nicola Waddell(University of Copenhagen), Jeremiah A. Wala(Broad Institute), Joachim Weischenfeldt(University of Copenhagen), Lixing Yang(Seoul National University Hospital), Xiaotong Yao(Universidade de Santiago de Compostela), Sung-Soo Yoon(Broad Institute), Jorge Zamora(Universidade de Santiago de Compostela), Cheng‐Zhong Zhang(Broad Institute), Peter J. Campbell(University of Cambridge), José M. C. Tubío(Universidade de Santiago de Compostela), Lauri A. Aaltonen(The University of Melbourne), Federico Abascal, Adam Abeshouse, Hiroyuki Aburatani, David J. Adams, Nishant Agrawal, Keun Soo Ahn, Sung-Min Ahn, Hiroshi Aikata(The University of Texas MD Anderson Cancer Center), Rehan Akbani, Kadir C. Akdemir(The University of Texas MD Anderson Cancer Center), Hikmat Al‐Ahmadie, Sultan T. Al‐Sedairy, Fátima Al‐Shahrour, Malik Alawi, Monique Albert, Kenneth Aldape(University of Cambridge), Ludmil B. Alexandrov, Adrian Ally(Universidade de Santiago de Compostela), Kathryn Alsop, Eva G. Álvarez(Universidade de Santiago de Compostela), Fernanda Amary, Samirkumar B. Amin, Brice Aminou, Ole Ammerpohl(University of Chicago), 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(Barcelona Supercomputing Center), Laurent Arnould, L. Sylvia, Yassen Assenov, Gurnit Atwal, Sietse Aukema, J. Todd Auman, Miriam R. R. Aure(Universidade de Vigo), Philip Awadalla, Marta Aymerich(University of Cambridge), Gary D. Bader, Adrian Baez‐Ortega(University of Cambridge), Matthew H. Bailey, Peter J. Bailey, Miruna Balasundaram, Saianand Balu, Pratiti Bandopadhayay, Rosamonde E. Banks, Stefano Barbi, Andrew P. Barbour, Jonathan Barenboim(Universitat de Vic - Universitat Central de Catalunya), Jill S. Barnholtz‐Sloan, Hugh Barr(The University of Queensland), Elisabet Barrera(Universidade de Santiago de Compostela), John Bartlett, Javier Bartolomé, Claudio Bassi(Johns Hopkins University), Oliver F. Bathe, Daniel Baumhoer, Prashant Bavi, Stephen B. Baylin, Wojciech Bażant, Duncan Beardsmore, Timothy A. Beck, Sam Behjati, Andreas Behren(Wellcome Sanger Institute), Beifang Niu, Cindy Bell, Sergi Beltrán(Broad Institute), Christopher C. Benz, Andrew Berchuck, Anke K. Bergmann, Erik N. Bergstrom, Benjamin P. Berman, Daniel M. Berney(Broad Institute), Stephan H. Bernhart, Rameen Beroukhim(Broad Institute), Mario Berríos, Samantha Bersani(Universidade de Santiago de Compostela), Johanna Bertl, 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(University of Cambridge), Tom Bodenheimer, Lori Boice, Giada Bonizzato, Johann S. de Bono, Arnoud Boot, Moiz S. Bootwalla, Åke Borg, Arndt Borkhardt, Keith A. Boroevich, Ivan Borozan, Christoph W. Borst, Marcus Bosenberg, Mattia Bosio(McGill University), Jacqueline Boultwood(Ontario Institute for Cancer Research), Guillaume Bourque(McGill University), Paul C. Boutros(Ontario Institute for Cancer Research), G. Steven Bova, David Bowen(The University of Melbourne), Reanne Bowlby, David D.L. Bowtell(The University of Melbourne), Sandrine Boyault, Rich Boyce, Jeffrey M. Boyd(University of Cambridge), Alvis Brāzma, Paul M. Brennan, Daniel S. Brewer, Arie B. Brinkman, Robert G. Bristow, Russell R. Broaddus, Jane E. Brock, Malcolm V. Brock, Annegien Broeks, Angela N. Brooks(National Center for Tumor Diseases), Denise Brooks, Benedikt Brors(German Cancer Research Center), Søren Brunak(Universidade de Vigo), Timothy J. C. Bruxner(Cornell University), Alicia L. Bruzos(Universidade de Santiago de Compostela), Alex Buchanan, Ivo Buchhalter, Christiane Buchholz, Susan Bullman, Hazel Burke(Johns Hopkins University), Birgit Burkhardt(The University of Queensland), Kathleen H. Burns(Johns Hopkins University), John Busanovich(Wellcome Sanger Institute), Carlos D. Bustamante, Adam P. Butler(Wellcome Sanger Institute), Atul J. Butte, Niall J. Byrne, Anne‐Lise Børresen‐Dale(University of St Andrews), Rory Johnson, Andy Cafferkey, Declan Cahill, Claudia Calabrese, Carlos Caldas, Fabien Calvo(Wellcome Sanger Institute), Niedzica Camacho, Peter J. Campbell(University of Cambridge), Elı́as Campo, Cinzia Cantù, Shaolong Cao, Thomas E. Carey(University of Cambridge), Joana Carlevaro-Fita, Rebecca Carlsen, Ivana Cataldo, Mario Cazzola(Washington State University), Jonathan Cebon, Robert J. Cerfolio, Dianne Chadwick, Dimple Chakravarty(University of Ottawa), Drc Chalmers(University of Ottawa), Calvin Wing Yiu Chan, Kin Chan(University of Ottawa), Michelle Chan‐Seng‐Yue, Vishal S. Chandan, David K. Chang, Stephen J. Chanock, Lorraine A. Chantrill, Aurélien Chateigner, Nilanjan Chatterjee(Broad Institute), Kazuaki Chayama(Broad Institute), Hsiao‐Wei Chen(The University of Texas MD Anderson Cancer Center), Jieming Chen(Broad Institute), Ken Chen(Broad Institute), Yiwen Chen, Zhaohong Chen, Andrew D. Cherniack, Jeremy Chien, Yoke-Eng Chiew(University of Alabama at Birmingham), Suet‐Feung Chin(University of Alabama at Birmingham), Juok Cho, Sunghoon Cho, Jung Kyoon Choi, Wan Choi(University of Alabama at Birmingham), Christine Chomienne, Zechen Chong(The University of Texas MD Anderson Cancer Center), Su Pin Choo, Angela Chou, Angelika N. Christ, Elizabeth L. Christie, Eric Chuah, Carrie Cibulskis, Kristian Cibulskis(Wellcome Sanger Institute), Sara Cingarlini(Cornell University), 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(Harvard University), Stephen Cordner, Isidro Cortés-Ciriano(Harvard University), Kyle R. Covington, Prue A. Cowin(Institució Catalana de Recerca i Estudis Avançats), Brian Craft, David Craft, Chad J. Creighton(Galicia Sur Biomedical Foundation), Yupeng Cun, Erin Curley, Ioana Cutcutache, Karolina Czajka(University of Cambridge), Bogdan Czerniak, Rebecca A. Dagg(Institució Catalana de Recerca i Estudis Avançats), 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(The University of Queensland), Olivier Delaneau(KU Leuven), John A. Demchok, Jonas Demeulemeester(The Francis Crick Institute), German Demidov, Deniz Demircioğlu, Nening M. Dennis(Open Data Institute), Robert E. Denroche, Stefan C. Dentro(The Francis Crick Institute), Nikita Desai, Vikram Deshpande, Amit G. Deshwar, Christine Desmedt, Jordi Deu-Pons, Noreen Dhalla, Neesha C. Dhani, Priyanka Dhingra, Rajiv Dhir, Anthony DiBiase(University of Chicago), Klev Diamanti, Li Ding, Shuai Ding, Huy Q. Dinh, Luc Dirix, HarshaVardhan Doddapaneni, Nilgun Donmez, Michelle T. Dow, Ronny Drapkin, Oliver Drechsel, Ruben M. Drews, Serge Serge(Universitat de Vic - Universitat Central de Catalunya), Tim Dudderidge(Broad Institute), Ana Dueso-Barroso(Universitat de Vic - Universitat Central de Catalunya), Andrew Dunford(Broad Institute), Michael Dunn, Lewis Jonathan Dursi(The University of Texas MD Anderson Cancer Center), Fraser R. Duthie, Ken Dutton‐Regester, Jenna Eagles, Douglas F. Easton(University of Cambridge), Stuart Edmonds(University of Cambridge), Paul A. Edwards(University of Cambridge), Sandra E. Edwards, Rosalind A. Eeles, Anna Ehinger, Juergen Eils, Roland Eils(University of Bern), Adel K. El‐Naggar, Matthew Eldridge, Kyle Ellrott, Serap Erkek, Geòrgia Escaramís, Shadrielle M. G. Espiritu(The University of Melbourne), Xavier Estivill, Dariush Etemadmoghadam(The University of Melbourne), Jorunn E. Eyfjord(Open Data Institute), Bishoy M. Faltas(Open Data Institute), Daiming Fan, Fan Yu, William C. Faquin, Claudiu Farcas, Matteo Fassan(University of Milan), Aquila Fatima, Francesco Favero(Heidelberg University), Nodirjon Fayzullaev, Ina Felau, Sián Fereday, Martin L. Ferguson(German Cancer Research Center), Vincent Ferretti(University of Bern), Lars Feuerbach(The University of Queensland), Matthew A. Field, J. Lynn Fink(The University of Queensland), Gaetano Finocchiaro, Cyril Fisher(University of Cambridge), Matthew W. Fittall(University of Cambridge), Anna Fitzgerald, Rebecca C. Fitzgerald(University of Cambridge), Adrienne M. Flanagan(University of Cambridge), Neil Fleshner(The University of Queensland), Paul Flicek, John A. Foekens, Kwun M. Fong, Nuno A. Fonseca, Christopher S. Foster, Natalie S. Fox, Michael Fraser(Bar-Ilan University), Scott Frazer, Milana Frenkel‐Morgenstern(Bar-Ilan University), William A. Friedman, Joan Frigola, Catrina C. Fronick, Akihiro Fujimoto, Masashi Fujita, Masashi Fukayama(Washington State University), Lucinda A. Fulton, Robert S. Fulton, Mayuko Furuta, P. Andrew Futreal, Anja Füllgrabe(Washington State University), Stacey Gabriel, Steven Gallinger, Carlo Gambacorti‐Passerini, Jianjiong Gao, Shengjie Gao, Levi A. Garraway, Øystein Garred(The University of Melbourne), Erik Garrison, Dale W. Garsed(The University of Melbourne), Nils Gehlenborg, Josep L. L. Gelpi, Joshy George, Daniela S. Gerhard, Clarissa Gerhäuser(Princeton University), Jeffrey E. Gershenwald, Mark Gerstein(Yale University), Moritz Gerstung, Gad Getz, 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 González(National Institute of Environmental Health Sciences), Abel González-Pérez(Brandeis University), Dmitry A. Gordenin(National Institute of Environmental Health Sciences), James Gossage, Kunihito Gotoh, Ramaswamy Govindan, Dorthe Grabau, Janet S. Graham, Robert C. Grant, Anthony R. Green, Eric Green(The University of Queensland), Liliana Greger(Universidade de Santiago de Compostela), Nicola Grehan, Sonia Grimaldi, Sean M. Grimmond(The University of Melbourne), Robert L. Grossman, Adam Grundhoff, Gunes Gundem, Qianyun Guo, Manaswi Gupta, Shailja Gupta(Universidade de Vigo), Marta Gut, Marta Gut(The University of Melbourne), Jonathan Göke, Gavin Ha(University of California, Santa Cruz), Andrea Haake, David Haan(University of California, Santa Cruz), Siegfried Haas(Brandeis University), Kerstin Haase, James E. Haber(Brandeis University), Nina Habermann, Faraz Hach, Syed Haider, Natsuko Hama, Freddie C. Hamdy, Anne Hamilton(Universitat Pompeu Fabra), Mark P. Hamilton, Leng Han(Cornell University), George B. Hanna, Martin L. Hansmann, Nicholas J. Haradhvala, Olivier Harismendy, Ivon Harliwong, Arif Harmanci, Eoghan Harrington(Institució Catalana de Recerca i Estudis Avançats), Takanori Hasegawa(Washington State University), David Haussler, Steve Hawkins, Shinya Hayami, Shuto Hayashi, D. Neil Hayes, Stephen J. Hayes(Washington State University), Nicholas K. Hayward(University of Bern), Steven Hazell, Yao He, Allison P. Heath(Institució Catalana de Recerca i Estudis Avançats), Simon Heath, David W. Hedley, Apurva M. Hegde, David I. Heiman, Michael C. Heinold, Zachary Heins(Universidade de Santiago de Compostela), Lawrence E. Heisler, Eva Hellstrom-Lindberg, Mohamed Helmy, Seong Gu Heo, Austin J. Hepperla, José María Heredia‐Genestar(Wellcome Sanger Institute), Carl Herrmann(Massachusetts General Hospital), Peter Hersey, Julian M. Hess(Broad Institute), Hólmfríður Hilmarsdóttir, Jonathan Hinton, Satoshi Hirano, Nobuyoshi Hiraoka, Katherine A. Hoadley, Asger Hobolth, Ermin Hodzic(Washington State University), Jessica I. Hoell, Steve Hoffmann, Oliver Hofmann, Andrea Holbrook, Aliaksei Z. Holik, Michael A. Hollingsworth(Washington State University), Oliver Holmes(Broad Institute), Robert A. Holt(Broad Institute), Hong Chen(Broad Institute), Eun Pyo Hong, Jongwhi H. Hong, Gerrit K. Hooijer, Henrik Hornshøj, Fumie Hosoda, Yong Hou, Volker Hovestadt, William Howat, Alan P. Hoyle(German Cancer Research Center), Ralph H. Hruban(German Cancer Research Center), Taobo Hu(University of Chicago), Taobo Hu, Xing Hua, Kuan‐lin Huang, Mei Huang, Mi Ni Huang(Wellcome Sanger Institute), Vincent Huang, Yi Huang, Wolfgang Huber, Thomas J. Hudson, Michael Hummel(Institució Catalana de Recerca i Estudis Avançats), Jillian A. Hung, David Huntsman, Ted R. Hupp, Jason T. Huse(German Cancer Research Center), Matthew R. Huska(German Cancer Research Center), Barbara Hutter(Johns Hopkins University), Carolyn M. Hutter, Daniel Hübschmann, Christine A. Iacobuzio–Donahue(Cornell University), Charles D. Imbusch, Marcin Imielinski(Cornell University), Seiya Imoto, William B. Isaacs, Keren Isaev, Shumpei Ishikawa, Murat Iskar, S. M. Ashiqul Islam, Michael Ittmann, Sinisa Ivkovic, José M. G. Izarzugaza, Jocelyne Jacquemier, Valerie Jakrot, Nigel B. Jamieson, Gun Ho Jang, Se Jin Jang, Joy C. Jayaseelan, Reyka G. Jayasinghe, Stuart R. Jefferys, Karine Jegalian, Jennifer L. Jennings, Seung-Hyup Jeon, Lara Jerman(University of Copenhagen), Yuan Ji(Wellcome Sanger Institute), Wei Jiao, Peter A. Johansson, Amber L. Johns, Jeremy Johns, Rory Johnson, Todd A. Johnson, Clemency Jolly, Yann Joly(German Cancer Research Center), Jón G. Jónasson(German Cancer Research Center), Corbin D. Jones(German Cancer Research Center), David R. Jones(German Cancer Research Center), David Jones(German Cancer Research Center), Nic Jones(Universidade de Santiago de Compostela), Steven J.M. Jones(Wellcome Sanger Institute), Jos Jonkers, Young Seok Ju(Broad Institute), Hartmut Juhl, Jongsun Jung, Malene Juul, Randi Istrup Juul, Randi Istrup Juul, Natalie Jäger(Broad Institute), Rolf Kabbe, André Kahles, Abdullah Kahraman, Vera B. Kaiser, Hojabr Kakavand, Sangeetha Kalimuthu, Christof von Kalle, Koo Jeong Kang, Katalin Karászi, Beth Y. Karlan, Rosa Karlić, Dennis Karsch, Katayoon Kasaian, Karin S. Kassahn, Hitoshi Katai, Mamoru Kato, Hiroto Katoh, Yoshiiku Kawakami, Jonathan D. Kay(Skolkovo Institute of Science and Technology), Stephen H. Kazakoff, Marat D. Kazanov(Skolkovo Institute of Science and Technology), Maria Keays, Electron Kebebew, Richard Kefford(The University of Texas MD Anderson Cancer Center), Manolis Kellis, James G. Kench, Catherine J. Kennedy(Institució Catalana de Recerca i Estudis Avançats), Jules N. A. Kerssemakers, David Khoo, Vincent Khoo, Narong Khuntikeo, Ekta Khurana, Helena Kilpinen, Hark Kyun Kim, Hyung‐Lae Kim, Hyung-Yong Kim, Hyunghwan Kim, Jaegil Kim, Jihoon Kim, Jong K. Kim, Young-Wook Kim, Tari A. King, Wolfgang Hiddemann(National Institute of Environmental Health Sciences), Kortine Kleinheinz(European Molecular Biology Laboratory), Leszek J. Klimczak(National Institute of Environmental Health Sciences), Stian Knappskog, Michael Kneba(Seoul National University Hospital), Bartha Maria Knoppers, Youngil Koh(Seoul National University Hospital), Jan Komorowski, Daisuke Komura(McGill University), Mitsuhiro Komura, Gu Kong(European Bioinformatics Institute), Marcel Kool, Jan O. Korbel(European Bioinformatics Institute), Viktoriya Korchina, Andrey Korshunov, Michael Koscher, Roelof Koster, Zsofia Kote‐Jarai, Antonios Koures(German Cancer Research Center), Milena Kovačević, Bárbara Kremeyer, Helene Kretzmer, Markus Kreuz, Savitri Krishnamurthy(Broad Institute), Dieter Kube(Broad Institute), Kiran Kumar(Broad Institute), Pardeep Kumar(Broad Institute), Sushant 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(The University of Melbourne), Fabien C. Lamaze, Adam Lambert, Eric Lander, Pablo Landgraf, Luca Landoni, Anita Langerød, Andrés Lanzós, Denis Larsimont(The University of Melbourne), Erik Larsson(McGill University), Mark Lathrop, Loretta M. S. Lau, Chris Lawerenz, Rita T. Lawlor, Michael S. Lawrence, Alexander J. Lazar(The University of Melbourne), Ana Mijalkovic Lazic, Xuan Le, Darlene Lee(Broad Institute), Dong-Hoon Lee, Eunjung Alice Lee(Boston Children's Hospital), Hee Jin Lee, Jake June-Koo Lee(Harvard University), Jeong‐Yeon Lee(Harvard University), Ju Hee Lee(Harvard University), Ming Ta Michael Lee, Henry Lee-Six, Kjong-Van Lehmann, Hans Lehrach, Dido Lenze(Johns Hopkins University), Conrad Leonard, Daniel Leongamornlert, Ignaty Leshchiner, Louis Létourneau, Ivica Letunić, Douglas A. Levine, Lora Lewis(University of Chicago), Tim Ley(University of Chicago), Chang Li(University of Chicago), Constance H. Li(Broad Institute), Haiyan Irene Li(Heidelberg University), Jun Li(University of Chicago), Lin Li(University of Chicago), Shantao Li(University of Chicago), Siliang Li(University of Chicago), Xiaobo Li(University of Chicago), Xiaotong Li(Wellcome Sanger Institute), Xinyue Li(Universitat Pompeu Fabra), Yilong Li(Wellcome Sanger Institute), Han Liang(Wellcome Sanger Institute), Sheng‐Ben Liang(Heidelberg University), Péter Lichter(Heidelberg University), Pei Lin(University of Bern), Ziao Lin, W. M. Linehan, Ole Christian Lingjærde, Dongbing Liu, Eric Minwei Liu, Fei-Fei Fei Liu, Fenglin Liu, Jia Liu, Xingmin Liu, Julie Livingstone, Dimitri Livitz, Naomi Livni, Lucas Lochovsky(McGill University), Markus Loeffler, Georgina V. Long, Armando López‐Guillermo, Shaoke Lou, David N. Louis, Laurence Lovat, Yiling Lu, Yong‐Jie Lu, Youyong Lu, Claudio Luchini, Ilinca M. Lungu, Xuemei Luo(University of St Andrews), Hayley J. Luxton, Andy G. Lynch(University of St Andrews), Lisa Lype, Cristina López(The University of Melbourne), Carlos López-Otı́n(The University of Melbourne), Z. Eric, Yussanne Ma, Gaëtan MacGrogan(University of Cambridge), Shona MacRae, Geoff Macintyre(University of Cambridge), Tobias Madsen, Kazuhiro Maejima, Andrea Mafficini, Dennis T. Maglinte, Arindam Maitra, Partha P. Majumder, Luca Malcovati, Salem Malikić, Giuseppe Malleo, Graham J. Mann(Johns Hopkins University), Luisa Mantovani‐Löffler, Kathleen Marchal, Giovanni Marchegiani(The University of Melbourne), Elaine R. Mardis(Universidade de Santiago de Compostela), Adam A. Margolin(University of Cambridge), Maximillian G. Marin(Massachusetts General Hospital), Florian Markowetz(The University of Melbourne), Julia Markowski, Jeffrey S. Marks(University of Cambridge), Tomàs Marquès‐Bonet, Marco A. Marra, Luke Marsden(Cornell University), John W.M. Martens, Sancha Martin(Wellcome Sanger Institute), José I. Martín‐Subero(Cornell University), Iñigo Martincorena(Wellcome Sanger Institute), Alexander Martinez‐Fundichely(Cornell University), Yosef E. Maruvka, R. Jay Mashl(University of Bern), Charlie E. Massie, Thomas J. Matthew, Lucy Matthews, Erik Mayer, Simon Mayes, Michael Mayo, Faridah Mbabaali, Karen McCune, Ultan McDermott, Patrick D. McGillivray, Michael D. McLellan, John D. McPherson, John R. McPherson, Treasa A. McPherson(Broad Institute), Samuel R. Meier, Alice Meng(Broad Institute), Shaowu Meng, Andrew Menzies, Neil D. Merrett(University of Bern), Sue Merson(University of Bern), Matthew Meyerson(Broad Institute), William Meyerson, Piotr A. Mieczkowski, George L. Mihaiescu, Sanja Mijalković, Tom Mikkelsen, Michèle Milella, Linda Mileshkin, Christopher A. Miller, David K. Miller, Jessica K. Miller(Bar-Ilan University), Gordon B. Mills, Ana Milovanovic(University of Cambridge), Sarah Minner, Marco Miotto, Gisela Mir Arnau, Lisa Mirabello, Thomas J. Mitchell(The University of Tokyo), Thomas J. Mitchell, Satoru Miyano(The University of Tokyo), Naoki Miyoshi, Shinichi Mizuno, Fruzsina Molnár‐Gábor, Malcolm J. Moore, Richard A. Moore, Sandro Morganella, Quaid Morris, Carl D. Morrison, Lisle E. Mose, Catherine D. Moser, Ferran Muiños(Broad Institute), Loris Mularoni, Andrew J. Mungall, Karen Mungall, Elizabeth A. Musgrove(Institució Catalana de Recerca i Estudis Avançats), Ville Mustonen(University of Milan), David G. Mutch, Francesc Muyas, Donna M. Muzny, Alfonso Muñoz(The University of Queensland), Jerome Myers(Wellcome Sanger Institute), Ola Myklebost, Peter Möller, Genta Nagae, Adnan Nagrial, Hardeep K. Nahal-Bose(RIKEN Center for Integrative Medical Sciences), Hitoshi Nakagama, Hidewaki Nakagawa(RIKEN Center for Integrative Medical Sciences), Hiromi Nakamura, Toru Nakamura, Kaoru Nakano, Tannistha Nandi(Broad Institute), Jyoti Nangalia(Yale University), Mia Nastic(Yale University), Arcadi Navarro, Fábio C. P. Navarro(Yale University), David E. Neal, Gerd Nettekoven, Felicity Newell, Steven Newhouse(Cornell University), Yulia Newton(Cornell University), Alvin Wei Tian Ng, Chi‐Fai Ng(The University of Queensland), Jonathan Nicholson(Johns Hopkins University), David M. Nicol, Yongzhan Nie, G. Petur Nielsen, Morten Muhlig Nielsen, Serena Nik‐Zainal, Michael S. Noble(University of Cambridge), Kátia Nones, Paul A. Northcott, Faiyaz Notta(Wellcome Sanger Institute), Brian D. O’Connor, Peter H. O’Donnell, Maria O’Donovan, Sarah O’Meara, Brian Patrick O’Neill(Institució Catalana de Recerca i Estudis Avançats), 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(Cornell University), Larsson Omberg(Universitat Pompeu Fabra), Choon Kiat Ong, Stephan Ossowski(Universitat Pompeu Fabra), German Ott, B. F. Francis Ouellette(Universidade de Vigo), Christine P’ng, Marta Paczkowska, Salvatore Paiella(Universidade de Santiago de Compostela), Chawalit Pairojkul, Marina Pajic, Qiang Pan‐Hammarström, Elli Papaemmanuil, Irene Papatheodorou(Harvard University), Nagarajan Paramasivam(Harvard University), Ji Wan Park(Harvard University), Joong‐Won Park(Harvard University), Keunchil Park(Harvard University), Kiejung Park, Peter J. Park(Harvard University), Joel S. Parker, Simon L. Parsons, Harvey I. Pass, Danielle Pasternack, Alessandro Pastore, Ann‐Marie Patch(The University of Queensland), Iris Pauporté(The University of Queensland), Antonio Pea, John V. Pearson(The University of Queensland), Chandra Sekhar Pedamallu, Jakob Skou Pedersen(Cornell University), Paolo Pederzoli, Martin Peifer, Nathan A. Pennell, Charles M. Perou, Marc D. Perry, Gloria M. Petersen, Myron Peto(Washington State University), Nicholas J. Petrelli, Robert Petryszak(The University of Melbourne), Stefan M. Pfister, Mark Phillips, Oriol Pich, Hilda A. Pickett, Todd Pihl, Nischalan Pillay(The University of Melbourne), Sarah Pinder, Mark Pinese, Andreia V. Pinho, Esa Pitkänen, Xavier Pivot, Elena Piñeiro-Yáñez, Laura Planko, Christoph Plass, Paz Polak, Tirso Pons, Irinel Popescu, Olga Potapova, Aparna Prasad, Shaun R. Preston, Manuel Prinz, Antonia L. Pritchard, Stephenie D. Prokopec, Elena Provenzano(Barcelona Supercomputing Center), Xosé S. Puente(Barcelona Supercomputing Center), Sonia Puig, Montserrat Puiggròs(Barcelona Supercomputing Center), Sergio Pulido-Tamayo, Gulietta M. Pupo, Colin A. Purdie, Michael C. Quinn, Raquel Rabionet, Janet S. Rader, Bernhard Radlwimmer, Petar Radovic(Wellcome Sanger Institute), Benjamin Raeder, Keiran M. Raine(Wellcome Sanger Institute), Manasa Ramakrishna, Kamna Ramakrishnan, Suresh Ramalingam, Benjamin J. Raphael, W. Kimryn Rathmell, Tobias Rausch, Guido Reifenberger(Universidade de Santiago de Compostela), Jüri Reimand, Jorge S. Reis‐Filho, Victor E. Reuter(University of Bern), Iker Reyes-Salazar, Matthew A. Reyna, Sheila M. Reynolds, Esther Rheinbay, Yasser Riazalhosseini(Massachusetts General Hospital), Andrea L. Richardson(University of Bern), Julia Richter, Matthew D. Ringel, Markus Ringnér(German Cancer Research Center), Yasushi Rino, Karsten Rippe(German Cancer Research Center), Jeffrey Roach(Wellcome Sanger Institute), Lewis R. Roberts(Washington State University), Nicola D. Roberts(Wellcome Sanger Institute), Steven A. Roberts(Washington State University), A. Gordon Robertson(Universidade de Santiago de Compostela), Alan J. Robertson(Universidade de Santiago de Compostela), Javier Bartolomé Rodriguez, Bernardo Rodriguez-Martin(Universidade de Santiago de Compostela), F. Germán Rodríguez-González, Michael H. A. Roehrl, Marius Rohde, Hirofumi Rokutan, Gilles Romieu, Ilse Rooman(Johns Hopkins University), Tom Roques(Skolkovo Institute of Science and Technology), Daniel Rosebrock, Mara Rosenberg, Philip Rosenstiel, Andreas Rosenwald, Edward Rowe, Romina Royo, Steve Rozen(The University of Melbourne), Yulia Rubanova, Mark A. Rubin, Carlota Rubio-Pérez, Vasilisa A. Rudneva, Borislav C. Rusev, Andrea Ruzzenente, Gunnar Rätsch, Radhakrishnan Sabarinathan, Veronica Y. Sabelnykova, Sara Sadeghi, S. Cenk Şahinalp, Natalie Saini, Mihoko Saito-Adachi, Gordon Saksena, Adriana Salcedo, Roberto Salgado, Leonidas Salichos, Richard Sallari, Charles Saller, Roberto Salvia, Michelle Sam, Jaswinder S. Samra, Francisco Sánchez-Vega, Chris Sander, 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(Open Data Institute), Sarah‐Jane Schramm, Stefan Schreiber(Broad Institute), Nikolaus Schultz, Steven E. Schumacher(Broad Institute), Roland F. Schwarz(Institució Catalana de Recerca i Estudis Avançats), Richard A. Scolyer(Beth Israel Deaconess Medical Center), David W. Scott, Ralph Scully(Beth Israel Deaconess Medical Center), Raja S. Seethala, Ayellet V. Segrè, Iris Selander, Colin A. Semple, Yasin Şenbabaoğlu, Subhajit Sengupta(Barcelona Supercomputing Center), Elisabetta Sereni, Stefano Serra(The University of Melbourne), Dennis C. Sgroi, Mark Shackleton(The University of Melbourne), Nimish Shah, Sagedeh Shahabi, Catherine A. Shang, Ping Shang, Ofer Shapira, Troy Shelton, Ciyue Shen(University of Cambridge), Hui Shen, Rebecca Shepherd(University of Chicago), 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, Raunak Shrestha, Suyash Shringarpure, Craig D. Shriver(University of Copenhagen), Shimin Shuai, Nikos Sidiropoulos(University of Copenhagen), Reiner Siebert(Heidelberg University), Anieta M. Sieuwerts, Lina Sieverling(German Cancer Research Center), Sabina Signoretti, Katarzyna Sikora, Michele Simbolo, Ronald Simon, Janae V. Simons, Jared T. Simpson, Peter T. Simpson, Samuel Singer, Nasa Sinnott-Armstrong, 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(The University of Queensland), Paul T. Spellman(Broad Institute), Nicola Sperandio, Andrew J. Spillane, Oliver Spiro, Jonathan Spring, Johan Staaf(Wellcome Sanger Institute), Peter F. Stadler, Peter Staib, Stefan G. Stark, Lucy Stebbings, Ólafur Andri Stefánsson(Princeton University), Oliver Stegle, Lincoln D. Stein(Broad Institute), Alasdair Stenhouse(Universitat Pompeu Fabra), Chip Stewart(Broad Institute), Stephan Stilgenbauer, Miranda D. Stobbe, Michael R. Stratton, Jonathan R. Stretch, Adam J. Struck, Joshua M. Stuart(Seoul National University Hospital), Henk G. Stunnenberg(Seoul National University Hospital), Hong Su(Seoul National University Hospital), Xiaoping Su, Ren Sun, Stéphanie Sungalee, Hana Sušak, Akihiro Suzuki, Fred C.G.J. Sweep, Monika Szczepanowski, Holger Sültmann(Universidade de Santiago de Compostela), Takashi Yugawa(Institució Catalana de Recerca i Estudis Avançats), Angela Tam, David Tamborero, 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(Universidade de Santiago de Compostela), Varsha Tembe, Javier Temes(Universidade de Santiago de Compostela), Kevin Thai, Sarah P. Thayer, Nina Thiessen, Gilles Thomas, Sarah Thomas, Alan Thompson, Alastair M. Thompson, John F. Thompson, R. Houston Thompson, Heather Thorne(University of Cambridge), Leigh B. Thorne, Adrian Thorogood, Grace Tiao, Nebojša Tijanić, Lee E. Timms(Universidade de Vigo), Roberto Tirabosco, Marta Tojo(Universidade de Vigo), Stefania Tommasi, Christopher W. Toon(Institució Catalana de Recerca i Estudis Avançats), Umut H. Toprak, David Torrents(Institució Catalana de Recerca i Estudis Avançats), Giampaolo Tortora, Jörg Tost(Institució Catalana de Recerca i Estudis Avançats), Yasushi Totoki, David Townend, Nadia Traficante, Isabelle Treilleux, Jean-Rémi Trotta, Lorenz Trümper, Ming‐Sound Tsao(Universidade de Santiago de Compostela), Tatsuhiko Tsunoda, José M. C. Tubío(Universidade de Santiago de Compostela), Olga Tucker, Richard Turkington(Broad Institute), Daniel J. Turner, Andrew Tutt, Masaki Ueno, Naoto T. Ueno, Christopher B. Umbricht, Husen M. Umer, Tim Underwood, Lara Urban, Tomoko Urushidate, Tetsuo Ushiku, Liis Uusküla-Reimand, Alfonso Valencia(Washington State University), David Van Den Berg(The Francis Crick Institute), Steven Van Laere, Peter Van Loo(The Francis Crick Institute), Erwin G. Van Meir, Gert G. Van den Eynden, Theodorus van der Kwast(Universidade de Santiago de Compostela), Naveen Vasudev, Miguél Vázquez, Ravikiran Vedururu, Umadevi Veluvolu, Shankar Vembu(Wellcome Sanger Institute), Chao Li, Peter Vermeulen, Clare Verrill(Institució Catalana de Recerca i Estudis Avançats), Alain Viari, David Vicente(University of Copenhagen), Caterina Vicentini, K. VijayRaghavan, Juris Vīksna(Barcelona Supercomputing Center), Ricardo E. Vilain, Izar Villasante(Barcelona Supercomputing Center), Anne Vincent‐Salomon, Tapio Visakorpi, Douglas Voet, Paresh Vyas(The University of Queensland), Ignacio Vázquez-Garćıa(The University of Queensland), Nick M. Waddell(The University of Queensland), Nicola Waddell(The University of Queensland), Claes Wadelius, Lina Wadi(Broad Institute), Rabea Wagener, Jeremiah A. Wala(Broad Institute), Jian Wang, Jiayin Wang, Linghua Wang, Qi Wang, Wenyi Wang, Yumeng Wang, Zhining Wang, Paul Waring, Hans-Jörg Warnatz, Jonathan Warrell(European Molecular Biology Laboratory), Anne Y. Warren(Oxford BioMedica (United Kingdom)), Sebastian M. Waszak(European Molecular Biology Laboratory), David C. Wedge(University of Cambridge), Dieter Weichenhan, Paul Weinberger(University of Copenhagen), John N. Weinstein, Joachim Weischenfeldt(University of Copenhagen), Daniel J. Weisenberger, Ian Welch, Michael C. Wendl, Johannes Werner(Institució Catalana de Recerca i Estudis Avançats), Justin P. Whalley, David A. Wheeler, 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(Universitat Pompeu Fabra), 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, Guanming Wu, Jianmin Wu(University of Chicago), Kui Wu, Yang Wu(Cornell University), Zhenggang Wu(Cornell University), Xi Liu, Tian Xia(Cornell University), Qian Xiang(University of Chicago), Xiao Xiao(Broad Institute), Rui Xing, Heng Xiong, Qinying Xu(Broad Institute), Yanxun Xu, Hong Xue, Shinichi Yachida, Sergei Yakneen, Rui Yamaguchi, Takafumi N. Yamaguchi, Masakazu Yamamoto, Shogo Yamamoto(University of Chicago), Hiroki Yamaue(University of Chicago), Fan Yang(University of Chicago), Huanming Yang(University of Chicago), Jean Yang(University of Chicago), Liming Yang(University of Chicago), Lixing Yang(University of Chicago), Shanlin Yang(University of Chicago), Yeng Ang(Cornell University), Yang Yang, Xiaotong Yao(Cornell University), Marie‐Laure Yaspo, Lucy Yates(University of Bern), Christina Yau(University of Bern), Chen Ye, Kai Ye(Seoul National University Hospital), Venkata D. Yellapantula(Seoul National University Hospital), Christopher J. Yoon, Sung-Soo Yoon(Seoul National University Hospital), Fouad Yousif, Jun Yu, Kaixian Yu, Willie Yu, Yingyan Yu, Ke Yuan, Yuan Yuan, Denis Yuen, Christina K. Yung(Universidade de Santiago de Compostela), Olga Zaikova(Cornell University), Jorge Zamora(Universidade de Santiago de Compostela), Marc Zapatka, Jean C. Zenklusen, Thorsten Zenz(Broad Institute), Nikolajs Zeps(Broad Institute), Cheng‐Zhong Zhang(Broad Institute), Fan Zhang(Broad Institute), Hailei Zhang(Broad Institute), Hongwei Zhang(Broad Institute), Hongxin Zhang(Broad Institute), Jiashan Zhang(Broad Institute), Jing Zhang(Broad Institute), Junjun Zhang(Broad Institute), Xiuqing Zhang(Broad Institute), Xuanping Zhang(Broad Institute), Yan Zhang, Zemin Zhang, Zhongming Zhao, Liangtao Zheng, Xiuqing Zheng, Wanding Zhou, Yong Zhou, Bin Zhu, Hongtu Zhu, Jingchun Zhu, Shida Zhu, Lihua Zou, Xueqing Zou, Anna DeFazio, Nicholas van As, Carolien H. M. van Deurzen(University of Chicago), Marc J. van de Vijver, L. van’t Veer, Christian von Mering
Cited by 473Open Access
Abstract
About half of all cancers have somatic integrations of retrotransposons. Here, to characterize their role in oncogenesis, we analyzed the patterns and mechanisms of somatic retrotransposition in 2,954 cancer genomes from 38 histological cancer subtypes within the framework of the Pan-Cancer Analysis of Whole Genomes (PCAWG) project. We identified 19,166 somatically acquired retrotransposition events, which affected 35% of samples and spanned a range of event types. Long interspersed nuclear element (LINE-1; L1 hereafter) insertions emerged as the first most frequent type of somatic structural variation in esophageal adenocarcinoma, and the second most frequent in head-and-neck and colorectal cancers. Aberrant L1 integrations can delete megabase-scale regions of a chromosome, which sometimes leads to the removal of tumor-suppressor genes, and can induce complex translocations and large-scale duplications. Somatic retrotranspositions can also initiate breakage-fusion-bridge cycles, leading to high-level amplification of oncogenes. These observations illuminate a relevant role of L1 retrotransposition in remodeling the cancer genome, with potential implications for the development of human tumors.
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