ArticleNature genetics2018
Integrative detection and analysis of structural variation in cancer genomes.
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Article in Nature genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 232 papers.
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232citing papers in PubMed
24.9field-weighted citation impact, top 1% of its field
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232 citing papers in PubMed, 489 citations in OpenAlex.
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172 more citing papers are in PubMed but not listed here.
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Authors and funding
37 authors at 12 institutions in 3 countries.
Jesse R DixonSalk Institute for Biological Studies, La Jolla, CA, USA. jedixon@salk.edu.ORCID http://orcid.org/0000-0002-6273-2181
Jie XuDepartment of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA, USA.
Vishnu DileepDepartment of Biological Science, Florida State University, Tallahassee, FL, USA.
Ye ZhanProgram in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.ORCID http://orcid.org/0000-0001-9280-1718
Fan SongBioinformatics and Genomics Program, The Pennsylvania State University, University Park, State College, PA, USA.
Victoria T LeSalk Institute for Biological Studies, La Jolla, CA, USA.
Galip Gürkan YardımcıDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.
Abhijit ChakrabortyLa Jolla Institute for Allergy and Immunology, La Jolla, CA, USA.
Darrin V BannDivision of Otolaryngology, Head & Neck Surgery, Milton S. Hershey Medical Center, Hershey, PA, USA.
Yanli WangBioinformatics and Genomics Program, The Pennsylvania State University, University Park, State College, PA, USA.
Royden ClarkPenn State College of Medicine, Informatics and Technology, Hershey, PA, USA.
Lijun ZhangDepartment of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA, USA.
Hongbo YangDepartment of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA, USA.
Tingting LiuDepartment of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA, USA.
Sriranga IyyankiDepartment of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA, USA.
Lin AnBioinformatics and Genomics Program, The Pennsylvania State University, University Park, State College, PA, USA.
Christopher PoolDivision of Otolaryngology, Head & Neck Surgery, Milton S. Hershey Medical Center, Hershey, PA, USA.
Takayo SasakiDepartment of Biological Science, Florida State University, Tallahassee, FL, USA.
Juan Carlos Rivera-MuliaDepartment of Biological Science, Florida State University, Tallahassee, FL, USA.
Hakan OzadamProgram in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.
Bryan R LajoieProgram in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.
Rajinder KaulAltius institute for Biomedical Sciences, Seattle, WA, USA.
Michael BuckleyAltius institute for Biomedical Sciences, Seattle, WA, USA.ORCID http://orcid.org/0000-0002-7529-6112
Kristen LeeAltius institute for Biomedical Sciences, Seattle, WA, USA.
Morgan DiegelAltius institute for Biomedical Sciences, Seattle, WA, USA.
Dubravka PezicResearch Department of Cancer Biology, Cancer Institute, University College London, London, UK.
Christina ErnstCancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.ORCID http://orcid.org/0000-0002-3569-2209
Suzana HadjurResearch Department of Cancer Biology, Cancer Institute, University College London, London, UK.
Duncan T OdomCancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.ORCID http://orcid.org/0000-0001-6201-5599
John A StamatoyannopoulosAltius institute for Biomedical Sciences, Seattle, WA, USA.
James R BroachDepartment of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA, USA.
Ross C HardisonCenter for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA, USA.
Ferhat AyLa Jolla Institute for Allergy and Immunology, La Jolla, CA, USA. ferhatay@lji.org.ORCID http://orcid.org/0000-0002-0708-6914
William Stafford NobleDepartment of Genome Sciences, University of Washington, Seattle, WA, USA. william-noble@uw.edu.ORCID http://orcid.org/0000-0001-7283-4715
Job DekkerProgram in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA. job.dekker@umassmed.edu.ORCID http://orcid.org/0000-0001-5631-0698
David M GilbertDepartment of Biological Science, Florida State University, Tallahassee, FL, USA. gilbert@bio.fsu.edu.ORCID http://orcid.org/0000-0001-8087-9737
Feng YueDepartment of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA, USA. fyue@hmc.psu.edu.ORCID http://orcid.org/0000-0002-7954-5462
Pennsylvania State University · USAltius Institute for Biomedical Sciences · USFlorida State University · USPenn State Milton S. Hershey Medical Center · USUniversity of Massachusetts Chan Medical School · USLa Jolla Institute for Immunology · USSalk Institute for Biological Studies · USUniversity College London · GBUniversity of Washington · USGerman Cancer Research Center · DEHoward Hughes Medical Institute · USUniversity of Cambridge · GB
Funding
UNDERSTANDING MECHANISMS OF hESC SELF-RENEWAL AND CELL FATE COMMITMENTP01GM085354 · NIGMS · UNIVERSITY OF GEORGIA · PI CORCES, VICTOR G. · 2008 to 2018
$18.3MStructural Annotation of the Human GenomeR01HG003143 · NHGRI · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI Job Dekker · 2003 to 2026
$15.4MA Comprehensive catalog of human DNasel hypersensitive sitesU54HG004592 · NHGRI · UNIVERSITY OF WASHINGTON · PI STAMATOYANNOPOULOS, JOHN A · 2007 to 2011
$15.0MCenter for 3D Structure and Physics of the GenomeU54DK107980 · NIDDK · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI DEKKER, JOB, MIRNY, LEONID A · 2015 to 2019
$14.9MEDAC: ENCODE Data Analysis CenterU41HG007000 · NHGRI · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI WENG, ZHIPING · 2012 to 2016
$9.8MMapping Technology DevelopmentU54DK107965 · NIDDK · UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN · PI BELMONT, ANDREW STEVEN · 2015 to 2019
$8.6MVISION: ValIdated Systematic IntegratiON of epigenomic dataR24DK106766 · NIDDK · PENNSYLVANIA STATE UNIVERSITY, THE · PI BLOBEL, GERD A, BODINE, DAVID M. · 2016 to 2020
$6.2MGenome Plasticity during ES Cell Differentiation to Neural LineagesR01GM083337 · NIGMS · SAN DIEGO BIOMEDICAL RESEARCH INSTITUTE · PI David M Gilbert · 2007 to 2026
$6.1MImpact of genetic variants on gene regulation and 3D genome organization in human diseasesR35GM124820 · NIGMS · PENNSYLVANIA STATE UNIV HERSHEY MED CTR · PI Feng Yue · 2017 to 2026
$4.0MMechanisms of formation of 3D genome structuresDP5OD023071 · OD · SALK INSTITUTE FOR BIOLOGICAL STUDIES · PI DIXON, JESSE R · 2016 to 2020
$2.4MVisualization, modeling and validation of chromatin interaction dataR01HG009906 · NHGRI · PENNSYLVANIA STATE UNIV HERSHEY MED CTR · PI YUE, FENG · 2018 to 2022
$2.0MThe WashU 4DN Network Data Coordination and Integration CenterU01CA200060 · NCI · WASHINGTON UNIVERSITY · PI WANG, TING · 2015 to 2019
$1.9MCancer Research UK 20412Cancer Research UK 22398European Research Council 615584NCI NIH HHS U01 CA200060NHGRI NIH HHS R01 HG003143NHGRI NIH HHS R01 HG009906NHGRI NIH HHS U41 HG007000NHGRI NIH HHS U54 HG004592NIDDK NIH HHS R24 DK106766NIDDK NIH HHS U54 DK107965NIDDK NIH HHS U54 DK107980NIGMS NIH HHS P01 GM085354NIGMS NIH HHS R01 GM083337NIGMS NIH HHS R35 GM124820NIH HHS DP5 OD023071Wellcome Trust 202878/Z/16/Z
Abstract
Structural variants (SVs) can contribute to oncogenesis through a variety of mechanisms. Despite their importance, the identification of SVs in cancer genomes remains challenging. Here, we present a framework that integrates optical mapping, high-throughput chromosome conformation capture (Hi-C), and whole-genome sequencing to systematically detect SVs in a variety of normal or cancer samples and cell lines. We identify the unique strengths of each method and demonstrate that only integrative approaches can comprehensively identify SVs in the genome. By combining Hi-C and optical mapping, we resolve complex SVs and phase multiple SV events to a single haplotype. Furthermore, we observe widespread structural variation events affecting the functions of noncoding sequences, including the deletion of distal regulatory sequences, alteration of DNA replication timing, and the creation of novel three-dimensional chromatin structural domains. Our results indicate that noncoding SVs may be underappreciated mutational drivers in cancer genomes.
Indexed as
Genome, HumanGenomic Structural VariationA549 CellsCell Line, TumorChromosome MappingDNA, NeoplasmGenes, NeoplasmGenetic VariationHigh-Throughput Nucleotide SequencingHumansK562 CellsLinkage DisequilibriumNeoplasmsSequence Analysis, DNASystems BiologySystems IntegrationDNA, Neoplasm
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