Genotyping was done with the Illumina Human 1M beadchip by the Center for Inherited Diseases Research (CIDR) at Johns Hopkins University. A thorough data cleaning procedure on the genotype samples was applied to ensure the highest possible data quality, including using HapMap controls, detection of gender and chromosomal anomalies, hidden relatedness, population structure, missing call rates, plate effects, duplication error detection, and Hardy-Weinberg equilibrium (excluding SNPs with p < 10−6) (Laurie et al., 2009; Bierut et al., 2010). The final number of autosomal and X-chromosome markers consisted of 948,142 SNPs (only autosomal SNPs were used). The software package EIGENSTRAT/EIGENSOFT(Price et al., 2006) was used to calculate principal components reflecting continuous variation in allele frequencies representing ancestral differences in subjects. Two principal components distinguishing African-American participants from European-American participants and Hispanic and non-Hispanic subjects, were identified (Bierut et al., 2010).
