A Haplotype Reference Panel of over 31,000 individuals and Next Generation Imputation Methods. S. Das on behalf of Haplotype Reference Consortium University of Michigan, Ann Arbor, Michigan.

   Genotype imputation is now a key tool in the analysis of human genetic studies, enabling array-based genetic association studies to examine the millions of variants that are being discovered by advances in whole genome sequencing. Examining these variants increases power and resolution of genetic association studies and makes it easier to compare the results of studies conducted using different arrays. Genotype imputation improves in accuracy with increasing numbers of sequenced samples, particularly for low frequency variants. The goal of the Haplotype Reference Consortium is to combine haplotype information from ongoing whole genome sequencing studies to create a large imputation resource. To date, we have collected information on 31,500 sequenced whole genomes, aggregated over 20 studies of predominantly European ancestry, to create a very large reference panel of human haplotypes where ~50M genetic variants are observed 5 or more times. These haplotypes can be used to guide genotype imputation and haplotype estimation. In preliminary empirical evaluations, our panel provides substantial increases in accuracy relative to the 1000 Genomes Project Phase 1 reference panel and other smaller panels, particularly for variants with frequency 5%. I will describe our evaluation of strategies for merging haplotypes and variant lists across studies and advances in methods for genotype likelihood-based haplotype estimation that can be applied to 10,000s of samples. I will also summarize new methods for next generation imputation that perform faster and require less memory than contemporary methods while attaining similar levels of imputation accuracy. Our full resource is available to the community through imputation servers that enable scientists to impute missing variants in any study and respect the privacy of subjects contributing to the studies that constitute the Haplotype Reference Consortium. The majority of haplotypes will also be deposited in the European Genotype Archive.

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