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- July 10, 2017.
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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
Author Information
- Christina K. Yung1*,
- Brian D. O’Connor1,2*,
- Sergei Yakneen1,3*,
- Junjun Zhang1*,
- Kyle Ellrott4,
- Kortine Kleinheinz5,6,
- Naoki Miyoshi7,
- Keiran M. Raine8,
- Romina Royo9,
- Gordon B. Saksena10,
- Matthias Schlesner5,
- Solomon I. Shorser1,
- Miguel Vazquez11,
- Joachim Weischenfeldt3,12,
- Denis Yuen1,
- Adam P. Butler8,
- Brandi N. Davis-Dusenbery13,
- Roland Eils14,6,
- Vincent Ferretti1,
- Robert L. Grossman15,
- Olivier Harismendy16,17,
- Youngwook Kim18,
- Hidewaki Nakagawa19,
- Steven J. Newhouse20,
- David Torrents9,21,
- Lincoln D. Stein1,22,‡,
- on behalf of the PCAWG Technical Working Group23,
- Javier Bartolomé Rodriguez1,
- Keith A. Boroevich2,
- Rich Boyce3,
- Angela N. Brooks4,
- Alex Buchanan5,
- Ivo Buchhalter6,7,
- Niall J. Byrne8,
- Andy Cafferkey9,
- Peter J. Campbell10,
- Zhaohong Chen11,
- Sunghoon Cho12,
- Wan Choi13,
- Peter Clapham14,
- Francisco M. De La Vega15,16,
- Jonas Demeulemeester17,18,
- Michelle T. Dow19,
- Lewis J. Dursi8,20,
- Juergen Eils21,
- Claudiu Farcas22,
- Francesco Favero23,
- Nodirjon Fayzullaev8,
- Paul Flicek3,
- Nuno A. Fonseca3,
- Josep L.l. Gelpi24,25,
- Gad Getz26,27,
- Bob Gibson8,
- Michael C. Heinold6,7,
- Julian M. Hess26,
- Oliver Hofmann28,
- Jongwhi H. Hong29,
- Thomas J. Hudson30,31,
- Daniel Huebschmann6,7,
- Barbara Hutter32,33,
- Carolyn M. Hutter34,
- Seiya Imoto35,
- Sinisa Ivkovic36,
- Seung-Hyup Jeon13,
- Wei Jiao8,
- Jongsun Jung37,
- Rolf Kabbe6,
- Andre Kahles38,39,
- Jules Kerssemakers40,
- Hyunghwan Kim13,
- Hyung-Lae Kim41,42,
- Jihoon Kim11,
- Jan O. Korbel3,43,
- Michael Koscher40,
- Antonios Koures11,
- Milena Kovacevic36,
- Chris Lawerenz6,
- Ignaty Leshchiner26,
- Dimitri G. Livitz26,
- George L. Mihaiescu8,
- Sanja Mijalkovic36,
- Ana Mijalkovic Lazic36,
- Satoru Miyano44,
- Hardeep K. Nahal8,
- Mia Nastic36,
- Jonathan Nicholson14,
- David Ocana3,
- Kazuhiro Ohi44,
- Lucila Ohno-Machado22,
- Larsson Omberg45,
- B.F. Francis Ouellette8,46,
- Nagarajan Paramasivam6,47,
- Marc D. Perry8,
- Todd D. Pihl48,
- Manuel Prinz6,
- Montserrat Puiggròs24,
- Petar Radovic36,
- Esther Rheinbay26,49,
- Mara W. Rosenberg26,49,
- Charles Short3,
- Heidi J. Sofia50,
- Jonathan Spring51,
- Adam J. Struck5,
- Grace Tiao26,
- Nebojsa Tijanic36,
- Peter Van Loo17,18,
- David Vicente1,
- Jeremiah A. Wala26,52,
- Zhining Wang53,
- Johannes Werner6,
- Ashley Williams11,
- Youngchoon Woo13,
- Adam J. Wright8,
- Qian Xiang8,
- the PCAWG Network
- 1Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, M5G 0A3, Canada.
- 2UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, 95065, USA.
- 3Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Baden-Württemberg, 69120, Germany.
- 4Department of Computational Biology, Oregon Health and Science University, Portland, Oregon, 97239, USA.
- 5Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg, 69120, Germany.
- 6Department for Bioinformatics and Functional Genomics, Institutefor Pharmacy and Molecular Biotechnology and BioQuant, Heidelberg University, Heidelberg, Baden-Württemberg, 69120, Germany.
- 7Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo,108-8639, Japan.
- 8Cancer Ageing and Somatic Mutation Programme, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA,United Kingdom.
- 9Department of Life Sciences, Barcelona Supercomputing Center, Barcelona, Catalunya, 8034, Spain.
- 10Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, 02142, USA.
- 11Structural Computational Biology Group, Centro Nacional de Investigaciones Oncologicas, Madrid, Madrid, 28029, Spain.
- 12BRIC/Finsen Laboratory, Rigshospitalet, Copenhagen, 2200, Denmark.
- 13Seven Bridges, Cambridge, Massachusetts, 02142, USA.
- 14Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg, 69120, Germany.
- 15Center for Data Intensive Science, University of Chicago, Chicago, Illinois,60637, USA.
- 16Department of Medicine, University of California San Diego, San Diego, California, 92093, USA.
- 17Moores Cancer Center, Department of Medicine, Division of Biomedical Informatics, University of California San Diego, San Diego, California, 92093, USA.
- 18Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University, School of Medicine, Seoul, 135-710, South Korea.
- 19Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, 108-8639, Japan.
- 20Technical Services Cluster, European Molecular Biology Laboratory, European Bioinforamtics Institute, Hinxton, Cambridge, CB10 1SD,United Kingdom.
- 21Institució Catalana de Recerca i Estudis Avançats, Barcelona, Catalunya, 8010, Spain.
- 22Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A1, Canada.
- 1Department of Operations, Barcelona Supercomputing Center, Barcelona, Catalunya, 8034, Spain.
- 2Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.
- 3European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, United Kingdom.
- 4Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, 95065, USA.
- 5Department of Computational Biology, Oregon Health and Science University, Portland, Oregon,97239, USA.
- 6Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg, 69120, Germany.
- 7Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology and BioQuant, Heidelberg University, Heidelberg, Baden-Württemberg, 69120, Germany.
- 8Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, M5G 0A3, Canada.
- 9Technical Services Cluster, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, United Kingdom.
- 10Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom.
- 11Department of Medicine, University of California San Diego, San Diego, California, 92093, USA.
- 12PDXen Biosystems Inc., Seoul, 4900, South Korea.
- 13Electronics and Telecommunications Research Institute, Daejon, 34129, South Korea.
- 14Informatics Support Group, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom.
- 15Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, California, 94305, USA.
- 16Annai Systems, Inc., Carlsbad, California, 92011, USA.
- 17The Francis Crick Institute, London, NW1 1AT, United Kingdom.
- 18Department of Human Genetics, University of Leuven, B-3000 Leuven, Belgium.
- 19Biomedical Informatics, University of California San Diego, San Diego, California, 92093, USA.
- 20The Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada.
- 21Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg, 69120, Germany.
- 22Health System Department of Biomedical Informatics, University of California San Diego, La Jolla, California, 92093, USA.
- 23BRIC/Finsen Laboratory, Rigshospitalet, Copenhagen, 2200, Denmark.
- 24Department of Life 528 Sciences, Barcelona Supercomputing Center, Barcelona, Catalunya, 8034, Spain.
- 25Department of Biochemistry and Molecular Biomedicine, University of Barcelona, Barcelona, Catalunya, 8028, Spain.
- 26Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, 02142, USA.
- 27Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, 02114, USA.
- 28Center for Cancer Research, University of Melbourne, Melbourne, VIC 3001, Australia.
- 29Genome Data Integration Center, Syntekabio Inc., Daejon, 34025, South Korea.
- 30Genomics Program, Ontario Institute for Cancer Research, Toronto, Ontario, M5G 534 0A3, Canada.
- 31Oncology Discovery and Early Development, AbbVie, Redwood City, California, 94063, USA.
- 32Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg, 536 69120, Germany.
- 33Division of Applied Bioinformatics, National Center for Tumor Diseases, Heidelberg, Baden-Württemberg, 69120, Germany.
- 34Division of Genomic Medicine, National Human Genome Research Institute Bethesda, Maryland, 20852, USA.
- 35Health Intelligence Center, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan.
- 36Seven Bridges, Cambridge, Massachusetts, 02142, USA.
- 37Genome Data Integration Center, Syntekabio Inc., Daejon, 34025, South Korea.
- 38Department of Computer Science, ETH Zurich, Zurich, Zurich, 8092, Switzerland.
- 39Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, New York, 10065, USA.
- 40German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg, 69120, Germany.
- 41Department of Biochemistry, Ewha Womans University, Seoul, O7985, South Korea.
- 42PGM21, Seoul, O7985, South Korea.
- 43Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Baden-Württemberg, 69120, Germany.
- 44Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan.
- 45Systems Biology, Sage Bionetworks, Seattle, Washington, 98112, USA.
- 46Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, M5S 3G5, Canada.
- 47Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Baden-Württemberg, 69120, Germany.
- 48CSRA Incorporated, Fairfax, Virginia, 22042, USA.
- 49Cancer Center, Massachusetts General Hospital, Boston, Massachusetts, 02114, USA.
- 50National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, 20892-551 9305, USA.
- 51Center for Data Intensive Science, University of Chicago, Chicago, Illinois, 60637, USA.
- 52Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, 02115, USA.
- 53TCGA 553 Program Office, National Cancer Institute, Bethesda, Maryland, 20892, USA.
- ↵‡Corresponding author: lincoln.stein{at}gmail.com
↵* These authors contributed equally to this work.