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Cited by 719Cancer Genomics and DiagnosticsGenomic variations and chromosomal abnormalitiesChromatin Remodeling and Cancer

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

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Cortés-Ciriano, Isidro, Lee, Jake June-Koo, Xi, Ruibin, Jain, Dhawal, Jung, Youngsook L., Yang, Lixing, Gordenin, Dmitry, Klimczak, Leszek J. +1400 more·2020·Nature Genetics
DOI 10.1038/s41588-019-0576-7PMC PMC7058534

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Abstract

Chromothripsis is a mutational phenomenon characterized by massive, clustered genomic rearrangements that occurs in cancer and other diseases. Recent studies in selected cancer types have suggested that chromothripsis may be more common than initially inferred from low-resolution copy-number data. Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), we analyze patterns of chromothripsis across 2,658 tumors from 38 cancer types using whole-genome sequencing data. We find that chromothripsis events are pervasive across cancers, with a frequency of more than 50% in several cancer types. Whereas canonical chromothripsis profiles display oscillations between two copy-number states, a considerable fraction of events involve multiple chromosomes and additional structural alterations. In addition to non-homologous end joining, we detect signatures of replication-associated processes and templated insertions. Chromothripsis contributes to oncogene amplification and to inactivation of genes such as mismatch-repair-related genes. These findings show that chromothripsis is a major process that drives genome evolution in human cancer.

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Crossref · 10.1038/s41588-019-0576-7

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  • The genomic landscape of osteosarcoma tumours is usually dominated by widespread structural rearrangements, suggesting that several mutational mechanisms, including chromothripsis, chromoplexy, kataegis and other structure-altering mechanisms, are involved.

    “The genomic landscape of osteosarcoma tumours is usually dominated by widespread structural rearrangements, suggesting that several different mutational mechanisms, including chromothripsis, chromoplexy, kataegis and other structure-altering mechanisms, are involved 32,33,34 .”

    From Osteosarcoma (2022) · cites this paper as [32]

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Cortés-Ciriano, I., Lee, J. J.-K., Xi, R., Jain, D., Jung, Y. L., Yang, L., Gordenin, D., Klimczak, L. J., Zhang, C.-Z., Pellman, D. S., PCAWG Structural Variation Working Group, Akdemir, K. C., Alvarez, E. G., Baez-Ortega, A., Beroukhim, R., Boutros, P. C., Bowtell, D. D. L., Brors, B., Burns, K. H., Campbell, P. J., Chan, K., Chen, K., Cortés-Ciriano, I., Dueso-Barroso, A., Dunford, A. J., Edwards, P. A., Estivill, X., Etemadmoghadam, D., Feuerbach, L., Fink, J. L., Frenkel-Morgenstern, M., Garsed, D. W., Gerstein, M., Gordenin, D. A., Haan, D., Haber, J. E., Hess, J. M., Hutter, B., Imielinski, M., Jones, D. T. W., Ju, Y. S., Kazanov, M. D., Klimczak, L. J., Koh, Y., Korbel, J. O., Kumar, K., Lee, E. A., Lee, J. J.-K., Li, Y., Lynch, A. G., Macintyre, G., Markowetz, F., Martincorena, I., Martinez-Fundichely, A., Miyano, S., Nakagawa, H., Navarro, F. C. P., Ossowski, S., Park, P. J., Pearson, J. V., Puiggròs, M., Rippe, K., Roberts, N. D., Roberts, S. A., Rodriguez-Martin, B., Schumacher, S. E., Scully, R., Shackleton, M., Sidiropoulos, N., Sieverling, L., Stewart, C., Torrents, D., Tubio, J. M. C., Villasante, I., Waddell, N., Wala, J. A., Weischenfeldt, J., Yang, L., Yao, X., Yoon, S.-S., Zamora, J., Zhang, C.-Z., Park, P. J., PCAWG Consortium, Aaltonen, L. A., Abascal, F., Abeshouse, A., Aburatani, H., Adams, D. J., Agrawal, N., Ahn, K. S., Ahn, S.-M., Aikata, H., Akbani, R., Akdemir, K. C., Al-Ahmadie, H., Al-Sedairy, S. T., Al-Shahrour, F., Alawi, M., Albert, M., Aldape, K., Alexandrov, L. B., Ally, A., Alsop, K., Alvarez, E. G., Amary, F., Amin, S. B., Aminou, B., Ammerpohl, O., Anderson, M. J., Ang, Y., Antonello, D., Anur, P., Aparicio, S., Appelbaum, E. L., Arai, Y., Aretz, A., Arihiro, K., Ariizumi, S.-I., Armenia, J., Arnould, L., Asa, S., Assenov, Y., Atwal, G., Aukema, S., Auman, J. T., Aure, M. R. R., Awadalla, P., Aymerich, M., Bader, G. D., Baez-Ortega, A., Bailey, M. H., Bailey, P. 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Affiliations
  • Peking University (CN)
  • Harvard University (US)
  • Howard Hughes Medical Institute (US)
  • The University of Texas MD Anderson Cancer Center (US)
  • University of Helsinki (FI)
  • The University of Melbourne (AU)
  • Memorial Sloan Kettering Cancer Center (US)
  • Research Center for Advanced Science and Technology, The University of Tokyo (JP)
  • Wellcome Sanger Institute (GB)
  • University of Chicago (US)
  • Keimyung University Dongsan Medical Center (KR)
  • Gachon University (KR)
  • Hiroshima University (JP)
  • Leibniz Institute of Virology (LIV) (DE)
  • Ontario Institute for Cancer Research (CA)
  • University of Cambridge (GB)
  • BC Cancer Agency (CA)
  • Royal National Orthopaedic Hospital (GB)
  • Universität Ulm (DE)
  • The University of Queensland (AU)
  • Salford Royal NHS Foundation Trust (GB)
  • University of Verona (IT)
  • Oregon Health & Science University (US)
  • Washington University in St. Louis (US)
  • National Cancer Centre Japan (JP)
  • Deutsches Zentrum für Luft- und Raumfahrt e. V. (DLR) (DE)
  • Tokyo Women's Medical University (JP)
  • Los Alamos National Laboratory (US)
  • University of North Carolina at Chapel Hill (US)
  • German Cancer Research Center (DE)
  • Oslo University Hospital (NO)
  • Consorci Institut D'Investigacions Biomediques August Pi I Sunyer (ES)
  • University of Toronto (CA)
  • University of Glasgow (GB)
  • Broad Institute (US)
  • University of Leeds (GB)
  • Gloucestershire Royal Hospital (GB)
  • European Bioinformatics Institute (GB)
  • University of Calgary (CA)
  • Johns Hopkins University (US)
  • Royal Stoke University Hospital (GB)
  • La Trobe University (AU)
  • Chinese Academy of Sciences (CN)
  • Genome Canada (CA)
  • Duke Medical Center (US)
  • Medizinische Hochschule Hannover (DE)
  • University of California San Diego (US)
  • Cedars-Sinai Medical Center (US)
  • Queen Mary University of London (GB)
  • Aarhus University (DK)
  • Instituto Carlos Slim de la Salud (MX)
  • Garvan Institute of Medical Research (AU)
  • Leipzig University (DE)
  • Massachusetts General Hospital (US)
  • National Institute of Biomedical Genomics (IN)
  • Duke-NUS Medical School (SG)
  • University of Southern California (US)
  • Heinrich Heine University Düsseldorf (DE)
  • RIKEN Center for Integrative Medical Sciences (JP)
  • Friedrich-Ebert-Krankenhaus (DE)
  • Yale University (US)
  • Universitat Pompeu Fabra (ES)
  • University of Oxford (GB)
  • Tampere University (FI)
  • Leeds Teaching Hospitals NHS Trust (GB)
  • Centre Léon Bérard (FR)
  • Fox Chase Cancer Center (US)
  • Centre international de recherche sur le cancer (FR)
  • University of East Anglia (GB)
  • Radboud University Nijmegen (NL)
  • Brigham and Women's Hospital (US)
  • The Netherlands Cancer Institute (NL)
  • University of Copenhagen (DK)
  • Universidade de Santiago de Compostela (ES)
  • Bundesministerium für Forschung, Technologie und Raumfahrt (DE)
  • The University of Sydney (AU)
  • Stanford Medicine (US)
  • University of California, San Francisco (US)
  • Royal Marsden NHS Foundation Trust (GB)
  • Institut Gustave Roussy (FR)
  • Institute of Cancer Research (GB)
  • U-M Rogel Cancer Center (US)
  • University of Bern (CH)
  • University of Pavia (IT)
  • University of Alabama at Birmingham (US)
  • University Health Network (CA)
  • Icahn School of Medicine at Mount Sinai (US)
  • University of Ottawa (CA)
  • Mayo Clinic (US)
  • National Institutes of Health (US)
  • Korea Advanced Institute of Science and Technology (KR)
  • Electronics and Telecommunications Research Institute (KR)
  • Institut National du Cancer (FR)
  • National Cancer Centre Singapore (SG)
  • University Hospital Schleswig-Holstein (DE)
  • University of Auckland (NZ)
  • Royal Children's Hospital (AU)
  • Vancouver Prostate Centre (CA)
  • Mount Sinai Hospital (CA)
  • Baylor College of Medicine (US)
  • University of California, Santa Cruz (US)
  • University of Cologne (DE)
  • International Genomics Consortium (US)
  • Barking, Havering And Redbridge University Hospitals NHS Trust (GB)
  • SIB Swiss Institute of Bioinformatics (CH)
  • University of Padua (IT)
  • University of Geneva (CH)
  • The Francis Crick Institute (GB)
  • National University of Singapore (SG)
  • Institut Jules Bordet (BE)
  • Princess Margaret Cancer Centre (CA)
  • Weill Cornell Medicine (US)
  • Shadyside Hospital (US)
  • Uppsala University (SE)
  • Hefei University of Technology (CN)
  • University of Antwerp (BE)
  • Simon Fraser University (CA)
  • University of Pennsylvania (US)
  • Wellcome Trust (GB)
  • Lund University (SE)
  • Heidelberg University (DE)
  • European Molecular Biology Laboratory (DE)
  • Icelandic Cancer Society (IS)
  • Xijing Hospital (CN)
  • Dana-Farber Cancer Institute (US)
  • Rigshospitalet (DK)
  • Fondazione IRCCS Istituto Neurologico Carlo Besta (IT)
  • Bioplatforms Australia (AU)
  • University College London (GB)
  • Erasmus MC (NL)
  • University of Liverpool (GB)
  • University of Florida Health (US)
  • Institute for Research in Biomedicine (ES)
  • The University of Tokyo (JP)
  • University of Milano-Bicocca (IT)
  • BGI Group (China) (CN)
  • Barcelona Supercomputing Center (ES)
  • The Jackson Laboratory for Genomic Medicine (US)
  • University of Würzburg (DE)
  • University of Miami (US)
  • St Thomas' Hospital (GB)
  • Osaka International Cancer Institute (JP)
  • Beatson West of Scotland Cancer Centre (GB)
  • Government of India (IN)
  • University of British Columbia (CA)
  • Barcelona Institute of Science and Technology (ES)
  • The University of Texas Health Science Center at Houston (US)
  • Goethe University Frankfurt (DE)
  • UC San Diego Health System (US)
  • Oxford Nanopore Technologies (United Kingdom) (GB)
  • Wakayama Medical University (JP)
  • Institute of Medical Science, The University of Tokyo (JP)
  • Children's Hospital of Philadelphia (US)
  • Hallym University (KR)
  • Hokkaido University (JP)
  • National Cancer Center Hospital (JP)
  • Leibniz Institute on Aging - Fritz Lipmann Institute (FLI) (DE)
  • University of Nebraska Medical Center (US)
  • Amsterdam UMC Location University of Amsterdam (NL)
  • Aarhus University Hospital (DK)
  • Cambridge University Hospitals NHS Foundation Trust (GB)
  • Hong Kong University of Science and Technology (HK)
  • Xi'an Jiaotong University (CN)
  • Charité – Universitätsmedizin Berlin (DE)
  • Edinburgh Royal Infirmary (GB)
  • Michael E. DeBakey VA Medical Center (US)
  • Seven Bridges Genomics (United States) (US)
  • Hanyang University (KR)
  • Glasgow Royal Infirmary (GB)
  • Asan Medical Center (KR)
  • University of Ljubljana (SI)
  • Endeavor Health (US)
  • QIMR Berghofer Medical Research Institute (AU)
  • McGill University and Génome Québec Innovation Centre (CA)
  • Boston Children's Hospital (US)
  • Institute of Genetics and Cancer (GB)
  • University of Zagreb (HR)
  • South Australia Pathology (AU)
  • National Cancer Center Research Institute (JP)
  • Skolkovo Institute of Science and Technology (RU)
  • Melanoma Institute Australia (AU)
  • Ewha Womans University (KR)
  • Christian-Albrechts-Universität zu Kiel (DE)
  • Seoul National University (KR)
  • University of Duisburg-Essen (DE)
  • King's College London (GB)
  • Van Andel Institute (US)
  • McGill University (CA)
  • Children's Medical Research Institute (AU)
  • Berlin Institute of Health at Charité - Universitätsmedizin Berlin (DE)
  • Institute of Biomedical Sciences, Academia Sinica (TW)
  • Max Planck Institute for Molecular Genetics (DE)
  • University of Oslo (NO)
  • Leidos Biomedical Research Inc. (United States) (US)
  • University of St Andrews (GB)
  • Institute for Systems Biology (US)
  • Australian National University (AU)
  • Max Delbrück Center (DE)
  • Duke University (US)
  • Henry Ford Hospital (US)
  • Bar-Ilan University (IL)
  • University Medical Center Hamburg-Eppendorf (DE)
  • Kyushu University (JP)
  • Heidelberg Academy of Sciences and Humanities (DE)
  • Genome Institute of Singapore (SG)
  • Institució Catalana de Recerca i Estudis Avançats (ES)
  • German Cancer Aid (DE)
  • Chinese University of Hong Kong (HK)
  • St. Jude Children's Research Hospital (US)
  • Carleton College (US)
  • Keio University (JP)
  • Sage Bionetworks (US)
  • Robert Bosch Hospital (DE)
  • Nottingham University Hospitals NHS Trust (GB)
  • NYU Langone Health (US)
  • Cleveland Clinic (US)
  • Christiana Care Health System (US)
  • SRA International (United States) (US)
  • Guy's Hospital (GB)
  • Macquarie University (AU)
  • Inserm (FR)
  • Spanish National Cancer Research Centre (ES)
  • Institutul Clinic Fundeni (RO)
  • Royal Surrey County Hospital (GB)
  • Ghent University (BE)
  • Ninewells Hospital (GB)
  • Medical College of Wisconsin (US)
  • Winship Cancer Institute (US)
  • Princeton University (US)
  • Vanderbilt University (US)
  • The Ohio State University Comprehensive Cancer Center – Arthur G. James Cancer Hospital and Richard J. Solove Research Institute (US)
  • Universitätsklinikum Gießen und Marburg (DE)
  • Institut Regional du Cancer de Montpellier (FR)
  • Norfolk and Norwich University Hospital (GB)
  • North Bristol NHS Trust (GB)
  • Tata Institute of Fundamental Research (IN)
  • National Institute of Environmental Health Sciences (US)
  • GZA Ziekenhuizen Campus Sint-Augustinus (BE)
  • Analytical Biological Services (United States) (US)
  • Tata Memorial Hospital (IN)
  • Cancer Research UK (GB)
  • University of Pittsburgh (US)
  • Japan Agency for Medical Research and Development (JP)
  • Korea University (KR)
  • Walter Reed National Military Medical Center (US)
  • University Hospitals Coventry and Warwickshire NHS Trust (GB)
  • Sankt-Antonius-Hospital Eschweiler (DE)
  • University of Iceland (IS)
  • Radboud University Medical Center (NL)
  • Singapore General Hospital (SG)
  • SingHealth (SG)
  • Universidade de Vigo (ES)
  • Istituto Tumori Bari (IT)
  • Commissariat à l'Énergie Atomique et aux Énergies Alternatives (FR)
  • Maastricht University (NL)
  • Lyon 1 Université (FR)
  • University of Göttingen (DE)
  • Tokyo Medical and Dental University (JP)
  • University Hospitals Birmingham NHS Foundation Trust (GB)
  • Queen's University Belfast (GB)
  • Tallinn University of Technology (EE)
  • John Radcliffe Hospital (GB)
  • Augusta University (US)
  • Wythenshawe Hospital (GB)
  • Centre for Human Genetics (GB)
  • Nationwide Children's Hospital (US)
  • Poznan University of Medical Sciences (PL)
  • MRC University of Glasgow Centre for Virus Research (GB)
  • Huazhong University of Science and Technology (CN)
  • Peking University Cancer Hospital (CN)
  • Buck Institute for Research on Aging (US)
  • First Affiliated Hospital of Xi'an Jiaotong University (CN)
  • National Center for Tumor Diseases (DE)
  • Epworth Hospital (AU)
  • Northwestern University (US)
ORCID
Venue
Nature Genetics
Publisher
Springer Science and Business Media LLC
Published
2020-02-05
Volume
52
Issue
3
Pages
331-341
ISSN
  • 1061-4036 (ISSN-L)
  • 1546-1718
DOI
10.1038/s41588-019-0576-7
PMC
PMC7058534
OpenAlex
W3005469082
Cited by
712
References
65
Citations by year
2026: 69 · 2025: 100 · 2024: 122 · 2023: 135 · 2022: 105 · 2021: 112 · 2020: 62 · 2019: 6 · 2018: 1
FWCI
36.00
Type
journal article
Language
en
Update notices
Open access
Licence
Locations
  • Nature Genetics (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Research Publications (Maastricht University) (publishedVersion, cc-by)
  • City Research Online (City University London) (acceptedVersion)
  • Informationszentrum Lebenswissenschaften (ZB MED) (submittedVersion, cc-by)
  • St Andrews Research Repository (St Andrews Research Repository) (submittedVersion, cc-by)
  • BOA (University of Milano-Bicocca) (submittedVersion, cc-by)
  • Dépôt institutionnel de l'Université libre de Bruxelles (Université Libre de Bruxelles) (submittedVersion, other-oa)
  • eScholarship (California Digital Library) (submittedVersion, cc-by)
  • Minerva Access (University of Melbourne) (submittedVersion, cc-by)
  • Lund University Publications (Lund University) (submittedVersion)
  • Rare & Special e-Zone (The Hong Kong University of Science and Technology) (submittedVersion)
  • Radboud Repository (Radboud University) (submittedVersion)
  • Padua Research Archive (University of Padova) (submittedVersion, cc-by)
Funders
  • Massachusetts General Hospital
  • Yale University
  • Princeton University
  • Brandeis University
  • Johns Hopkins University
  • University of Ottawa
  • Deutsches Krebsforschungszentrum
  • Francis Crick Institute (10202)
  • Sidra Medicine
  • Cancer Research UK (23924)
  • European Commission (703543, HORIZON2020)
  • Bar-Ilan University
  • University of Toronto
  • Peter MacCallum Cancer Centre
  • Barcelona Supercomputing Center
  • Universidade de Vigo
  • Korea Advanced Institute of Science and Technology
  • Skolkovo Institute of Science and Technology
  • Deutschen Konsortium für Translationale Krebsforschung
  • Universidade de Santiago de Compostela
  • Centro Singular de Investigación de Galicia
  • Nature
  • National Institutes of Health
  • University of California, Los Angeles
  • Weill Cornell Medical College
  • University of Texas MD Anderson Cancer Center
  • Ludwig Center at Harvard
  • Heidelberger Zentrum für Personalisierte Onkologie Deutsches Krebsforschungszentrum In Der Helmholtz-Gemeinschaft
  • Japan Society for the Promotion of Science (15H05912, 18H04049)
  • Institute for Molecular Bioscience, University Of Queensland
  • Cancer Research UK Cambridge Institute, University of Cambridge
  • National Cancer Institute (K22CA193848, R01CA095175, R01CA213404, R01CA217991, P30CA016672)
  • National Institute of General Medical Sciences (R35GM127029)
  • National Institute of Environmental Health Sciences (ZIAES103266)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
Keywords
chromothripsis, genome rearrangement, copy number alterations, cancer genome evolution, structural variants, non-homologous end joining, oncogene amplification
MeSH terms
Chromothripsis, Whole Genome Sequencing, Humans, Mutation, Neoplasms, Genome, Human, Evolution, Molecular, Genomics

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