s41586-019-1913-9.pdf (33.5 MB)
Patterns of somatic structural variation in human cancer genomes
journal contribution
posted on 2024-01-08, 11:47 authored by Yilong Li, Nicola D Roberts, Jeremiah A Wala, Ofer Shapira, Steven E Schumacher, Kiran Kumar, Ekta Khurana, Sebastian Waszak, Jan O Korbel, James E Haber, Marcin Imielinski, Kadir C Akdemir, Eva G Alvarez, Adrian Baez-Ortega, Rameen Beroukhim, Paul C Boutros, David DL Bowtell, Benedikt Brors, Kathleen H Burns, Peter J Campbell, Kin Chan, Ken Chen, Isidro Cortés-Ciriano, Ana Dueso-Barroso, Andrew J Dunford, Paul A Edwards, Xavier Estivill, Dariush Etemadmoghadam, Lars Feuerbach, J Lynn Fink, Milana Frenkel-Morgenstern, Dale W Garsed, Mark Gerstein, Dmitry A Gordenin, David Haan, Julian M Hess, Barbara Hutter, David TW Jones, Young Seok Ju, Marat D Kazanov, Leszek J Klimczak, Youngil Koh, Eunjung Alice Lee, Jake June-Koo Lee, Andy G Lynch, Geoff Macintyre, Florian Markowetz, Iñigo Martincorena, Alexander Martinez-Fundichely, Matthew Meyerson, Satoru Miyano, Hidewaki Nakagawa, Fabio CP Navarro, Stephan Ossowski, Peter J Park, John V Pearson, Montserrat Puiggròs, Karsten Rippe, Steven A Roberts, Bernardo Rodriguez-Martin, Ralph Scully, Mark Shackleton, Nikos Sidiropoulos, Lina Sieverling, Chip Stewart, David Torrents, Jose MC Tubio, Izar Villasante, Nicola Waddell, Joachim Weischenfeldt, Lixing Yang, Xiaotong Yao, Sung-Soo Yoon, Jorge Zamora, Cheng-Zhong Zhang, Lauri A Aaltonen, Federico Abascal, Adam Abeshouse, Hiroyuki Aburatani, David J Adams, Nishant Agrawal, Keun Soo Ahn, Sung-Min Ahn, Hiroshi Aikata, Rehan Akbani, Hikmat Al-Ahmadie, Sultan T Al-Sedairy, Fatima Al-Shahrour, Malik Alawi, Monique Albert, Kenneth Aldape, Ludmil B Alexandrov, Adrian Ally, Kathryn Alsop, Fernanda Amary, Samirkumar B Amin, Brice Aminou, Ole Ammerpohl, Matthew J Anderson, Yeng Ang, Davide Antonello, Pavana Anur, Samuel Aparicio, Elizabeth L Appelbaum, Yasuhito Arai, Axel Aretz, Koji Arihiro, Shun-ichi Ariizumi, Joshua Armenia, Laurent Arnould, Sylvia Asa, Yassen Assenov, Gurnit Atwal, Sietse Aukema, J Todd Auman, Miriam RR Aure, Philip Awadalla, Marta Aymerich, Gary D Bader, Matthew H Bailey, Peter J Bailey, Miruna Balasundaram, Saianand Balu, Pratiti Bandopadhayay, Rosamonde E Banks, Stefano Barbi, Andrew P Barbour, Jonathan Barenboim, Jill Barnholtz-Sloan, Hugh Barr, Elisabet Barrera, John Bartlett, Javier Bartolome, Claudio Bassi, Oliver F Bathe, Daniel Baumhoer, Prashant Bavi, Stephen B Baylin, Wojciech Bazant, Duncan Beardsmore, Timothy A Beck, Sam Behjati, Andreas Behren, Beifang Niu, Cindy Bell, Sergi Beltran, Christopher Benz, Andrew Berchuck, Anke K Bergmann, Erik N Bergstrom, Benjamin P Berman, Daniel M Berney, Stephan H Bernhart, Mario Berrios, Samantha Bersani, Johanna Bertl, Miguel Betancourt, Vinayak Bhandari, Shriram G Bhosle, Andrew V Biankin, Matthias Bieg, Darell Bigner, Hans Binder, Ewan Birney, Michael Birrer, Nidhan K Biswas, Bodil Bjerkehagen, Tom Bodenheimer, Lori Boice, Giada Bonizzato, Johann S De Bono, Arnoud Boot, Moiz S Bootwalla, Ake Borg, Arndt Borkhardt, Keith A Boroevich, Ivan Borozan, Christoph Borst, Marcus Bosenberg, Mattia Bosio, Jacqueline Boultwood, Guillaume Bourque, G Steven Bova, David T Bowen, Reanne Bowlby, Sandrine Boyault, Rich Boyce, Jeffrey Boyd, Alvis Brazma, Paul Brennan, Daniel S Brewer, Arie B Brinkman, Robert G Bristow, Russell R Broaddus, Jane E Brock, Malcolm Brock, Annegien Broeks, Angela N Brooks, Denise Brooks, Søren Brunak, Timothy JC Bruxner, Alicia L Bruzos, Alex Buchanan, Ivo Buchhalter, Christiane Buchholz, Susan Bullman, Hazel Burke, Birgit Burkhardt, John Busanovich, Carlos D Bustamante, Adam P Butler, Atul J Butte, Niall J Byrne, Anne-Lise Børresen-Dale, Samantha J Caesar-Johnson, Andy Cafferkey, Declan Cahill, Claudia Calabrese, Carlos Caldas, Fabien Calvo, Niedzica Camacho, Elias Campo, Cinzia Cantù, Shaolong Cao, Thomas E Carey, Joana Carlevaro-Fita, Rebecca Carlsen, Ivana Cataldo, Mario Cazzola, Jonathan Cebon, Robert Cerfolio, Dianne E Chadwick, Dimple Chakravarty, Don Chalmers, Calvin Wing Yiu Chan, Michelle Chan-Seng-Yue, Vishal S Chandan, David K Chang, Stephen J Chanock, Lorraine A Chantrill, 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, Jung Kyoon Choi, 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 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 M Cordner, Kyle 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 Davi, 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 P Dei Tos, Olivier Delaneau, John A Demchok, Jonas Demeulemeester, German M Demidov, Deniz Demircioğlu, Nening M Dennis, Robert E Denroche, Stefan C Dentro, Nikita Desai, Vikram Deshpande, Amit G Deshwar, Christine Desmedt, Jordi Deu-Pons, Noreen Dhalla, Neesha C Dhani, Priyanka Dhingra, Rajiv Dhir, Anthony DiBiase, 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, Tim Dudderidge, Michael Dunn, Lewis Jonathan Dursi, Fraser R Duthie, Ken Dutton-Regester, Jenna Eagles, Douglas F Easton, Stuart Edmonds, Sandra E Edwards, Rosalind A Eeles, Anna Ehinger, Juergen Eils, Roland Eils, Adel El-Naggar, Matthew Eldridge, Kyle Ellrott, Serap Erkek, Georgia Escaramis, Shadrielle MG Espiritu, Jorunn E Eyfjord, Bishoy M Faltas, Daiming Fan, Yu Fan, William C Faquin, Claudiu Farcas, Matteo Fassan, Aquila Fatima, Francesco Favero, Nodirjon Fayzullaev, Ina Felau, Sian 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 E Fleshner, Paul Flicek, John A Foekens, Kwun M Fong, Nuno A Fonseca, Christopher S Foster, Natalie S Fox, Michael Fraser, Scott Frazer, William Friedman, Joan Frigola, Catrina C Fronick, Akihiro Fujimoto, Masashi Fujita, Masashi Fukayama, Lucinda A Fulton, Robert S Fulton, Mayuko Furuta, P Andrew Futreal, Anja Füllgrabe, Stacey B Gabriel, Steven Gallinger, Carlo Gambacorti-Passerini, Jianjiong Gao, Shengjie Gao, Levi Garraway, Øystein Garred, Erik Garrison, Nils Gehlenborg, Josep LL Gelpi, Joshy George, Daniela S Gerhard, Clarissa Gerhauser, Jeffrey E Gershenwald, 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 Glodzik, Vincent J Gnanapragasam, Maria Elisabeth Goebler, Mary J Goldman, Carmen Gomez, Santiago Gonzalez, Abel Gonzalez-Perez, 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, Qianyun Guo, Manaswi Gupta, Shailja Gupta, Ivo G Gut, Marta Gut, Jonathan Göke, Gavin Ha, Andrea Haake, Siegfried Haas, Kerstin Haase, Nina Habermann, Faraz Hach, Syed Haider, Natsuko Hama, Freddie C Hamdy, Anne Hamilton, Mark P Hamilton, Leng Han, George B Hanna, Martin Hansmann, Nicholas J Haradhvala, 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, Yao He, Allison P Heath, Simon C Heath, David Hedley, Apurva M Hegde, David I Heiman, Michael C Heinold, Zachary Heins, Lawrence E Heisler, Eva Hellstrom-Lindberg, Mohamed Helmy, Seong Gu Heo, Austin J Hepperla, José María Heredia-Genestar, Carl Herrmann, Peter Hersey, Holmfridur Hilmarsdottir, Jonathan Hinton, Satoshi Hirano, Nobuyoshi Hiraoka, Katherine A Hoadley, Asger Hobolth, Ermin Hodzic, Jessica I Hoell, Steve Hoffmann, Oliver Hofmann, Andrea Holbrook, Aliaksei Z Holik, Michael A Hollingsworth, Oliver HolmesAbstractA key mutational process in cancer is structural variation, in which rearrangements delete, amplify or reorder genomic segments that range in size from kilobases to whole chromosomes1–7. Here we develop methods to group, classify and describe somatic structural variants, using data from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), which aggregated whole-genome sequencing data from 2,658 cancers across 38 tumour types8. Sixteen signatures of structural variation emerged. Deletions have a multimodal size distribution, assort unevenly across tumour types and patients, are enriched in late-replicating regions and correlate with inversions. Tandem duplications also have a multimodal size distribution, but are enriched in early-replicating regions—as are unbalanced translocations. Replication-based mechanisms of rearrangement generate varied chromosomal structures with low-level copy-number gains and frequent inverted rearrangements. One prominent structure consists of 2–7 templates copied from distinct regions of the genome strung together within one locus. Such cycles of templated insertions correlate with tandem duplications, and—in liver cancer—frequently activate the telomerase gene TERT. A wide variety of rearrangement processes are active in cancer, which generate complex configurations of the genome upon which selection can act.
