Spurious association between a marker and a phenotype can arise from population stratification, especially in admixed populations such as AAs. To account for the effect of population stratification in AAs, we estimated the individual global ancestry using STRUCTURE program and included it as a covariate in the association analysis. To obtain a more consistent estimate of individual global ancestry for SAGE and our replication AA samples, we selected 2475 AIMs that were genotyped in both the SAGE AA sample and a subset of our replication sample (931 subjects). These AIMs were common to a reported AIMs panel for AAs based on a subset of SNPs on the ILLUMINA Human 1 M platform (45). The log likelihood of each analysis at varying numbers of assumed population groups (k) was estimated from the average of 3 independent runs (5,000 burn in and 5,000 iterations). As expected, the results favored a two-ancestry population model. The average proportion of European ancestry was 0.186 in the SAGE AA sample and 0.166 in our replication AA sample.
