To help to capture putative disease loci not on the Affymetrix chip we used a new multilocus method in which a population genetics model is applied to our genotype data and the HapMap reference samples to simulate, or impute, genotype data at 2,193,483 HapMap SNPs not on the Affymetrix chip. These imputed, or in silico, genotypes are then tested for association in the same ways as SNPs genotyped in the project.
