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Haplotype Reference Consortium

The Haplotype Reference Consortium (HRC) was a collaboration to create a large reference panel of human haplotypes by combining together sequencing data from multiple cohorts.

The reference panel can be used for genotype imputation and phasing in other cohorts, typically genome-wide association studies (GWAS), where genotypes are available from genome-wide SNP microarrays. To do this it is possible to use either the impute server here or at the University of Michigan (links below), or to download from the EGA a slightly reduced copy of the panel for local imputation and phasing, subject to completion of a Data Access Agreement (see external links below).

By combining together multiple cohorts, the reference panel produced by the project was as large as possible at the time in terms of both number of haplotypes, and numbers of variants, containing 64,976 human haplotypes at 39,235,157 SNPs constructed using whole-genome sequence data from 20 studies of predominantly European ancestry. This increases the accuracy of the genotype imputation, especially at low-frequency variants as low as 0.1% minor allele frequency, and the number of imputable variants, thus increasing the power of GWAS.

The final reference panel was published in Nature Genetics in 2016, with a link given below.


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