We ran the program STRUCTURE (Falush et al., 2003) to infer the individual ancestry proportions based on the genotype data for 37 ancestry informative markers (AIMs) (Yang et al., 2005a, 2005b; Stein et al., 2004). Four hundred seventeen of the 636 AA subjects had AIMs; an additional 105 European American (EA) subjects were included in the STRUCTURE run to set EA ancestral allele frequencies (to increase the accuracy when inferring admixture). The Monte Carlo simulation parameters were set to 50,000 burn-ins followed by 50,000 iterations, and K was set to 2. The inferred ancestry proportions were used as a covariate in the subsequent logistic regression.
