Additional quality control measures were applied to the dbGaP data for both the samples and the SNPs. Samples having genotypes for at least 98% of the SNPs were considered for inclusion in analyses. These samples were rigorously checked for cryptic relatedness, population stratification, consistency with reported sex, and related quality control issues [Edenberg et al., 2010]. For the theta ERO sample subset (N = 1,064) used in the GWAS analysis (see below), 771 individuals were classified as European-American and 293 as African-American. The inclusion thresholds for SNPs were a minimum call rate of 98%, minor allele frequency (MAF) greater than 0.01, and Hardy-Weinberg P-values greater than 0.001 for the European-American and African-American groups. Based on these criteria, 90,394 SNPs were removed, reducing the number of SNP markers in the final genotype dataset to 951,071.
