Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

Adrian Baez‐Ortega,Jorge Zamora,Fran Supek,Jonas Demeulemeester,Martín Santamarina,Young Ju,Javier Temes,Daniel García‐Souto,Harald Detering,Yilong Li,Jorge Rodríguez‐Castro,Ana Dueso-Barroso,Alicia Bruzos,Stefan Dentro,Miguel Blanco,Gianmarco Contino,Daniel Ardeljan,Marta Tojo,Nicola Roberts,Sonia Zumalave,Paul Edwards,Joachim Weischenfeldt,Montserrat Puiggròs,Zechen Chong,Ken Chen,Eunjung Lee,Jeremiah Wala,Keiran Raine,Adam Butler,Sebastian Waszak,Fábio Navarro,Steven Schumacher,Jean Monlong,Francesco Maura,Niccolò Bolli,Guillaume Bourque,Mark Gerstein,Peter Park,David Wedge,Rameen Beroukhim,David Torrents,Jan Korbel,Iñigo Martincorena,Rebecca Fitzgerald,Peter Loo,Haig Kazazian,Kathleen Burns,Kadir Akdemir,Paul Boutros,David Bowtell,Benedikt Brors,Peter Campbell,Kin Chan,Isidro Cortés‐Ciriano,Andrew Dunford,Xavier Estivill,Dariush Etemadmoghadam,Lars Feuerbach,J. Fink,Milana Frenkel‐Morgenstern,Dale Garsed,Dmitry Gordenin,David Haan,James Haber,Julian Hess,Barbara Hutter,Marcin Imieliński,David Jones,Marat Kazanov,Leszek Klimczak,Youngil Koh,Kiran Kumar,Jake Lee,Andy Lynch,Geoff Macintyre,Florian Markowetz,Alexander Martínez-Fundichely,Matthew Meyerson,Satoru Miyano,Hidewaki Nakagawa,Stephan Ossowski,John Pearson,Karsten Rippe,Steven Roberts,Ralph Scully,Mark Shackleton,Nikos Sidiropoulos,Lina Sieverling,Chip Stewart,José Tubío,Izar Villasante,Nicola Waddell,Lixing Yang,Xiaotong Yao,Sung-Soo Yoon,Cheng‐Zhong Zhang,Lauri Aaltonen,Federico Abascal,Adam Abeshouse,Hiroyuki Aburatani,David Adams,Nishant Agrawal,Keun Ahn,Sung-Min Ahn,Hiroshi Aikata,Rehan Akbani,Hikmat Al‐Ahmadie,Sultan Al‐Sedairy,Fátima Al‐Shahrour,Malik Alawi,Monique Albert,Kenneth Aldape,Ludmil Alexandrov,Adrian Ally,Kathryn Alsop,Fernanda Amary,Samirkumar Amin,Brice Aminou,Ole Ammerpohl,Matthew Anderson,Yeng Ang,Davide Antonello,Pavana Anur,Samuel Aparício,Elizabeth Appelbaum,Yasuhito Arai,Axel Aretz,Koji Arihiro,Shun‐ichi Ariizumi,Joshua Armenia,Laurent Arnould,L. Sylvia,Yassen Assenov,Gurnit Atwal,Sietse Aukema,J. Auman,Miriam Aure,Philip Awadalla,Marta Aymerich,Gary Bader,Matthew Bailey,Peter Bailey,Miruna Balasundaram,Saianand Balu,Pratiti Bandopadhayay,Rosamonde Banks,Stefano Barbi,Andrew Barbour,Jonathan Barenboim,Jill Barnholtz‐Sloan,Hugh Barr,Elisabet Barrera,John Bartlett,Javier Bartolomé,Claudio Bassi,Oliver Bathe,Daniel Baumhoer,Prashant Bavi,Stephen Baylin,Wojciech Bażant,Duncan Beardsmore,Timothy Beck,Sam Behjati,Andreas Behren,Beifang Niu,Cindy Bell,Sergi Beltrán,Christopher Benz,Andrew Berchuck,Anke Bergmann,Erik Bergstrom,Benjamin Berman,Daniel Berney,Stephan Wolf,Mario Berríos,Samantha Bersani,Johanna Bertl,Miguel Betancourt,Vinayak Bhandari,Shriram Bhosle,Andrew Biankin,Matthias Bieg,Darell Bigner,Hans Binder,Ewan Birney,Michael Birrer,Nidhan Biswas,Bodil Bjerkehagen,Tom Bodenheimer,Lori Boice,Giada Bonizzato,Johann Bono,Arnoud Boot,Åke Borg,Arndt Borkhardt,Keith Boroevich,Ivan Borozan,Christoph Borst,Marcus Bosenberg,Mattia Bosio,Jacqueline Boultwood,G. Bova,David Bowen,Reanne Bowlby,Sandrine Boyault,Rich Boyce,Jeffrey Boyd,Alvis Brāzma,Paul Brennan,Daniel Brewer,Arie Brinkman,Robert Bristow,Russell Broaddus,Jane Brock,Malcolm Brock,Annegien Broeks,Angela Brooks,Denise Brooks,Søren Brunak,Timothy Bruxner,Alex Buchanan,Ivo Buchhalter,Christiane Buchholz,Susan Bullman,Hazel Burke,Birgit Burkhardt,John Busanovich,Carlos Bustamante,Atul Butte,Niall Byrne,Anne‐Lise Børresen‐Dale,Rory Johnson,Andy Cafferkey,Declan Cahill,Claudia Calabrese,Carlos Caldas,Fabien Calvo,Niedzica Camacho,Elı́as Campo,Cinzia Cantù,Shaolong Cao,Thomas Carey,Joana Carlevaro-Fita,Rebecca Carlsen,Ivana Cataldo,Mario Cazzola,Jonathan Cebon,Robert Cerfolio,Dianne Chadwick,Dimple Chakravarty,Drc Chalmers,Calvin Chan,Michelle Chan‐Seng‐Yue,Vishal Chandan,David Chang,Stephen Chanock,Aurélien Chateigner,Nilanjan Chatterjee,Kazuaki Chayama,Hsiao‐Wei Chen,Jieming Chen,Yiwen Chen,Zhaohong Chen,Andrew Cherniack,Jeremy Chien,Yoke-Eng Chiew,Suet‐Feung Chin,Juok Cho,Sunghoon Cho,Jung Choi,Wan Choi,Christine Chomienne,Su Choo,Angela Chou,Angelika Christ,Elizabeth Christie,Eric Chuah,Carrie Cibulskis,Kristian Cibulskis,Sara Cingarlini,Peter Clapham,Alexander Claviez,Sean Cleary,Nicole Cloonan,Marek Cmero,Colin Collins,Ashton Connor,Susanna Cooke,Colin Cooper,Leslie Cope,Vincenzo Corbo,Matthew Cordes,Stephen Cordner,Kyle Covington,Prue Cowin,Brian Craft,David Craft,Chad Creighton,Yupeng Cun,Erin Curley,Ioana Cutcutache,Karolina Czajka,Bogdan Czerniak,Rebecca Dagg,Ludmila Danilova,Maria Davì,Natalie Davidson,Helen Davies,Ian Davis,Brandi Davis‐Dusenbery,Kevin Dawson,Francisco Vega,Ricardo Paoli‐Iseppi,Timothy Defreitas,Angelo Tos,Olivier Delaneau,John Demchok,German Demidov,Deniz Demircioğlu,Nening Dennis,Robert Denroche,Nikita Desai,Vikram Deshpande,Amit Deshwar,Christine Desmedt,Jordi Deu-Pons,Noreen Dhalla,Neesha Dhani,Priyanka Dhingra,Rajiv Dhir,Anthony DiBiase,Klev Diamanti,Li Ding,Shuai Ding,Huy Dinh,Luc Dirix,HarshaVardhan Doddapaneni,Nilgun Donmez,Michelle Dow,Ronny Drapkin,Oliver Drechsel,Ruben Drews,Serge Serge,Tim Dudderidge,Michael Dunn,Lewis Dursi,Fraser Duthie,Ken Dutton‐Regester,Jenna Eagles,Douglas Easton,Stuart Edmonds,Sandra Edwards,Rosalind Eeles,Anna Ehinger,Roland Eils,Adel El‐Naggar,Matthew Eldridge,Kyle Ellrott,Serap Erkek,Geòrgia Escaramís,Shadrielle Espiritu,Jorunn Eyfjord,Bishoy Faltas,Daiming Fan,Fan Yu,William Faquin,Claudiu Farcas,Matteo Fassan,Aquila Fatima,Francesco Favero,Nodirjon Fayzullaev,Ina Felau,Sián Fereday,Martin Ferguson,Vincent Ferretti,Matthew Field,Gaetano Finocchiaro,Cyril Fisher,Matthew Fittall,Anna Fitzgerald,Adrienne Flanagan,Neil Fleshner,Paul Flicek,John Foekens,Kwun Fong,Nuno Fonseca,Christopher Foster,Natalie Fox,Michael Fraser,Scott Frazer,William Friedman,Joan Frigola,Catrina Fronick,Akihiro Fujimoto,Masashi Fujita,Masashi Fukayama,Lucinda Fulton,Robert Fulton,Mayuko Furuta,P. Futreal,Anja Füllgrabe,Stacey Gabriel,Steven Gallinger,Carlo Gambacorti‐Passerini,Jianjiong Gao,Shengjie Gao,Levi Garraway,Øystein Garred,Erik Garrison,Nils Gehlenborg,Josep Gelpi,Joshy George,Daniela Gerhard,Clarissa Gerhäuser,Hui Shen,Moritz Gerstung,Gad Getz,Mohammed Ghori,Ronald Ghossein,Nasra Giama,Richard Gibbs,Bob Gibson,Anthony Gill,Pelvender Gill,Dilip Giri,Dominik Głodzik,Vincent Gnanapragasam,Maria Goebler,Mary Goldman,Carmen Gómez,Santiago González,Abel González-Pérez,James Gossage,Kunihito Gotoh,Ramaswamy Govindan,Dorthe Grabau,Janet Graham,Robert Grant,Anthony Green,Eric Green,Liliana Greger,Nicola Grehan,Sonia Grimaldi,Sean Grimmond,Robert Grossman,Adam Grundhoff,Gunes Gundem,Qianyun Guo,Manaswi Gupta,Shailja Gupta,Marta Gut,Jonathan Göke,Gavin Ha,Andrea Haake,Siegfried Haas,Kerstin Haase,Faraz Hach,Syed Haider,Natsuko Hama,Freddie Hamdy,Anne Hamilton,Mark Hamilton,Leng Han,George Hanna,Martin Hansmann,Nicholas Haradhvala,Olivier Harismendy,Ivon Harliwong,Arif Harmanci,Eoghan Harrington,Takanori Hasegawa,David Haussler,Steve Hawkins,Shinya Hayami,Shuto Hayashi,D. Hayes,Stephen Hayes,Nicholas Hayward,Steven Hazell,Yao He,Allison Heath,Simon Heath,David Hedley,Apurva Hegde,David Heiman,Michael Heinold,Zachary Heins,Lawrence Heisler,Eva Hellstrom-Lindberg,Mohamed Helmy,Seong Heo,Austin Hepperla,José Heredia‐Genestar,Carl Herrmann,Peter Hersey,Hólmfríður Hilmarsdóttir,Jonathan Hinton,Satoshi Hirano,Nobuyoshi Hiraoka,Katherine Hoadley,Asger Hobolth,Ermin Hodzic,Jessica Hoell,Steve Hoffmann,Oliver Hofmann,Andrea Holbrook,Aliaksei Holik,Michael Hollingsworth,Oliver Holmes,Robert Holt,Hong Chen,Eun Hong,Jongwhi Hong,Gerrit Hooijer,Henrik Hornshøj,Fumie Hosoda,Yong Hou,Volker Hovestadt,William Howat,Alan Hoyle,Ralph Hruban,Taobo Hu,Xing Hua,Kuan‐lin Huang,Mei Huang,Mi Huang,Vincent Huang,Yifei Huang,Wolfgang Huber,Thomas Hudson,Michael Hummel,Jillian Hung,David Huntsman,Ted Hupp,Jason Huse,Matthew Huska,Carolyn Hutter,Daniel Hübschmann,Christine Iacobuzio‐Donahue,Charles Imbusch,Seiya Imoto,William Isaacs,Keren Isaev,Shumpei Ishikawa,Murat Iskar,S. Islam,Michael Ittmann,Sinisa Ivkovic,José Izarzugaza,Jocelyne Jacquemier,Valerie Jakrot,Nigel Jamieson,Gun Jang,Se Jang,Joy Jayaseelan,Reyka Jayasinghe,Joshua Stuart,Karine Jegalian,Jennifer Jennings,Seung-Hyup Jeon,Lara Jerman,Yuan Ji,Wei Jiao,Peter Johansson,Amber Johns,Jeremy Johns,Todd Johnson,Clemency Jolly,Yann Joly,Jón Jónasson,Corbin Jones,Nic Jones,Steven Jones,Jos Jonkers,Hartmut Juhl,Jongsun Jung,Malene Juul,Randi Juul,Natalie Jäger,Rolf Kabbe,André Kahles,Abdullah Kahraman,Vera Kaiser,Hojabr Kakavand,Sangeetha Kalimuthu,Christof Kalle,Koo Kang,Katalin Karászi,Beth Karlan,Rosa Karlić,Dennis Karsch,Karin Kassahn,Hitoshi Katai,Mamoru Kato,Hiroto Katoh,Yoshiiku Kawakami,Jonathan Kay,Stephen Kazakoff,Maria Keays,Electron Kebebew,Richard Kefford,Manolis Kellis,James Kench,Catherine Kennedy,Jules Kerssemakers,David Khoo,Vincent Khoo,Narong Khuntikeo,Ekta Khurana,Helena Kilpinen,Hark Kim,Hyung‐Lae Kim,Hyung-Yong Kim,Hyunghwan Kim,Jaegil Kim,Jihoon Kim,Jong Kim,Young-Wook Kim,Tari King,Wolfram Klapper,Kortine Kleinheinz,Stian Knappskog,Michael Kneba,Bartha Knoppers,Jan Komorowski,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,Pardeep Kumar,Sushant Kumar,Yogesh Kumar,Ritika Kundra,Kirsten Kübler,Ralf Küppers,Jesper Lagergren,Phillip Lai,Peter Laird,Sunil Lakhani,Christopher Lalansingh,Emilie Lalonde,Fabien Lamaze,Adam Lambert,Eric Lander,Pablo Landgraf,Luca Landoni,Anita Langerød,Andrés Lanzós,Denis Larsimont,Erik Larsson,Mark Lathrop,Loretta Lau,Chris Lawerenz,Rita Lawlor,Michael Lawrence,Alexander Lazar,Ana Lazic,Xuan Le,Darlene Lee,Dong Lee,Hee Lee,Jeong‐Yeon Lee,Ju Lee,Ming Lee,Henry Lee-Six,Kjong-Van Lehmann,Hans Lehrach,Dido Lenze,Conrad Leonard,Daniel Leongamornlert,Ignaty Leshchiner,Louis Létourneau,Ivica Letunić,Douglas Levine,Lora Lewis,Tim Ley,Chang Li,Constance Li,Haiyan Li,Jun Li,Lin Li,Shantao Li,Siliang Li,Xiaobo Li,Xiaotong Li,Xinyue Li,Han Liang,Sheng‐Ben Liang,Péter Lichter,Pei Lin,Ziao Lin,W. Linehan,Ole Lingjærde,Dongbing Liu,Eric Liu,Fei-Fei Liu,Fenglin Liu,Jia Liu,Xingmin Liu,Julie Livingstone,Dimitri Livitz,Naomi Livni,Lucas Lochovsky,Markus Loeffler,Georgina Long,Armando López‐Guillermo,Shaoke Lou,David Louis,Laurence Lovat,Yiling Lu,Yong‐Jie Lu,Youyong Lu,Claudio Luchini,Ilinca Lungu,Xuemei Luo,Hayley Luxton,Lisa Lype,Cristina López,Carlos López‐Otín,Z. Eric,Yussanne Ma,Gaëtan MacGrogan,Shona MacRae,Tobias Madsen,Kazuhiro Maejima,Andrea Mafficini,Dennis Maglinte,Arindam Maitra,Partha Majumder,Luca Malcovati,Salem Malikić,Giuseppe Malleo,Graham Mann,Luisa Mantovani‐Löffler,Kathleen Marchal,Giovanni Marchegiani,Elaine Mardis,Adam Margolin,Maximillian Marin,Julia Markowski,Jeffrey Marks,Tomás Marquès‐Bonet,Marco Marra,Luke Marsden,John Martens,Sancha Martin,José Martín‐Subero,Yosef Maruvka,R. Mashl,Charlie Massie,Thomas Matthew,Lucy Matthews,Erik Mayer,Simon Mayes,Michael Mayo,Faridah Mbabaali,Karen McCune,Ultan McDermott,Patrick McGillivray,Michael McLellan,John McPherson,Treasa McPherson,Samuel Meier,Alice Meng,Shaowu Meng,Andrew Menzies,Neil Merrett,Sue Merson,Piotr Mieczkowski,George Mihaiescu,Sanja Mijalkovic,Tom Mikkelsen,Michèle Milella,Linda Mileshkin,Christopher Miller,David Miller,Jessica Miller,Gordon Mills,Ana Milovanovic,Sarah Minner,Marco Miotto,Gisela Arnau,Lisa Mirabello,Thomas Mitchell,Naoki Miyoshi,Shinichi Mizuno,Fruzsina Molnár‐Gábor,Malcolm Moore,Richard Moore,Sandro Morganella,Quaid Morris,Carl Morrison,Lisle Mose,Catherine Moser,Ferran Muiños,Loris Mularoni,Andrew Mungall,Karen Mungall,Elizabeth Musgrove,Ville Mustonen,David Mutch,Francesc Muyas,Donna Muzny,Alfonso Muñoz,Jerome Myers,Ola Myklebost,Peter Möller,Genta Nagae,Adnan Nagrial,Hardeep Nahal-Bose,Hitoshi Nakagama,Hiromi Nakamura,Toru Nakamura,Kaoru Nakano,Tannistha Nandi,Jyoti Nangalia,Mia Nastic,Arcadi Navarro,David Neal,Gerd Nettekoven,Felicity Newell,Steven Newhouse,Yulia Newton,Alvin Ng,Chi‐Fai Ng,Jonathan Nicholson,David Nicol,Yongzhan Nie,G. Nielsen,Morten Nielsen,Serena Nik-Zainal,Michael Noble,Kátia Nones,Paul Northcott,Faiyaz Notta,Brian O’Connor,Peter O’Donnell,Maria O’Donovan,Sarah O’Meara,Brian O’Neill,J. O’Neill,David Ocana,Angelica Ochoa,Layla Oesper,Christopher Ogden,Hideki Ohdan,Kazuhiro Ohi,Lucila Ohno‐Machado,Karin Oien,Akinyemi Ojesina,Hidenori Ojima,Takuji Okusaka,Larsson Omberg,Choon Ong,German Ott,B. Ouellette,Christine P’ng,Marta Paczkowska,Salvatore Paiella,Chawalit Pairojkul,Marina Pajic,Qiang Pan‐Hammarström,Elli Papaemmanuil,Irene Papatheodorou,Nagarajan Paramasivam,Ji Park,Joong‐Won Park,Keunchil Park,Kiejung Park,Joel Parker,Simon Parsons,Harvey Pass,Danielle Pasternack,A. 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Rathmell,Tobias Rausch,Guido Reifenberger,Jüri Reimand,Jorge Reis‐Filho,Victor Reuter,Iker Reyes-Salazar,Matthew Reyna,Sheila Reynolds,Esther Rheinbay,Yasser Riazalhosseini,Andrea Richardson,Julia Richter,Matthew Ringel,Markus Ringnér,Yasushi Rino,Jeffrey Roach,Lewis Roberts,A. Robertson,Alan Robertson,Javier Rodriguez,F. Rodríguez-González,Michael 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,Mark Rubin,Carlota Rubio-Pérez,Vasilisa Rudneva,Borislav Rusev,Andrea Ruzzenente,Gunnar Rätsch,Radhakrishnan Sabarinathan,Veronica Sabelnykova,Sara Sadeghi,S. 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