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A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing.

dc.rights.licenseopenen_US
dc.contributor.authorDENOMMÉ-PICHON, Anne-Sophie
dc.contributor.authorMATALONGA, Leslie
dc.contributor.authorDE BOER, Elke
dc.contributor.authorJACKSON, Adam
dc.contributor.authorBENETTI, Elisa
dc.contributor.authorBANKA, Siddharth
dc.contributor.authorBRUEL, Ange-Line
dc.contributor.authorCIOLFI, Andrea
dc.contributor.authorCLAYTON-SMITH, Jill
dc.contributor.authorDALLAPICCOLA, Bruno
dc.contributor.authorDUFFOURD, Yannis
dc.contributor.authorELLWANGER, Kornelia
dc.contributor.authorFALLERINI, Chiara
dc.contributor.authorGILISSEN, Christian
dc.contributor.authorGRAESSNER, Holm
dc.contributor.authorHAACK, Tobias B
dc.contributor.authorHAVLOVICOVA, Marketa
dc.contributor.authorHOISCHEN, Alexander
dc.contributor.authorJEAN-MARÇAIS, Nolwenn
dc.contributor.authorKLEEFSTRA, Tjitske
dc.contributor.authorLÓPEZ-MARTÍN, Estrella
dc.contributor.authorMACEK, Milan
dc.contributor.authorMENCARELLI, Maria Antonietta
dc.contributor.authorMOUTTON, Sébastien
dc.contributor.authorPFUNDT, Rolph
dc.contributor.authorPIZZI, Simone
dc.contributor.authorPOSADA, Manuel
dc.contributor.authorRADIO, Francesca Clementina
dc.contributor.authorRENIERI, Alessandra
hal.structure.identifierLaboratoire Maladies Rares: Génétique et Métabolisme (Bordeaux) [U1211 INSERM/MRGM]
dc.contributor.authorROORYCK, Caroline
dc.contributor.authorRYBA, Lukas
dc.contributor.authorSAFRAOU, Hana
dc.contributor.authorSCHWARZ, Martin
dc.contributor.authorTARTAGLIA, Marco
dc.contributor.authorTHAUVIN-ROBINET, Christel
dc.contributor.authorTHEVENON, Julien
dc.contributor.authorTRAN MAU-THEM, Frédéric
hal.structure.identifierLaboratoire Maladies Rares: Génétique et Métabolisme (Bordeaux) [U1211 INSERM/MRGM]
dc.contributor.authorTRIMOUILLE, Aurelien
dc.contributor.authorVOTYPKA, Pavel
dc.contributor.authorDE VRIES, Bert B A
dc.contributor.authorWILLEMSEN, Marjolein H
dc.contributor.authorZUREK, Birte
dc.contributor.authorVERLOES, Alain
dc.contributor.authorPHILIPPE, Christophe
dc.contributor.authorVITOBELLO, Antonio
dc.contributor.authorVISSERS, Lisenka E. L. M.
dc.contributor.authorFAIVRE, Laurence
dc.date.accessioned2024-02-16T09:03:01Z
dc.date.available2024-02-16T09:03:01Z
dc.date.issued2023-04-01
dc.identifier.issn1530-0366en_US
dc.identifier.urihttps://oskar-bordeaux.fr/handle/20.500.12278/188189
dc.description.abstractEnWithin the Solve-RD project (https://solve-rd.eu/), the European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies aimed to investigate whether a reanalysis of exomes from unsolved cases based on ClinVar annotations could establish additional diagnoses. We present the results of the "ClinVar low-hanging fruit" reanalysis, reasons for the failure of previous analyses, and lessons learned. Data from the first 3576 exomes (1522 probands and 2054 relatives) collected from European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies was reanalyzed by the Solve-RD consortium by evaluating for the presence of single-nucleotide variant, and small insertions and deletions already reported as (likely) pathogenic in ClinVar. Variants were filtered according to frequency, genotype, and mode of inheritance and reinterpreted. We identified causal variants in 59 cases (3.9%), 50 of them also raised by other approaches and 9 leading to new diagnoses, highlighting interpretation challenges: variants in genes not known to be involved in human disease at the time of the first analysis, misleading genotypes, or variants undetected by local pipelines (variants in off-target regions, low quality filters, low allelic balance, or high frequency). The "ClinVar low-hanging fruit" analysis represents an effective, fast, and easy approach to recover causal variants from exome sequencing data, herewith contributing to the reduction of the diagnostic deadlock.
dc.language.isoENen_US
dc.rightsAttribution 3.0 United States*
dc.rights.urihttp://creativecommons.org/licenses/by/3.0/us/*
dc.subject.enClinVar
dc.subject.enDevelopmental disorder
dc.subject.enExome reanalysis
dc.subject.enRare diseases
dc.title.enA Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing.
dc.title.alternativeGenet Meden_US
dc.typeArticle de revueen_US
dc.identifier.doi10.1016/j.gim.2023.100018en_US
dc.subject.halSciences du Vivant [q-bio]/Génétiqueen_US
dc.identifier.pubmed36681873en_US
dc.description.sponsorshipEuropeEuropean Union's Horizon 2020 research and innovation programen_US
dc.description.sponsorshipEuropeRD-CONNECT: An integrated platform connecting registries, biobanks and clinical bioinformatics for rare disease researchen_US
dc.description.sponsorshipEuropeEuropean Joint Programme on Rare Diseasesen_US
bordeaux.journalGenetics in Medicineen_US
bordeaux.page100018en_US
bordeaux.volume25en_US
bordeaux.hal.laboratoriesMaladies Rares : Génétique et Métabolisme (MRGM) - UMR 1211en_US
bordeaux.issue4en_US
bordeaux.institutionUniversité de Bordeauxen_US
bordeaux.institutionINSERMen_US
bordeaux.peerReviewedouien_US
bordeaux.inpressnonen_US
bordeaux.import.sourcepubmed
hal.identifierhal-04461276
hal.version1
hal.date.transferred2024-02-16T09:03:06Z
hal.popularnonen_US
hal.audienceInternationaleen_US
hal.exporttrue
workflow.import.sourcepubmed
dc.rights.ccCC BYen_US
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Genetics%20in%20Medicine&rft.date=2023-04-01&rft.volume=25&rft.issue=4&rft.spage=100018&rft.epage=100018&rft.eissn=1530-0366&rft.issn=1530-0366&rft.au=DENOMM%C3%89-PICHON,%20Anne-Sophie&MATALONGA,%20Leslie&DE%20BOER,%20Elke&JACKSON,%20Adam&BENETTI,%20Elisa&rft.genre=article


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