Based on the GWAS results in EAs, six SNPs (rs406001, rs382903, rs450378, rs6812849, rs1503292, and rs7691872) from two genomic regions (7p12 and 4q32) were scheduled for genotyping using TaqMan assays (Life Technologies, Carlsbad, California) in another 3112 subjects for follow-up and in 5504 of the 5799 GWAS subjects to estimate genotyping error rates. Single nucleotide polymorphisms rs382903 and rs1503292 failed quality control. In the 3112 follow-up subjects, 2752 were genotyped for 96 ancestry informative markers (AIMs), all SNPs, to estimate ancestry proportion by STRUCTURE software (28). Ninety of these AIMs were selected from SNPs included on the Illumina OminQuad genotyping microarray using a Bayesian strategy to maximize allele frequency differences between European, African, Asian, and other ancestry; the remainders were markers of frequent interest in psychiatric genetics. Subjects with African ancestry proportion scores <.5 were classified as EAs; otherwise, they were classified as AAs. We did not have AIMs information for the remaining 360 subjects, and self-reported population group was used to classify them. Of the 2752 subjects for whom AIMs were available, only 1.05% of the self-reported EAs were not grouped as EAs by analysis of the AIMs, indicating that overall, the self-identification of race was highly accurate.
