High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations

• DOI: 10.1038/s41467-019-13885-w
• Publication Date: 2020-02-05T19:03:29Z
• Authors: Yiqun Zhang; Fengju Chen; Nuno A. Fonseca; Yao He; Masashi Fujita; Hidewaki Nakagawa; Zemin Zhang; Alvis Brazma; ; Samirkumar B. Amin; Philip Awadalla; Peter J. Bailey; Alvis Brazma; Angela N. Brooks; Claudia Calabrese; Aurélien Chateigner; Isidro Cortés-Cir...; Brian Craft; David Craft; Chad J. Creighton; Natalie R. Davidson; Deniz Demircioğlu; Serap Erkek; Nuno A. Fonseca; Milana Frenkel-Mo...; Mary J. Goldman; Liliana Greger; Jonathan Göke; Yao He; Katherine A. Hoadley; Yong Hou; Matthew R. Huska; Andre Kahles; Ekta Khurana; Helena Kilpinen; Jan O. Korbel; Fabien C. Lamaze; Kjong-Van Lehmann; Chang Li; Siliang Li; Xiaobo Li; Xinyue Li; Dongbing Liu; Fenglin Liu; Xingmin Liu; Maximillian G. Marin; Julia Markowski; Matthew Meyerson; Tannistha Nandi; Morten Muhlig Nie...; Akinyemi I. Ojesina; B. F. Francis Oue...; Qiang Pan-Hammars...; Peter J. Park; Chandra Sekhar Pe...; Jakob Skou Pedersen; Marc D. Perry; Gunnar Rätsch; Roland F. Schwarz; Yuichi Shiraishi; Reiner Siebert; Cameron M. Soulette; Stefan G. Stark; Oliver Stegle; Hong Su; Patrick Tan; Bin Tean Teh; Lara Urban; Jian Wang; Sebastian M. Waszak; Kui Wu; Qian Xiang; Heng Xiong; Sergei Yakneen; Huanming Yang; Chen Ye; Christina K. Yung; Fan Zhang; Junjun Zhang; Xiuqing Zhang; Zemin Zhang; Liangtao Zheng; Jingchun Zhu; Shida Zhu; ; Kadir C. Akdemir; Eva G. Alvarez; Adrian Baez-Ortega; Rameen Beroukhim; Paul C. Boutros; David D. L. Bowtell; Benedikt Brors; Kathleen H. Burns; Peter J. Campbell; Kin Chan; Ken Chen; Isidro Cortés-Cir...; Ana Dueso-Barroso; Andrew J. Dunford; Paul A. Edwards; Xavier Estivill; Dariush Etemadmog...; Lars Feuerbach; J. Lynn Fink; Milana Frenkel-Mo...; Dale W. Garsed; Mark Gerstein; Dmitry A. Gordenin; David Haan; James E. Haber; Julian M. Hess; Barbara Hutter; Marcin Imielinski; David T. W. Jones; Young Seok Ju; Marat D. Kazanov; Leszek J. Klimczak; Youngil Koh; Jan O. Korbel; Kiran Kumar; Eunjung Alice Lee; Jake June-Koo Lee; Yilong Li; Andy G. Lynch; Geoff Macintyre; Florian Markowetz; Iñigo Martincorena; Alexander Martine...; Matthew Meyerson; Satoru Miyano; Hidewaki Nakagawa; Fabio C. P. Navarro; Stephan Ossowski; Peter J. Park; John V. Pearson; Montserrat Puiggròs; Karsten Rippe; Nicola D. Roberts; Steven A. Roberts; Bernardo Rodrigue...; Steven E. Schumacher; Ralph Scully; Mark Shackleton; Nikos Sidiropoulos; Lina Sieverling; Chip Stewart; David Torrents; Jose M. C. Tubio; Izar Villasante; Nicola Waddell; Jeremiah A. Wala; Joachim Weischenf...; Lixing Yang; Xiaotong Yao; Sung-Soo Yoon; Jorge Zamora; Cheng-Zhong Zhang; Chad J. Creighton; ; Lauri A. Aaltonen; Federico Abascal; 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; Fatima Al-Shahrour; Malik Alawi; Monique Albert; Kenneth Aldape; Ludmil B. Alexandrov; Adrian Ally; Kathryn Alsop; Eva G. Alvarez; Fernanda Amary; Samirkumar B. Amin; Brice Aminou; Ole Ammerpohl; Matthew J. Anderson; Yeng Ang; Davide Antonello; Pavana Anur; Samuel Aparicio; Elizabeth L. Appe...; 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 R. R. Aure; Philip Awadalla; Marta Aymerich; Gary D. Bader; Adrian Baez-Ortega; Matthew H. Bailey; Peter J. Bailey; Miruna Balasundaram; Saianand Balu; Pratiti Bandopadh...; 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; Rameen Beroukhim; 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; Paul C. Boutros; G. Steven Bova; David T. Bowen; Reanne Bowlby; David D. L. Bowtell; 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; Benedikt Brors; Søren Brunak; Timothy J. C. Bru...; Alicia L. Bruzos; Alex Buchanan; Ivo Buchhalter; Christiane Buchholz; Susan Bullman; Hazel Burke; Birgit Burkhardt; Kathleen H. Burns; John Busanovich; Carlos D. Bustamante; Adam P. Butler; Atul J. Butte; Niall J. Byrne; Anne-Lise Børrese...; Samantha J. Caesa...; Andy Cafferkey; Declan Cahill; Claudia Calabrese; Carlos Caldas; Fabien Calvo; Niedzica Camacho; Peter J. Campbell; 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; Kin Chan; Michelle Chan-Sen...; Vishal S. Chandan; David K. Chang; Stephen J. Chanock; Lorraine A. Chant...; Aurélien Chateigner; Nilanjan Chatterjee; Kazuaki Chayama; Hsiao-Wei Chen; Jieming Chen; Ken 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. Chri...; 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; Isidro Cortés-Cir...; 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-D...; Kevin J. Dawson; Francisco M. De L...; Ricardo De Paoli-...; 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 Dod...; Nilgun Donmez; Michelle T. Dow; Ronny Drapkin; Oliver Drechsel; Ruben M. Drews; Serge Serge; Tim Dudderidge; Ana Dueso-Barroso; Andrew J. Dunford; Michael Dunn; 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; Juergen Eils; Roland Eils; Adel El-Naggar; Matthew Eldridge; Kyle Ellrott; Serap Erkek; Georgia Escaramis; Shadrielle M. G. ...; Xavier Estivill; Dariush Etemadmog...; 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. 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Giri; Dominik Glodzik; Vincent J. Gnanap...; Maria Elisabeth G...; Mary J. Goldman; Carmen Gomez; Santiago Gonzalez; Abel Gonzalez-Perez; 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; Qianyun Guo; Manaswi Gupta; Shailja Gupta; Ivo G. Gut; Marta Gut; Jonathan Göke; Gavin Ha; Andrea Haake; David Haan; Siegfried Haas; Kerstin Haase; James E. Haber; 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. Harad...; 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-Lin...; Mohamed Helmy; Seong Gu Heo; Austin J. Hepperla; José María Heredi...; Carl Herrmann; Peter Hersey; Julian M. Hess; Holmfridur Hilmar...; 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. Hollin...; Oliver Holmes; Robert A. Holt; Chen Hong; Eun Pyo Hong; Jongwhi H. Hong; Gerrit K. Hooijer; Henrik Hornshøj; Fumie Hosoda; Yong Hou; Volker Hovestadt; William Howat; Alan P. Hoyle; Ralph H. Hruban; Jianhong Hu; 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 Huntsman; Ted R. Hupp; Jason Huse; Matthew R. Huska; Barbara Hutter; Carolyn M. Hutter; Daniel Hübschmann; Christine A. Iaco...; Charles David Imb...; Marcin Imielinski; Seiya Imoto; William B. Isaacs; Keren Isaev; Shumpei Ishikawa; Murat Iskar; S. M. Ashiqul Islam; Michael Ittmann; Sinisa Ivkovic; Jose M. G. Izarzu...; Jocelyne Jacquemier; Valerie Jakrot; Nigel B. Jamieson; Gun Ho Jang; Se Jin Jang; Joy C. Jayaseelan; Reyka Jayasinghe; Stuart R. Jefferys; Karine Jegalian; Jennifer L. Jennings; Seung-Hyup Jeon; Lara Jerman; Yuan Ji; Wei Jiao; Peter A. Johansson; Amber L. Johns; Jeremy Johns; Rory Johnson; Todd A. Johnson; Clemency Jolly; Yann Joly; Jon G. Jonasson; Corbin D. Jones; David R. Jones; David T. W. Jones; Nic Jones; Steven J. M. Jones; Jos Jonkers; Young Seok Ju; Hartmut Juhl; Jongsun Jung; Malene Juul; Randi Istrup Juul; Sissel Juul; Natalie Jäger; Rolf Kabbe; Andre Kahles; Abdullah Kahraman; Vera B. Kaiser; Hojabr Kakavand; Sangeetha Kalimuthu; Christof von Kalle; Koo Jeong Kang; Katalin Karaszi; Beth Karlan; Rosa Karlić; Dennis Karsch; Katayoon Kasaian; Karin S. 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• Keywords: 0301 basic medicine; Cancer Research; Medizin; General Physics and Astronomy; Regulatory Sequences, Nucleic Acid; Genome, Cancer; Ecology,Evolution & Ethology; Neoplasms; Databases, Genetic; Cancer genomics; 2.1 Biological and endogenous factors; 3100 Physics and Astronomy; Genes, Tumor Suppressor; Aetiology; Càncer; Cancer; 0303 health sciences; Human Biology & Physiology; Q; 3rd-DAS; 1600 Chemistry; 3. Good health; Gene Expression Regulation, Neoplastic; Enhancer Elements, Genetic; PCAWG Structural Variation Working Group; Genetics & Genomics; Tumor Suppressor; Biotechnology; PCAWG Transcriptome Working Group; 1300 Biochemistry; Enhancer Elements; Science; General Biochemistry,Genetics and Molecular Biology; Radboudumc 17: Women's cancers RIHS: Radboud Institute for Health Sciences; 610; Genetics and Molecular Biology; QH426 Genetics; Article; RC0254; Databases; 03 medical and health sciences; Rare Diseases; SDG 3 - Good Health and Well-being; Genetic; Genetics; Humans; QH426; Computational & Systems Biology; Neoplastic; Nucleic Acid; Whole Genome Sequencing; RC0254 Neoplasms. Tumors. Oncology (including Cancer); Human Genome; PCAWG Consortium; General Chemistry; Oncogenes; DNA Methylation; Tumour Biology; Radboudumc 17: Women's cancers RIMLS: Radboud Institute for Molecular Life Sciences; Genòmica; Gene Expression Regulation; Genes; General Biochemistry; Genomic Structural Variation; Gene expression; Digestive Diseases; Regulatory Sequences; Genètica

AbstractThe impact of somatic structural variants (SVs) on gene expression in cancer is largely unknown. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole-genome sequencing data and RNA sequencing from a common set of 1220 cancer cases, we report hundreds of genes for which the presence within 100 kb of an SV breakpoint associates with altered expression. For the majority of these genes, expression increases rather than decreases with corresponding breakpoint events. Up-regulated cancer-associated genes impacted by this phenomenon include TERT, MDM2, CDK4, ERBB2, CD274, PDCD1LG2, and IGF2. TERT-associated breakpoints involve ~3% of cases, most frequently in liver biliary, melanoma, sarcoma, stomach, and kidney cancers. SVs associated with up-regulation of PD1 and PDL1 genes involve ~1% of non-amplified cases. For many genes, SVs are significantly associated with increased numbers or greater proximity of enhancer regulatory elements near the gene. DNA methylation near the promoter is often increased with nearby SV breakpoint, which may involve inactivation of repressor elements.