Goal The Haplotype Reference Consortium (HRC) will create a large reference panel of human haplotypes by combining together sequencing data from multiple cohorts.
Uses The reference panel will 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.
Benefits By combining together multiple cohorts, the reference panels produced by the project will be as large as possible in terms of both number of haplotypes, and numbers of variants. This will increase the accuracy of the genotype imputation, especially at low-frequency variants, and the number of imputable variants, thus increasing the power of GWAS.
Ancestry Initially, the reference panel will contain haplotypes from individuals with predominantly European ancestry, although the HRC will include the 1000 Genomes Project data. In the future, we envisage the reference panel increasing in size and consisting of samples from a more diverse set of world-wide populations.
Timelines The first release will consist of 65,828 haplotypes at 50,313,740 SNPs, all with an estimated minor allele count of >= 5. Our current plan is to complete the first release by the end of 2014.