Encouraged by these initial results, we proceeded to apply our method to impute genotypes for untyped markers in the Finland United States Investigation of NIDDM genetics (FUSION) GWAS [Scott et al., 2007]. Since a previous analysis suggested LD patterns in the HapMap CEU and in FUSION are similar [Willer et al., 2006], we used genotypes for 290,690 autosomal markers with allele frequency >5% in the Illumina 317K SNP chip and haplotypes for 2.5M polymorphic markers in the phased HapMap CEU chromosomes as input. After running the haplotyping procedure described above, we estimated the most likely genotype at each position (taking a majority vote across all iterations) and the expected number of copies of the minor allele at each position (a fractional value between 0 and 2) for each individual. We obtained similar results running the haplotyping procedure for 50–100 iterations or using only a smaller number of iterations (10–20) to estimate model parameters and then calculating maximum likelihood estimates for the missing genotypes and allele counts. Different chromosomes were analyzed in parallel and, overall, imputing genotypes for 2,335 unrelated individuals
