Genome-wide genotyping was performed using the Affymetrix Genome-Wide Human SNP Array 6.0 and genotypes calls were made using the Birdseed algorithm, version 2 [Korn et al., 2008]. We had four genotype inclusion criteria: the individual sample success rate had to be ≥90% (no samples excluded), the SNP success rate had to be ≥95% (41,885 SNPs excluded), the minor allele frequency had to be ≥0.01 (19,154 SNPs excluded), and the p-value for the test of Hardy-Weinberg equilibrium had to be ≥1.0×10-3 (6,317 SNPs excluded). We retained 10,788 SNPs from chromosome 22 (Fig. 1) as the analysis set for this investigation.
