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Accès ouvert déclaré 2020 article

Genomic basis for RNA alterations in cancer

425Citations signalées — pas une note de qualité
474Institutions déclarées
36Pays d’affiliation déclarés

Résumé fourni par la source

Abstract Transcript alterations often result from somatic changes in cancer genomes 1 . Various forms of RNA alterations have been described in cancer, including overexpression 2 , altered splicing 3 and gene fusions 4 ; however, it is difficult to attribute these to underlying genomic changes owing to heterogeneity among patients and tumour types, and the relatively small cohorts of patients for whom samples have been analysed by both transcriptome and whole-genome sequencing. Here we present, to our knowledge, the most comprehensive catalogue of cancer-associated gene alterations to date, obtained by characterizing tumour transcriptomes from 1,188 donors of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA) 5 . Using matched whole-genome sequencing data, we associated several categories of RNA alterations with germline and somatic DNA alterations, and identified probable genetic mechanisms. Somatic copy-number alterations were the major drivers of variations in total gene and allele-specific expression. We identified 649 associations of somatic single-nucleotide variants with gene expression in cis , of which 68.4% involved associations with flanking non-coding regions of the gene. We found 1,900 splicing alterations associated with somatic mutations, including the formation of exons within introns in proximity to Alu elements. In addition, 82% of gene fusions were associated with structural variants, including 75 of a new class, termed ‘bridged’ fusions, in which a third genomic location bridges two genes. We observed transcriptomic alteration signatures that differ between cancer types and have associations with variations in DNA mutational signatures. This compendium of RNA alterations in the genomic context provides a rich resource for identifying genes and mechanisms that are functionally implicated in cancer.

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Contrôle bibliographique ouvert

DOI retrouvé dans Crossref DOI retrouvé ; titre concordant.

Titre Crossref
Genomic basis for RNA alterations in cancer
Date Crossref
05/02/2020
Éditeur
Springer Science and Business Media LLC
Type
journal-article

Ce recoupement confirme des métadonnées liées au DOI. Il ne confirme ni la méthode ni les conclusions de l’étude et ne compte pas comme une seconde source scientifique indépendante.

Institutions déclarées

European Bioinformatics InstituteSIB Swiss Institute of BioinformaticsMemorial Sloan Kettering Cancer CenterCornell UniversityETH ZurichUniversity Hospital ZurichEuropean Molecular Biology LaboratoryNational University of SingaporeGenome Institute of SingaporeUniversidade do PortoPeking UniversityCenter for Life SciencesUniversity of TorontoPrincess Margaret Cancer CentreThe University of TokyoUniversity of California, Santa CruzBGI Group (China)China National GeneBankYale UniversityOntario Institute for Cancer ResearchUniversity of California, San FranciscoNational Institutes of HealthNational Cancer InstituteUniversity of GlasgowUniversity of North Carolina at Chapel HillMax Delbrück CenterUniversity College LondonKarolinska InstitutetBroad InstituteHarvard UniversityDana-Farber Cancer InstituteUniversität UlmKorea UniversityChristian-Albrechts-Universität zu KielDuke-NUS Medical SchoolSingHealthNational University Cancer Institute, SingaporeNational Heart Centre SingaporeBaylor College of MedicineThe University of Texas MD Anderson Cancer CenterQuantitative BioSciencesJackson LaboratoryThe Jackson Laboratory for Genomic MedicineInstitut National de Recherche pour l'Agriculture, l'Alimentation et l'EnvironnementBar-Ilan UniversityWeill Cornell MedicineAarhus UniversityAarhus University HospitalNational Cancer Centre SingaporeInstitute of Molecular and Cell BiologyJames S. McDonnell FoundationXi'an Jiaotong UniversityHeidelberg UniversityThe University of Texas Health Science Center at HoustonGerman Cancer Research CenterGerman Cancer SocietyDeutsches Konsortium für Translationale KrebsforschungUniversity of HelsinkiWellcome Sanger InstituteUniversity of ChicagoKeimyung University Dongsan Medical CenterKeimyung UniversityGachon University Gil Medical CenterHiroshima UniversityKing Faisal Specialist Hospital & Research CentreSpanish National Cancer Research CentreUniversität HamburgUniversity Medical Center Hamburg-EppendorfLeibniz Institute of Virology (LIV)Center for Cancer ResearchCanada's Michael Smith Genome Sciences CentreThe University of MelbournePeter MacCallum Cancer CentreUC San Diego Health SystemUniversity of California San DiegoMoores Cancer CenterUniversidade de Santiago de CompostelaCenter for Research in Molecular Medicine and Chronic DiseasesUniversidade de VigoRoyal National Orthopaedic HospitalThe University of QueenslandSalford Royal NHS Foundation TrustOregon Health & Science UniversityTokyo Women's Medical UniversityMolecular Oncology (United States)Los Alamos National LaboratoryUniversity Health NetworkNottingham University Hospitals NHS TrustToronto General HospitalEpigenomics (Germany)Vector InstituteOslo University HospitalConsorci Institut D'Investigacions Biomediques August Pi I SunyerUniversitat de BarcelonaUniversity of CambridgeWashington University in St. LouisAlvin J. Siteman Cancer CenterDana-Farber/Boston Children's Cancer and Blood Disorders CenterUniversity of LeedsSt James's University HospitalPrincess Alexandra HospitalUniversity Hospitals of ClevelandCase Western Reserve UniversityGloucestershire Royal HospitalBarcelona Supercomputing CenterUniversitat Politècnica de CatalunyaUniversity of CalgaryInstitute of Cancer ResearchJohns Hopkins UniversitySidney Kimmel Comprehensive Cancer CenterRoyal Stoke University HospitalUniversity Hospital Southampton NHS Foundation TrustHuman Longevity (United States)La Trobe UniversityOlivia Newton-John Cancer Wellness & Research CentreOlivia Newton-John Cancer Research InstituteChinese Academy of SciencesComputer Network Information CenterGenome CanadaUniversitat Pompeu FabraCentre for Genomic RegulationBuck Institute for Research on AgingDuke Medical CenterMedizinische Hochschule HannoverCedars-Sinai Medical CenterQueen Mary University of LondonHebrew University of JerusalemLeipzig UniversityUniversity of Southern CaliforniaSecretaria de SaludBerlin Institute of Health at Charité - Universitätsmedizin BerlinGarvan Institute of Medical ResearchGlasgow Royal InfirmaryUNSW SydneyDuke University HospitalSouth Western Sydney Local Health DistrictMassachusetts General HospitalNational Institute of Biomedical GenomicsUniversity of OsloInstitute of Cancer ResearchLund UniversityHeinrich Heine University DüsseldorfRIKEN Center for Integrative Medical SciencesFriedrich-Ebert-KrankenhausUniversity of OxfordMcGill UniversityTampere University HospitalTampere UniversityUniversity of California, Los AngelesLeeds Teaching Hospitals NHS TrustCentre Léon BérardFox Chase Cancer CenterCentre international de recherche sur le cancerUniversity of East AngliaEarlham InstituteRadboud University NijmegenRadboud University Medical CenterRadboud Institute for Molecular Life SciencesBrigham and Women's HospitalUniversity of ManchesterCancer Research UK Manchester InstituteJohns Hopkins MedicineThe Netherlands Cancer InstituteOncode InstituteNational Center for Tumor DiseasesUniversity of CopenhagenNovo Nordisk FoundationTechnical University of DenmarkBundesministerium für Forschung, Technologie und RaumfahrtThe University of SydneyMelanoma Institute AustraliaUniversity Hospital MünsterStanford UniversityFoundation Medicine (United States)Royal Marsden NHS Foundation TrustInstitut Gustave RoussyCancer Research UK Cambridge CenterCambridge University Hospitals NHS Foundation TrustUniversity of MichiganMichigan Center for Translational PathologyUniversity of BernUniversity Hospital of BernUniversity of PaviaUniversity of Alabama at BirminghamIcahn School of Medicine at Mount SinaiUniversity of TasmaniaUniversity of OttawaMayo Clinic in ArizonaWollongong HospitalMayo ClinicWinnMedWestmead HospitalWestmead Institute for Medical ResearchKorea Advanced Institute of Science and TechnologyElectronics and Telecommunications Research InstituteInstitut National du CancerUniversity Hospital Schleswig-HolsteinUniversity of LübeckUniversity of AucklandRoyal Children's HospitalWalter and Eliza Hall Institute of Medical ResearchMurdoch Children's Research InstituteMount Sinai HospitalLunenfeld-Tanenbaum Research InstituteVictorian Institute of Forensic MedicineNorfolk and Norwich University HospitalUniversity of CologneCenter for Systems BiologyInternational Genomics ConsortiumChildren's Hospital at WestmeadBarking, Havering And Redbridge University Hospitals NHS TrustUniversity of VeronaPediatrics and GeneticsMRC Cancer UnitSeven Bridges Genomics (United States)Addenbrooke's HospitalUniversity of PaduaCa' Foncello HospitalUniversity of GenevaUniversity of LausanneThe Francis Crick InstituteKU LeuvenUniversity of TübingenInstitut Jules BordetInstitute for Research in BiomedicineShadyside HospitalWellesley CollegeUppsala UniversityScience for Life LaboratoryHefei University of TechnologyUniversity of AntwerpGZA Ziekenhuizen Campus Sint-AugustinusSimon Fraser UniversityUniversity of PennsylvaniaUniversitat de Vic - Universitat Central de CatalunyaWellcome TrustQIMR Berghofer Medical Research InstituteHospital for Sick ChildrenQueen Elizabeth University HospitalProstate Cancer CanadaMedicon VillageGroupe de Recherche en Droit, Économie, GestionCentro de Investigación Biomédica en Red de Epidemiología y Salud PúblicaIcelandic Cancer SocietyXijing HospitalAir Force Medical UniversityRigshospitaletAustralian Institute of Tropical Health and MedicineUniversité de MontréalJames Cook UniversityFondazione IRCCS Istituto Neurologico Carlo BestaBioplatforms AustraliaLondon CancerCancer Genomics CentrePrince Charles HospitalUniversity of LiverpoolUniversity of FloridaUniversity of Milano-BicoccaUniversity of WürzburgCambridge SchoolUniversity of MiamiSylvester Comprehensive Cancer CenterNational Institute of Environmental Health SciencesSt Thomas' HospitalHospital del Mar Research InstituteOsaka International Cancer InstituteSkåne University HospitalBeatson West of Scotland Cancer CentreNational Human Genome Research InstituteVictorian Comprehensive Cancer CentreGerman Center for Infection ResearchGovernment of IndiaDepartment of BiotechnologyMinistry of Science and TechnologyBrandeis UniversityUniversity of British ColumbiaImperial College LondonGoethe University FrankfurtUniversity of San DiegoHoward Hughes Medical InstituteWakayama Medical UniversityUniversity of Tennessee Health Science CenterWest Cancer CenterChildren's Hospital of PhiladelphiaHallym UniversityInstitut de Biologia EvolutivaUniversity Hospital HeidelbergHokkaido UniversityTokyo National HospitalLeibniz Institute on Aging - Fritz Lipmann Institute (FLI)University of Nebraska Medical CenterSyneos Health (South Korea)Amsterdam UMC Location University of AmsterdamHong Kong University of Science and TechnologyShenzhen Bioeasy Biotechnology (China)Charité - Universitätsmedizin BerlinAbbVie (United States)BC Cancer AgencyEdinburgh Royal InfirmaryHeidelberg Institute for Stem Cell Technology and Experimental MedicineNew York Genome CenterMichael E. DeBakey VA Medical CenterHanyang UniversityAsan Medical CenterEndeavor HealthChicago Department of Public HealthUniversity of LjubljanaMcGill University and Génome Québec Innovation CentreHopp Children's Cancer Center HeidelbergCancer Research HorizonsInstitute of Genetics and CancerUniversity of EdinburghUniversity of ZurichUniversity of ZagrebSouth Australia PathologyNational Cancer Centre JapanSkolkovo Institute of Science and TechnologyInstitute for Information Transmission ProblemsDmitry Rogachev National Research Center of Pediatric Hematology, Oncology and ImmunologyGeorge Washington UniversityMacquarie UniversityMassachusetts Institute of TechnologyRoyal Prince Alfred HospitalKhon Kaen UniversityNational Cancer CenterEwha Womans UniversitySamsung (South Korea)Sungkyunkwan UniversityDana-Farber Brigham Cancer CenterUniversity of BergenSeoul National University HospitalInstitute of Computer SciencePolish Academy of SciencesUniversity of GöttingenUniversity of Duisburg-EssenVan Andel InstituteKing's College LondonGuy's and St Thomas' NHS Foundation TrustRoyal Brisbane and Women's HospitalUniversity of GothenburgChildren's Medical Research InstituteBoston Children's HospitalInstitute of Biomedical Sciences, Academia SinicaMax Planck Institute for Molecular GeneticsBiobyte Solutions (Germany)Gynecologic Oncology GroupNew York UniversityHarvard University PressLeidos (United States)Leidos Biomedical Research Inc. (United States)Second Military Medical UniversityPeking University Cancer HospitalBeijing HospitalInstitute for Systems BiologyUniversity of St AndrewsUniversidad de OviedoInstitut BergoniéChildren's Hospital of Los AngelesOrthopädische PraxisGhent UniversityNationwide Children's HospitalDuke UniversityInstitució Catalana de Recerca i Estudis AvançatsUniversitat Autònoma de BarcelonaInstitut Català de Paleontologia Miquel CrusafontOxford Nanopore Technologies (United Kingdom)University of California, DavisWestern Sydney UniversityHenry Ford HospitalKyushu UniversityHeidelberg Academy of Sciences and HumanitiesRoswell Park Comprehensive Cancer CenterPenrose-St. Francis Health ServicesUniversity Hospital UlmGerman Cancer AidChinese University of Hong KongSt. Jude Children's Research HospitalCarleton CollegeHudsonAlpha Institute for BiotechnologyKeio UniversitySage BionetworksRobert Bosch HospitalSamsung Medical CenterSangmyung UniversityNYU Langone HealthCleveland ClinicMayo Clinic in FloridaChristiana Care Health SystemSRA International (United States)Guy's HospitalKings Health PartnersInsermCentre Hospitalier Universitaire de BesançonInstitutul Clinic FundeniRoyal Surrey County HospitalNIHR Cambridge Biomedical Research CentreNinewells HospitalMedical College of WisconsinEmory UniversityPrinceton UniversityVanderbilt UniversityThe Ohio State University Comprehensive Cancer Center – Arthur G. James Cancer Hospital and Richard J. Solove Research InstituteYokohama City UniversityWashington State UniversityUniversitätsklinikum Gießen und MarburgInstitut de Recherche en Cancérologie de MontpellierNorth Bristol NHS TrustNewYork–Presbyterian HospitalNew York Hospital QueensPresbyterian HospitalVall d'Hebron Institut de RecercaTata Institute of Fundamental ResearchNational Centre for Biological SciencesIndiana University BloomingtonAnalytical Biological Services (United States)Tata Memorial HospitalAdvanced Centre for Treatment, Research and Education in CancerHunter WaterEssen University HospitalMartini-KlinikBeth Israel Deaconess Medical CenterCancer Research InstituteUniversity of PittsburghMassachusetts Eye and Ear InfirmaryJapan Agency for Medical Research and DevelopmentWalter Reed National Military Medical CenterUniversity Hospitals Coventry and Warwickshire NHS TrustSankt-Antonius-Hospital EschweilerUniversity of IcelandInstitut CurieSingapore General HospitalColumbia University Irving Medical CenterIstituto Tumori BariAgostino Gemelli University PolyclinicIstituti di Ricovero e Cura a Carattere ScientificoCommissariat à l'Énergie Atomique et aux Énergies AlternativesGenoscopeMaastricht UniversityLyon 1 UniversitéTokyo Medical and Dental UniversityTokyo University of ScienceJapan Science and Technology AgencyUniversity Hospitals Birmingham NHS Foundation TrustQueen's University BelfastUniversity of SouthamptonTallinn University of TechnologySickKids FoundationWinship Cancer InstituteNorwegian University of Science and TechnologyRED Consulting (Norway)John Radcliffe HospitalUniversity of LatviaColumbia UniversityOxford BioMedica (United Kingdom)Augusta UniversityGeorgia Regents Medical CenterWythenshawe HospitalLeibniz Institute for Baltic Sea Research WarnemündeCentre for Human GeneticsPoznan University of Medical SciencesInternational Institute for Molecular OncologyMRC University of Glasgow Centre for Virus ResearchHuazhong University of Science and TechnologyThe University of OsakaTri-Institutional PhD Program in Chemical BiologyFirst Affiliated Hospital of Xi'an Jiaotong UniversityRuijin HospitalEpworth HospitalEastern HealthMonash UniversityThe Ohio State UniversityUniversity of HoustonNorthwestern UniversityErasmus MC

Une affiliation ne permet pas de déduire la nationalité d’un auteur.

Sujets associés

RNA modifications and cancerCancer-related molecular mechanisms researchRNA Research and Splicing

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