DNA samples were genotyped on the Illumina Human 1 M beadchip (Illumina Inc., San Diego, CA, USA) by the Center for Inherited Diseases Research (CIDR) at Johns Hopkins University. A total of 948,658 SNPs passed data-cleaning procedures and further within sample filtering for autosomal and X-chromosome markers yielded 948,142 markers. HapMap genotyping controls, duplicates, related subjects and outliers were removed from the sample set (Bierut et al. 2010). A total of 771,842 SNPs on the autosomal chromosomes with MAF greater than equal to 5% were used for further analysis. The software package EIGENSTRAT (Price et al. 2006) was used to calculate principal components reflecting continuous variation in allele frequencies representing ancestral differences. First principal component (PC1) distinguished African-American participants from European-American (EA) participants. The EA subset of the SAGE sample was used for the final association analysis.
