A major application of SNP AIMs is to reduce false positives in association studies. For traits associated with continental ancestry our modeling studies found that relatively small numbers of SNP AIMs (64 or more) could adequately adjust for differences in ancestry stratification between cases and controls. It is notable that without the use of AIMs we observed many false positives even when the surrogate models used loci were not in complete linkage disequilibrium with the true ancestry associated trait (i.e. r2 = 0.73 for model 2 and r2 = 0.53 for model 3). This suggests that it is necessary to adjust for population structure for traits that are only partially association with continental ancestry and underscores the importance of the application of these or similar methods when subjects of mixed ancestry are studied. Our modeling studies also examined the use of AIMs in association tests for an admixed population (African Americans). Similar to the subject sets containing individuals from multiple continents, these studies showed that relatively small numbers of highly informative SNP AIMs (64 or more) can adequately adjust for
