For the simulated HapMap data, polymorphic sites were ascertained and thinned to match the corresponding (CEU) Phase II HapMap International HapMap Consortium [2007] marker density, allele frequency spectrum and LD patterns, resulting in ≈1,000 SNPs for each region for the panel of 120 HapMap chromosomes. Based on the thinned HapMap panel, we selected a set of 100 tagSNPs for each region that included the 90 tagSNPs with the largest number of proxies and 10 additional SNPs picked at random among those remaining [Carlson et al., 2004]. The tagSNP selection approach taken above resulted in tagSNP sets that captured ≈78% of the common variants (MAF >5%) in the simulated CEU HapMap, similar to the observed performance of the Illumina HumanHap300 Beadchip SNP genotyping platform. The genotypes at these 100 tagSNPs constituted the observed data for each simulated sample.
