A reference panel of 64,976 haplotypes for genotype imputation
Andrew R. Wood,
Hyun Min Kang,
Laura J Scott,
Cornelia Van Duijn,
Christopher E Gillies,
Dorret I. Boomsma,
Francis S. Collins,
George Davey Smith,
Ross M Fraser,
Oddgeir L Holmen,
Karen L. Mohlke,
P. Eline Slagboom,
Leonard Van den Berg,
Wouter Van Rheenen,
Matthew G. Sampson,
James F Wilson,
Paul de Bakker,
Mark I McCarthy,
Posted 23 Dec 2015
bioRxiv DOI: 10.1101/035170 (published DOI: 10.1038/ng.3643)
Posted 23 Dec 2015
We describe a reference panel of 64,976 human haplotypes at 39,235,157 SNPs constructed using whole genome sequence data from 20 studies of predominantly European ancestry. Using this resource leads to accurate genotype imputation at minor allele frequencies as low as 0.1%, a large increase in the number of SNPs tested in association studies and can help to discover and refine causal loci. We describe remote server resources that allow researchers to carry out imputation and phasing consistently and efficiently.
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