Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel

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dc.contributor.author Huang, Jie
dc.contributor.author Howie, Bryan
dc.contributor.author McCarthy, Shane
dc.contributor.author Memari, Yasin
dc.contributor.author Walter, Klaudia
dc.contributor.author Min, Josine L.
dc.contributor.author Danecek, Petr
dc.contributor.author Malerba, Giovanni
dc.contributor.author Trabetti, Elisabetta
dc.contributor.author Zheng, Hou-Feng
dc.contributor.author Gambaro, Giovanni
dc.contributor.author Richards, J. Brent
dc.contributor.author Durbin, Richard
dc.contributor.author Timpson, Nicholas J.
dc.contributor.author Marchini, Jonathan
dc.contributor.author Soranzo, Nicole
dc.contributor.author UK10K Consortium
dc.contributor.author Paunio, Tiina
dc.date.accessioned 2016-11-07T12:00:04Z
dc.date.available 2016-11-07T12:00:04Z
dc.date.issued 2015-09
dc.identifier.citation Huang , J , Howie , B , McCarthy , S , Memari , Y , Walter , K , Min , J L , Danecek , P , Malerba , G , Trabetti , E , Zheng , H-F , Gambaro , G , Richards , J B , Durbin , R , Timpson , N J , Marchini , J , Soranzo , N , UK10K Consortium & Paunio , T 2015 , ' Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel ' , Nature Communications , vol. 6 , 8111 . https://doi.org/10.1038/ncomms9111
dc.identifier.other PURE: 58957650
dc.identifier.other PURE UUID: 6b0e8035-d2dd-49c9-985d-fc3aa09624ec
dc.identifier.other WOS: 000362948800002
dc.identifier.other Scopus: 84941702459
dc.identifier.uri http://hdl.handle.net/10138/168631
dc.description Tiina Paunio on UK10K Consortium -työryhmän jäsen.
dc.description.abstract Imputing genotypes from reference panels created by whole-genome sequencing (WGS) provides a cost-effective strategy for augmenting the single-nucleotide polymorphism (SNP) content of genome-wide arrays. The UK10K Cohorts project has generated a data set of 3,781 whole genomes sequenced at low depth (average 7x), aiming to exhaustively characterize genetic variation down to 0.1% minor allele frequency in the British population. Here we demonstrate the value of this resource for improving imputation accuracy at rare and low-frequency variants in both a UK and an Italian population. We show that large increases in imputation accuracy can be achieved by re-phasing WGS reference panels after initial genotype calling. We also present a method for combining WGS panels to improve variant coverage and downstream imputation accuracy, which we illustrate by integrating 7,562WGS haplotypes from the UK10K project with 2,184 haplotypes from the 1000 Genomes Project. Finally, we introduce a novel approximation that maintains speed without sacrificing imputation accuracy for rare variants. en
dc.format.extent 9
dc.language.iso eng
dc.relation.ispartof Nature Communications
dc.rights cc_by
dc.rights.uri info:eu-repo/semantics/openAccess
dc.subject GENOME-WIDE ASSOCIATION
dc.subject GENOTYPE IMPUTATION
dc.subject TWINSUK
dc.subject FORMAT
dc.subject MAP
dc.subject 3111 Biomedicine
dc.title Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel en
dc.type Article
dc.contributor.organization Clinicum
dc.contributor.organization Department of Psychiatry
dc.description.reviewstatus Peer reviewed
dc.relation.doi https://doi.org/10.1038/ncomms9111
dc.relation.issn 2041-1723
dc.rights.accesslevel openAccess
dc.type.version publishedVersion

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