1
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Northcott PA, Buchhalter I, Morrissy AS, Hovestadt V, Weischenfeldt J, Ehrenberger T, Gröbner S, Segura-Wang M, Zichner T, Rudneva VA, Warnatz HJ, Sidiropoulos N, Phillips AH, Schumacher S, Kleinheinz K, Waszak SM, Erkek S, Jones DTW, Worst BC, Kool M, Zapatka M, Jäger N, Chavez L, Hutter B, Bieg M, Paramasivam N, Heinold M, Gu Z, Ishaque N, Jäger-Schmidt C, Imbusch CD, Jugold A, Hübschmann D, Risch T, Amstislavskiy V, Gonzalez FGR, Weber UD, Wolf S, Robinson GW, Zhou X, Wu G, Finkelstein D, Liu Y, Cavalli FMG, Luu B, Ramaswamy V, Wu X, Koster J, Ryzhova M, Cho YJ, Pomeroy SL, Herold-Mende C, Schuhmann M, Ebinger M, Liau LM, Mora J, McLendon RE, Jabado N, Kumabe T, Chuah E, Ma Y, Moore RA, Mungall AJ, Mungall KL, Thiessen N, Tse K, Wong T, Jones SJM, Witt O, Milde T, Von Deimling A, Capper D, Korshunov A, Yaspo ML, Kriwacki R, Gajjar A, Zhang J, Beroukhim R, Fraenkel E, Korbel JO, Brors B, Schlesner M, Eils R, Marra MA, Pfister SM, Taylor MD, Lichter P. The whole-genome landscape of medulloblastoma subtypes. Nature 2017; 547:311-317. [PMID: 28726821 PMCID: PMC5905700 DOI: 10.1038/nature22973] [Citation(s) in RCA: 667] [Impact Index Per Article: 95.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 05/10/2017] [Indexed: 12/14/2022]
Abstract
Current therapies for medulloblastoma, a highly malignant childhood brain tumour, impose debilitating effects on the developing child, and highlight the need for molecularly targeted treatments with reduced toxicity. Previous studies have been unable to identify the full spectrum of driver genes and molecular processes that operate in medulloblastoma subgroups. Here we analyse the somatic landscape across 491 sequenced medulloblastoma samples and the molecular heterogeneity among 1,256 epigenetically analysed cases, and identify subgroup-specific driver alterations that include previously undiscovered actionable targets. Driver mutations were confidently assigned to most patients belonging to Group 3 and Group 4 medulloblastoma subgroups, greatly enhancing previous knowledge. New molecular subtypes were differentially enriched for specific driver events, including hotspot in-frame insertions that target KBTBD4 and ‘enhancer hijacking’ events that activate PRDM6. Thus, the application of integrative genomics to an extensive cohort of clinical samples derived from a single childhood cancer entity revealed a series of cancer genes and biologically relevant subtype diversity that represent attractive therapeutic targets for the treatment of patients with medulloblastoma. Genomic analysis of 491 medulloblastoma samples, including methylation profiling of 1,256 cases, effectively assigns candidate drivers to most tumours across all molecular subgroups. Medulloblastomas are highly malignant brain tumours that develop during childhood. Paul Northcott and colleagues analysed the whole-genome sequences of 491 medulloblastomas in order to characterize the genomic landscape across tumours and identify new drivers and mutational signatures. Their integrative genomic analyses, including methylation profiling of 1,256 medulloblastomas, identifies subgroup-specific driver mutations and suggests additional tumour subtypes. The authors assign driver mutations to a high proportion of the less well characterized Group 3 and Group 4, which together contribute to more than 60% of all medulloblastomas.
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Affiliation(s)
- Paul A Northcott
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Ivo Buchhalter
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany
| | - A Sorana Morrissy
- Developmental &Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario
| | - Volker Hovestadt
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Joachim Weischenfeldt
- Biotech Research &Innovation Centre (BRIC), Copenhagen University and Finsen Laboratory, Rigshospitalet, Denmark
| | - Tobias Ehrenberger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Susanne Gröbner
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Maia Segura-Wang
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Thomas Zichner
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Vasilisa A Rudneva
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Hans-Jörg Warnatz
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | - Nikos Sidiropoulos
- Biotech Research &Innovation Centre (BRIC), Copenhagen University and Finsen Laboratory, Rigshospitalet, Denmark
| | - Aaron H Phillips
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | | | - Kortine Kleinheinz
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sebastian M Waszak
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Serap Erkek
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - David T W Jones
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Barbara C Worst
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Marcel Kool
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Marc Zapatka
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Natalie Jäger
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lukas Chavez
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Barbara Hutter
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthias Bieg
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Heidelberg Center for Personalized Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nagarajan Paramasivam
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Michael Heinold
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany
| | - Zuguang Gu
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Heidelberg Center for Personalized Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Naveed Ishaque
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Heidelberg Center for Personalized Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christina Jäger-Schmidt
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Charles D Imbusch
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alke Jugold
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Hübschmann
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany.,Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Thomas Risch
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | | | | | - Ursula D Weber
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stephan Wolf
- Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Giles W Robinson
- Department of Oncology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Xin Zhou
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Gang Wu
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - David Finkelstein
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Yanling Liu
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Florence M G Cavalli
- Developmental &Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario
| | - Betty Luu
- Developmental &Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario
| | - Vijay Ramaswamy
- Developmental &Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario
| | - Xiaochong Wu
- Developmental &Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario
| | - Jan Koster
- Department of Oncogenomics, Amsterdam Medical Center, Amsterdam, Netherlands
| | - Marina Ryzhova
- Department of Neuropathology, NN Burdenko Neurosurgical Institute, Moscow, Russia
| | - Yoon-Jae Cho
- Department of Pediatrics, Papé Family Pediatric Research Institute, Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon, USA
| | - Scott L Pomeroy
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Christel Herold-Mende
- Department of Neurosurgery, University Clinic, Heidelberg University, Heidelberg Hospital, Germany
| | - Martin Schuhmann
- Department of Neurosurgery, University Hospital Tübingen, Tübingen, Germany
| | - Martin Ebinger
- Department of Hematology and Oncology, Children's University Hospital Tübingen, Tübingen, Germany
| | - Linda M Liau
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Jaume Mora
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Roger E McLendon
- Department of Pathology, Duke University, Durham, North County, USA
| | - Nada Jabado
- Department of Pediatrics, McGill University, Montreal, Quebec, Canada
| | - Toshihiro Kumabe
- Department of Neurosurgery, Kitasato University School of Medicine, Sagamihara, Japan
| | - Eric Chuah
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Yussanne Ma
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Richard A Moore
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Andrew J Mungall
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Karen L Mungall
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Nina Thiessen
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Kane Tse
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Tina Wong
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Steven J M Jones
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Olaf Witt
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Till Milde
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Andreas Von Deimling
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - David Capper
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Andrey Korshunov
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Marie-Laure Yaspo
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | - Richard Kriwacki
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Amar Gajjar
- Department of Oncology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jinghui Zhang
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Rameen Beroukhim
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Ernest Fraenkel
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jan O Korbel
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Benedikt Brors
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Matthias Schlesner
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roland Eils
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Marco A Marra
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Michael D Taylor
- Developmental &Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario.,Division of Neurosurgery, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
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2
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Alioto TS, Buchhalter I, Derdak S, Hutter B, Eldridge MD, Hovig E, Heisler LE, Beck TA, Simpson JT, Tonon L, Sertier AS, Patch AM, Jäger N, Ginsbach P, Drews R, Paramasivam N, Kabbe R, Chotewutmontri S, Diessl N, Previti C, Schmidt S, Brors B, Feuerbach L, Heinold M, Gröbner S, Korshunov A, Tarpey PS, Butler AP, Hinton J, Jones D, Menzies A, Raine K, Shepherd R, Stebbings L, Teague JW, Ribeca P, Giner FC, Beltran S, Raineri E, Dabad M, Heath SC, Gut M, Denroche RE, Harding NJ, Yamaguchi TN, Fujimoto A, Nakagawa H, Quesada V, Valdés-Mas R, Nakken S, Vodák D, Bower L, Lynch AG, Anderson CL, Waddell N, Pearson JV, Grimmond SM, Peto M, Spellman P, He M, Kandoth C, Lee S, Zhang J, Létourneau L, Ma S, Seth S, Torrents D, Xi L, Wheeler DA, López-Otín C, Campo E, Campbell PJ, Boutros PC, Puente XS, Gerhard DS, Pfister SM, McPherson JD, Hudson TJ, Schlesner M, Lichter P, Eils R, Jones DTW, Gut IG. A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing. Nat Commun 2015; 6:10001. [PMID: 26647970 PMCID: PMC4682041 DOI: 10.1038/ncomms10001] [Citation(s) in RCA: 202] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/23/2015] [Indexed: 12/13/2022] Open
Abstract
As whole-genome sequencing for cancer genome analysis becomes a clinical tool, a full understanding of the variables affecting sequencing analysis output is required. Here using tumour-normal sample pairs from two different types of cancer, chronic lymphocytic leukaemia and medulloblastoma, we conduct a benchmarking exercise within the context of the International Cancer Genome Consortium. We compare sequencing methods, analysis pipelines and validation methods. We show that using PCR-free methods and increasing sequencing depth to ∼ 100 × shows benefits, as long as the tumour:control coverage ratio remains balanced. We observe widely varying mutation call rates and low concordance among analysis pipelines, reflecting the artefact-prone nature of the raw data and lack of standards for dealing with the artefacts. However, we show that, using the benchmark mutation set we have created, many issues are in fact easy to remedy and have an immediate positive impact on mutation detection accuracy.
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Affiliation(s)
- Tyler S. Alioto
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Ivo Buchhalter
- Division of Theoretical Bioinformatics, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg 69120, Germany
- Division of Applied Bioinformatics, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg 69120, Germany
| | - Sophia Derdak
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Barbara Hutter
- Division of Applied Bioinformatics, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg 69120, Germany
| | - Matthew D. Eldridge
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway
- Department of Informatics, University of Oslo, 0373 Oslo, Norway
| | - Lawrence E. Heisler
- Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3
| | - Timothy A. Beck
- Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3
| | - Jared T. Simpson
- Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3
| | - Laurie Tonon
- Synergie Lyon Cancer Foundation, Centre Léon Bérard, Cheney C, 28 rue Laennec, Lyon 69373, France
| | - Anne-Sophie Sertier
- Synergie Lyon Cancer Foundation, Centre Léon Bérard, Cheney C, 28 rue Laennec, Lyon 69373, France
| | - Ann-Marie Patch
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Natalie Jäger
- Division of Theoretical Bioinformatics, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg 69120, Germany
- Department of Genetics, Stanford University, Mail Stop-5120, Stanford, California 94305-5120, USA
| | - Philip Ginsbach
- Division of Theoretical Bioinformatics, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg 69120, Germany
| | - Ruben Drews
- Division of Theoretical Bioinformatics, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg 69120, Germany
| | - Nagarajan Paramasivam
- Division of Theoretical Bioinformatics, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg 69120, Germany
| | - Rolf Kabbe
- Division of Theoretical Bioinformatics, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg 69120, Germany
| | - Sasithorn Chotewutmontri
- Genome and Proteome Core Facility, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg, 69120 Germany
| | - Nicolle Diessl
- Genome and Proteome Core Facility, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg, 69120 Germany
| | - Christopher Previti
- Genome and Proteome Core Facility, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg, 69120 Germany
| | - Sabine Schmidt
- Genome and Proteome Core Facility, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg, 69120 Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg 69120, Germany
| | - Lars Feuerbach
- Division of Applied Bioinformatics, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg 69120, Germany
| | - Michael Heinold
- Division of Applied Bioinformatics, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg 69120, Germany
| | - Susanne Gröbner
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Im Neuenheimer Feld 430, Heidelberg 69120, Germany
| | - Andrey Korshunov
- Department of Neuropathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, Heidelberg 69120, Germany
| | | | - Adam P. Butler
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Jonathan Hinton
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - David Jones
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Andrew Menzies
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Keiran Raine
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Rebecca Shepherd
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Lucy Stebbings
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Jon W. Teague
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Paolo Ribeca
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Francesc Castro Giner
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Sergi Beltran
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Emanuele Raineri
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Marc Dabad
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Simon C. Heath
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Robert E. Denroche
- Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3
| | - Nicholas J. Harding
- Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3
| | - Takafumi N. Yamaguchi
- Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3
| | - Akihiro Fujimoto
- RIKEN Center for Integrative Medical Sciences, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Hidewaki Nakagawa
- RIKEN Center for Integrative Medical Sciences, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Víctor Quesada
- Universidad de Oviedo—IUOPA, C/Fernando Bongera s/n, 33006 Oviedo, Spain
| | - Rafael Valdés-Mas
- Universidad de Oviedo—IUOPA, C/Fernando Bongera s/n, 33006 Oviedo, Spain
| | - Sigve Nakken
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway
| | - Daniel Vodák
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway
- The Bioinformatics Core Facility, Institute for Cancer Genetics and Informatics, Oslo University Hospital, 0310 Oslo, Norway
| | - Lawrence Bower
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Andrew G. Lynch
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Charlotte L. Anderson
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Victorian Life Sciences Computation Initiative, The University of Melbourne, Melbourne, Victoria 3053, Australia
| | - Nicola Waddell
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - John V. Pearson
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Sean M. Grimmond
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
- WolfsonWohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland G61 1QH, UK
| | - Myron Peto
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239-3098, USA
| | - Paul Spellman
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239-3098, USA
| | | | - Cyriac Kandoth
- The Genome Institute, Washington University, St Louis, Missouri 63108, USA
| | - Semin Lee
- Harvard Medical School, Boston, Massachusetts 02115, USA
| | - John Zhang
- Harvard Medical School, Boston, Massachusetts 02115, USA
- MD Anderson Cancer Center, Houston, Texas 77030, USA
| | | | - Singer Ma
- Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA
| | - Sahil Seth
- MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - David Torrents
- IRB-BSC Joint Research Program on Computational Biology, Barcelona Supercomputing Center, 08034 Barcelona, Spain
| | - Liu Xi
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - David A. Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Carlos López-Otín
- Universidad de Oviedo—IUOPA, C/Fernando Bongera s/n, 33006 Oviedo, Spain
| | - Elías Campo
- Hematopathology Unit, Department of Pathology, Hospital Clinic, University of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer, 08036 Barcelona, Spain
| | | | - Paul C. Boutros
- Synergie Lyon Cancer Foundation, Centre Léon Bérard, Cheney C, 28 rue Laennec, Lyon 69373, France
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada M5G 1L7
| | - Xose S. Puente
- Universidad de Oviedo—IUOPA, C/Fernando Bongera s/n, 33006 Oviedo, Spain
| | - Daniela S. Gerhard
- National Cancer Institute, Office of Cancer Genomics, 31 Center Drive, 10A07, Bethesda, Maryland 20892-2580, USA
| | - Stefan M. Pfister
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Im Neuenheimer Feld 430, Heidelberg 69120, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany
| | - John D. McPherson
- Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada M5G 1L7
| | - Thomas J. Hudson
- Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada M5G 1L7
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Matthias Schlesner
- Division of Theoretical Bioinformatics, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg 69120, Germany
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120,Germany
- Heidelberg Center for Personalised Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roland Eils
- Division of Theoretical Bioinformatics, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg 69120, Germany
- Heidelberg Center for Personalised Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Heidelberg 69120, Germany
- Bioquant Center, University of Heidelberg, Im Neuenheimer Feld 267, Heidelberg 69120, Germany
| | - David T. W. Jones
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany
| | - Ivo G. Gut
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
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