Large-Scale Uniform Analysis of Cancer Whole Genomes in Multiple Computing Environments

Autor: Tijanic N, Solomon Shorser, Rosenberg Mw, Mijalkovic S, Byrne Nj, André Kahles, Rolf Kabbe, Larsson Omberg, Jules Kerssemakers, Olivier Harismendy, Romina Royo, Michael Heinold, Francis Ouellette B, Jonas Demeulemeester, Zhao Chen, Satoru Miyano, Peter J. Campbell, Short C, Ocana D, Oliver Hofmann, Raine Km, April E. Williams, Hong Jh, Mihaiescu Gl, Adam Butler, Denis Yuen, Jongsun Jung, Sergei Yakneen, Kovacevic M, Carolyn M. Hutter, Miyoshi N, Vicente D, Hidewaki Nakagawa, Steven Newhouse, Manuel Prinz, Andy Cafferkey, Johannes Werner, Yong Ho Kim, Nicholson J, Esther Rheinbay, Matthias Schlesner, David Torrents, Ivkovic S, Sung-Hoon Cho, Joachim Weischenfeldt, Lazic Am, Jeon S, Thomas J. Hudson, Julian M. Hess, Fayzullaev N, Nahal Hk, Gad Getz, Peter Van Loo, Dimitri Livitz, Perry, Ivo Buchhalter, Rodriguez Jb, Nagarajan Paramasivam, Michelle Dow, Young-Choon Woo, Ignaty Leshchiner, Paul Flicek, Robert L. Grossman, Jonathan Spring, Jeremiah Wala, Roland Eils, Grace Tiao, Kyle Ellrott, Angela N. Brooks, Heidi J. Sofia, Josep Lluís Gelpí, Barbara Hutter, Francesco Favero, Brian O'Connor, Lucila Ohno-Machado, Peter Clapham, Nastic M, Choi W, De La Vega Fm, L. J. Dursi, Montserrat Puiggròs, Ohi K, Wei Jiao, Brandi N. Davis-Dusenbery, Qian Xiang, Adam J Struck, Gibson B, Ferretti, Claudiu Farcas, Koscher M, Koures A, Lincoln Stein, Keith A. Boroevich, Jan O. Korbel, Gordon Saksena, Radovic P, Christian Lawerenz, Alex Buchanan, Christina K. Yung, Adam Wright, Nuno A. Fonseca, Todd Pihl, Jae H. Kim, Zhining Wang, Boyce R, Miguel Vazquez, Jürgen Eils, Kim H, Junjun Zhang, Seiya Imoto, Kortine Kleinheinz, Daniel Huebschmann

The International Cancer Genome Consortium (ICGC)’s Pan-Cancer Analysis of Whole Genomes (PCAWG) project aimed to categorize somatic and germline variations in both coding and non-coding regions in over 2,800 cancer patients. To provide this datase

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c90d76ea28cb1ca5039f28a82651baec

Author Correction: Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition.

Autor: Rodriguez-Martin B; Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.; Biomedical Research Centre (CINBIO), University of Vigo, Vigo, Spain.; Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain., Alvarez EG; Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.; Biomedical Research Centre (CINBIO), University of Vigo, Vigo, Spain.; Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain., Baez-Ortega A; Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK., Zamora J; Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.; Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.; The Biomedical Research Centre (CINBIO), Universidade de Vigo, Vigo, Spain.; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK., Supek F; Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.; Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain., Demeulemeester J; The Francis Crick Institute, London, UK.; Department of Human Genetics, University of Leuven, Leuven, Belgium., Santamarina M; Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.; Biomedical Research Centre (CINBIO), University of Vigo, Vigo, Spain.; Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain., Ju YS; Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.; Cancer Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Cambridge, UK., Temes J; Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.; Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain., Garcia-Souto D; Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain., Detering H; Biomedical Research Centre (CINBIO), University of Vigo, Vigo, Spain.; Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain.; Galicia Sur Health Research Institute, Vigo, Spain., Li Y; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK., Rodriguez-Castro J; Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain., Dueso-Barroso A; Faculty of Science and Technology, University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain.; Barcelona Supercomputing Center (BSC), Barcelona, Spain., Bruzos AL; Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.; Biomedical Research Centre (CINBIO), University of Vigo, Vigo, Spain.; Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain., Dentro SC; The Francis Crick Institute, London, UK.; Experimental Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK.; Oxford Big Data Institute, University of Oxford, Oxford, UK., Blanco MG; DNA Repair and Genome Integrity, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.; Department of Biochemistry and Molecular Biology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain., Contino G; Medical Research Council (MRC) Cancer Unit, University of Cambridge, Cambridge, UK., Ardeljan D; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Baltimore, MD, USA., Tojo M; The Biomedical Research Centre (CINBIO), Universidade de Vigo, Vigo, Spain.; Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain., Roberts ND; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK., Zumalave S; Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.; Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain., Edwards PA; University of Cambridge, Cambridge, UK.; Li Ka Shing Centre, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK., Weischenfeldt J; European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.; Finsen Laboratory and Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.; Department of Urology, Charité Universitätsmedizin Berlin, Berlin, Germany., Puiggròs M; Barcelona Supercomputing Center (BSC), Barcelona, Spain., Chong Z; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.; Department of Genetics and Informatics Institute, University of Alabama at Birmingham (UAB) School of Medicine, Birmingham, AL, USA., Chen K; University of Texas MD Anderson Cancer Center, Houston, TX, USA., Lee EA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA., Wala JA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA.; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.; Harvard Medical School, Boston, MA, USA., Raine KM; Cancer Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Cambridge, UK., Butler A; Cancer Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Cambridge, UK., Waszak SM; European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany., Navarro FCP; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA.; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.; Department of Computer Science, Yale University, New Haven, CT, USA., Schumacher SE; The Broad Institute of Harvard and MIT, Cambridge, MA, USA.; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA., Monlong J; Department of Human Genetics, McGill University, Montreal, Québec, Canada., Maura F; Cancer Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Cambridge, UK.; Department of Oncology and Onco-Hematology, University of Milan, Milan, Italy.; Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy., Bolli N; Department of Oncology and Onco-Hematology, University of Milan, Milan, Italy.; Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy., Bourque G; Canadian Center for Computational Genomics, McGill University, Montreal, Quebec, Canada., Gerstein M; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA.; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.; Department of Computer Science, Yale University, New Haven, CT, USA., Park PJ; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.; Ludwig Center at Harvard, Boston, MA, USA., Wedge DC; Cancer Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Cambridge, UK.; Experimental Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK.; Oxford NIHR Biomedical Research Centre, Oxford, UK., Beroukhim R; The Broad Institute of Harvard and MIT, Cambridge, MA, USA.; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.; Harvard Medical School, Boston, MA, USA., Torrents D; Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.; Barcelona Supercomputing Center (BSC), Barcelona, Spain., Korbel JO; European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK., Martincorena I; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK., Fitzgerald RC; Medical Research Council (MRC) Cancer Unit, University of Cambridge, Cambridge, UK., Van Loo P; The Francis Crick Institute, London, UK.; Department of Human Genetics, University of Leuven, Leuven, Belgium., Kazazian HH; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Baltimore, MD, USA., Burns KH; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Baltimore, MD, USA.; McKusick-Nathans Institute of Genetic Medicine, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University School of Medicine, Baltimore, MD, USA., Campbell PJ; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK. pc8@sanger.ac.uk.; Department of Haematology, University of Cambridge, Cambridge, UK. pc8@sanger.ac.uk., Tubio JMC; Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain. jose.mc.tubio@usc.es.; Biomedical Research Centre (CINBIO), University of Vigo, Vigo, Spain. jose.mc.tubio@usc.es.; Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain. jose.mc.tubio@usc.es.; Cancer Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Cambridge, UK. jose.mc.tubio@usc.es.

Publikováno v: Nature genetics [Nat Genet] 2023 Jun; Vol. 55 (6), pp. 1080.

Framework for quality assessment of whole genome cancer sequences.

Autor: Whalley JP; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Carrer Baldiri i Reixac 4, 08028, Barcelona, Spain.; Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK., Buchhalter I; Division of Theoretical Bioinformatics (B080), German Cancer Research Centre (DKFZ), Heidelberg, Germany.; Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany.; Omics IT and Data Management Core Facility (W610), German Cancer Research Center (DKFZ), Heidelberg, Germany.; Division of Applied Bioinformatics (G200), Cancer Research Centre (DKFZ), Heidelberg, Germany., Rheinbay E; Broad Institute of Harvard and MIT, Cambridge, MA, USA.; Massachusetts General Hospital Cancer Center and Department of Pathology, Boston, MA, USA., Raine KM; Wellcome Sanger Institute, Hinxton, UK., Stobbe MD; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Carrer Baldiri i Reixac 4, 08028, Barcelona, Spain., Kleinheinz K; Division of Theoretical Bioinformatics (B080), German Cancer Research Centre (DKFZ), Heidelberg, Germany., Werner J; Division of Theoretical Bioinformatics (B080), German Cancer Research Centre (DKFZ), Heidelberg, Germany.; Department of Biological Oceanography, Leibniz Institute of Baltic Sea Research, Seestraße 15, Rostock, Germany., Beltran S; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Carrer Baldiri i Reixac 4, 08028, Barcelona, Spain., Gut M; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Carrer Baldiri i Reixac 4, 08028, Barcelona, Spain., Hübschmann D; Division of Theoretical Bioinformatics (B080), German Cancer Research Centre (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 Immunology, Hematology and Oncology, University Hospital Heidelberg, Heidelberg, Germany.; Computational Oncology, Molecular Diagnostics Program, National Center for Tumor diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany.; Heidelberg Insititute for Stem cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany., Hutter B; Division of Applied Bioinformatics (G200), Cancer Research Centre (DKFZ), Heidelberg, Germany.; Computational Oncology, Molecular Diagnostics Program, National Center for Tumor diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany., Livitz D; Broad Institute of Harvard and MIT, Cambridge, MA, USA., Perry MD; Department of Radiation Oncology, University of California, San Francisco, CA, USA., Rosenberg M; Broad Institute of Harvard and MIT, Cambridge, MA, USA.; Massachusetts General Hospital Cancer Center and Department of Pathology, Boston, MA, USA., Saksena G; Broad Institute of Harvard and MIT, Cambridge, MA, USA., Trotta JR; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Carrer Baldiri i Reixac 4, 08028, Barcelona, Spain., Eils R; Center for Digital Health, Berlin Institute of Health (BIH) and Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany.; Health Data Science Unit, Heidelberg University Hospital and BioQuant, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany., Gerhard DS; Office of Cancer Genomics, National Cancer Institute, US National Institutes of Health, Bethesda, MD, USA., Campbell PJ; Wellcome Sanger Institute, Hinxton, UK., Schlesner M; Division of Theoretical Bioinformatics (B080), German Cancer Research Centre (DKFZ), Heidelberg, Germany.; Bioinformatics and Omics Data Analytics (B240), German Cancer Research Centre (DKFZ), Heidelberg, Germany., Gut IG; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Carrer Baldiri i Reixac 4, 08028, Barcelona, Spain. ivo.gut@cnag.crg.eu.; Universitat Pompeu Fabra (UPF), Barcelona, Spain. ivo.gut@cnag.crg.eu.

Publikováno v: Nature communications [Nat Commun] 2020 Oct 07; Vol. 11 (1), pp. 5040. Date of Electronic Publication: 2020 Oct 07.

Universal Patterns of Selection in Cancer and Somatic Tissues.

Autor: Martincorena I, Raine KM, Gerstung M, Dawson KJ, Haase K, Van Loo P, Davies H, Stratton MR, Campbell PJ

Publikováno v: Cell [Cell] 2018 Jun 14; Vol. 173 (7), pp. 1823.

cgpCaVEManWrapper: Simple Execution of CaVEMan in Order to Detect Somatic Single Nucleotide Variants in NGS Data.

Autor: Jones D; Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge, United Kingdom., Raine KM; Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge, United Kingdom., Davies H; Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge, United Kingdom., Tarpey PS; Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge, United Kingdom., Butler AP; Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge, United Kingdom., Teague JW; Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge, United Kingdom., Nik-Zainal S; Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge, United Kingdom., Campbell PJ; Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge, United Kingdom.

Publikováno v: Current protocols in bioinformatics [Curr Protoc Bioinformatics] 2016 Dec 08; Vol. 56, pp. 15.10.1-15.10.18. Date of Electronic Publication: 2016 Dec 08.