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

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http://hdl.handle.net/10138/168631

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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

Titel: Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel
Författare: 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
Upphovmannens organisation: Clinicum
Department of Psychiatry
Datum: 2015-09
Språk: eng
Sidantal: 9
Tillhör serie: Nature Communications
ISSN: 2041-1723
DOI: https://doi.org/10.1038/ncomms9111
Permanenta länken (URI): http://hdl.handle.net/10138/168631
Abstrakt: 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.
Beskrivning: Tiina Paunio on UK10K Consortium -työryhmän jäsen.
Subject: GENOME-WIDE ASSOCIATION
GENOTYPE IMPUTATION
TWINSUK
FORMAT
MAP
3111 Biomedicine
Referentgranskad: Ja
Licens: cc_by
Användningsbegränsning: openAccess
Parallelpublicerad version: publishedVersion


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