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Updated: Jun 14, 2026

Infinium Assay for Large-scale SNP Genotyping Applications
Published on: November 19, 2013
A reference panel of 64,976 haplotypes for genotype imputation
Shane McCarthy1, Sayantan Das2,3, Warren Kretzschmar4
1Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK.
Abstract:
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% and a large increase in the number of SNPs tested in association studies, and it 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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