We also obtained data from a GWA study of Type II diabetes in individuals of European descent [FUSION; Scott et al., 2007]. In 538 control samples, additional genotyping was conducted in a region of chromosome 14. This resulted in 521 markers for which we had both imputed genotypes from the HapMap, as well as genotypes typed on a custom microarray from Illumina. Imputation in these data set was carried out with MaCH 1.0 [Li et al., 2010], using the data from an Illumina 317K microarray platform as “tag SNPs”. Conditional on the typed genotypes at these 521 markers, we simulated quantitative trait data as above, keeping the genetic variance fixed to yield informative and interpretable summaries of power across multiple markers with varying allele frequencies. In addition to simulating phenotypes on the full set (538 individuals), we also simulated a larger effect on a subset of 50 individuals, selected at random. We repeated these simulations 100 times to obtain simulated phenotypes for 52,100 SNPs (100 × 521), for both “large” and small sample sizes.
