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How local reference panels improve imputation in French populations

dc.rights.licenseopenen_US
dc.contributor.authorHERZIG, Anthony
dc.contributor.authorVELO‐SUÁREZ, Lourdes
dc.contributor.authorCAMPION, Dominique
hal.structure.identifierBordeaux population health [BPH]
dc.contributor.authorDARTIGUES, Jean-François
dc.contributor.authorLAMBERT, Jean-Charles
dc.contributor.authorLUDWIG, Thomas
dc.contributor.authorGRENIER-BOLEY, Benjamin
dc.contributor.authorLETORT, Sébastien
dc.contributor.authorLINDENBAUM, Pierre
dc.contributor.authorMEYER, Vincent
dc.contributor.authorQUENEZ, Olivier
dc.contributor.authorBELLENGUEZ, Céline
dc.contributor.authorCLÉZIO, Camille Charbonnier-Le
dc.contributor.authorGIEMZA, Joanna
dc.contributor.authorCHATEL, Stéphanie
dc.contributor.authorFÉREC, Claude
dc.contributor.authorLE MAREC, Hervé
hal.structure.identifierBordeaux population health [BPH]
dc.contributor.authorLETENNEUR, Luc
dc.contributor.authorNICOLAS, Gaël
dc.contributor.authorROUAULT, Karen
dc.contributor.authorBACQ, Delphine
dc.contributor.authorBOLAND, Anne
dc.contributor.authorLECHNER, Doris
dc.contributor.authorADJOU, Chantal
dc.contributor.authorCHATEL, Stéphanie
dc.contributor.authorGOLDBERG, Marcel
dc.contributor.authorHALBOUT, Philippe-Antoine
dc.contributor.authorLE MAREC, Hervé
dc.contributor.authorL’HELGOUACH, David
dc.contributor.authorROUAULT, Karen
dc.contributor.authorSCHOTT, Jean-Jacques
dc.contributor.authorVOGELSPERGER, Anne
dc.contributor.authorZINS, Marie
dc.contributor.authorBACQ, Delphine
dc.contributor.authorBLANCHÉ, Hélène
dc.contributor.authorBOLAND, Anne
dc.contributor.authorOLASO, Robert
dc.contributor.authorLINDENBAUM, Pierre
dc.contributor.authorLUDWIG, Thomas
dc.contributor.authorMEYER, Vincent
dc.contributor.authorSANDRON, Florian
dc.contributor.authorDELAFOY, Damien
dc.contributor.authorVELO-SUÁREZ, Lourdes
dc.contributor.authorALVES, Isabel
dc.contributor.authorBOCHER, Ozvan
dc.contributor.authorHERZIG, Anthony, F
dc.contributor.authorKARAKACHOFF, Matilde
dc.contributor.authorMARENNE, Gaëlle
dc.contributor.authorSAINT-PIERRE, Aude
dc.contributor.authorGEOFFROY, Véronique
dc.contributor.authorDINA, Christian
dc.contributor.authorREDON, Richard
dc.contributor.authorDELEUZE, Jean-François
dc.contributor.authorGÉNIN, Emmanuelle
dc.date.accessioned2024-10-12T10:54:53Z
dc.date.available2024-10-12T10:54:53Z
dc.date.issued2024-01-03
dc.identifier.issn2045-2322en_US
dc.identifier.urihttps://oskar-bordeaux.fr/handle/20.500.12278/202461
dc.description.abstractEnImputation servers offer the exclusive possibility to harness the largest public reference panelswhich have been shown to deliver very high precision in the imputation of European genomes. Manystudies have nonetheless stressed the importance of ‘study specific panels’ (SSPs) as an alternativeand have shown the benefits of combining public reference panels with SSPs. But such combinedapproaches are not attainable when using external imputation servers. To investigate how toconfront this challenge, we imputed 550 French individuals using either the University of Michiganimputation server with the Haplotype Reference Consortium (HRC) panel or an in‑house SSP of 850whole‑genome sequenced French individuals. With approximate geo‑localization of both our targetand SSP individuals we are able to pinpoint different scenarios where SSP‑based imputation wouldbe preferred over server‑based imputation or vice‑versa. This is achieved by showing to a high degreeof resolution the importance of the proximity of the reference panel to target individuals; with afocus on the clear added value of SSPs for estimating haplotype phase and for the imputation of rarevariants (minor allele‑frequency below 0.01). Such benefits were most evident for individuals fromthe same geographical regions in France as the SSP individuals. Overall, only 42.3% of all 125,442variants evaluated were better imputed with an SSP from France compared to an external referencepanel, however this rises to 58.1% for individuals from geographic regions well covered by the SSP.By investigating haplotype sharing and population fine‑structure in France, we show the importanceof including SSP haplotypes for imputation but also that they should ideally be combined with largepublic panels. In the absence of the unattainable results from a combined panel of the HRC and ourFrench SSP, we put forward a pragmatic solution where server‑based and SSP‑based imputationoutcomes can be combined based on comparing posterior genotype probabilities. We show that suchan approach can give a level of imputation accuracy in excess of what could be achieved with eitherstrategy alone. The results presented provide detailed insights into the accuracy of imputation thatshould be expected from different strategies for European populations.
dc.description.sponsorshipMedical Genomicsen_US
dc.description.sponsorshipEtude Génétique de la Population Françaiseen_US
dc.language.isoENen_US
dc.rightsAttribution 3.0 United States*
dc.rights.urihttp://creativecommons.org/licenses/by/3.0/us/*
dc.title.enHow local reference panels improve imputation in French populations
dc.title.alternativeSci Repen_US
dc.typeArticle de revueen_US
dc.identifier.doi10.1038/s41598-023-49931-3en_US
dc.subject.halSciences du Vivant [q-bio]/Santé publique et épidémiologieen_US
dc.identifier.pubmed38172507en_US
bordeaux.journalScientific Reportsen_US
bordeaux.page370en_US
bordeaux.volume14en_US
bordeaux.hal.laboratoriesBordeaux Population Health Research Center (BPH) - UMR 1219en_US
bordeaux.issue1en_US
bordeaux.institutionUniversité de Bordeauxen_US
bordeaux.institutionINSERMen_US
bordeaux.teamACTIVE_BPHen_US
bordeaux.peerReviewedouien_US
bordeaux.inpressnonen_US
hal.identifierhal-04501605
hal.popularnonen_US
hal.audienceInternationaleen_US
hal.exportfalse
dc.rights.ccPas de Licence CCen_US
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Scientific%20Reports&rft.date=2024-01-03&rft.volume=14&rft.issue=1&rft.spage=370&rft.epage=370&rft.eissn=2045-2322&rft.issn=2045-2322&rft.au=HERZIG,%20Anthony&VELO%E2%80%90SU%C3%81REZ,%20Lourdes&CAMPION,%20Dominique&DARTIGUES,%20Jean-Fran%C3%A7ois&LAMBERT,%20Jean-Charles&rft.genre=article


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