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

Show simple item record Huang, Jie Howie, Bryan McCarthy, Shane Memari, Yasin Walter, Klaudia Min, Josine L. Danecek, Petr Malerba, Giovanni Trabetti, Elisabetta Zheng, Hou-Feng Gambaro, Giovanni Richards, J. Brent Durbin, Richard Timpson, Nicholas J. Marchini, Jonathan Soranzo, Nicole UK10K Consortium Paunio, Tiina 2016-11-07T12:00:04Z 2016-11-07T12:00:04Z 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 .
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.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 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.issn 2041-1723
dc.rights.accesslevel openAccess
dc.type.version publishedVersion

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