Our evaluation of imputed genotypes in the FUSION, HapMap, and HGDP samples clearly shows that imputation can be very accurate in a variety of populations. In this way, we believe it will be an important tool for combining results across studies that rely on different marker panels. To investigate whether using imputed genotypes might also improve power in individual studies, we carried out a simulation experiment. As previously described [Schaffner et al., 2005], we simulated 10,000 chromosomes for a series of 1 Mb regions. Within each region, simulated LD patterns mimicked the HapMap CEU or YRI [Schaffner et al., 2005]. We then used a subset of 120 simulated chromosomes to generate a region specific “HapMap.” As described in the methods, we then picked the minor allele for a randomly selected polymorphic site in each region as the “disease susceptibility allele” and simulated a set of 500 case and 500 control individuals using the remaining chromosomes. The susceptibility allele varied in frequency between 2.5 and 50%, with larger simulated effect sizes assigned to rarer alleles to ensure comparable power in a
