Analyses of population genetic structure have shown that continental population groups can be identified by examining differences in allele frequencies (Rosenberg, et al., 2005; Rosenberg, et al., 2002). Over the last several years studies have demonstrated that thousands of individual single nucleotide polymorphisms (SNPs) distributed through out the genome have very large differences in allele frequencies between two or more continental populations (Mao, et al., 2007; Price, et al., 2007; Smith, et al., 2004; Tian, et al., 2007; Tian, et al., 2006). These studies have set the framework for both admixture mapping and adjusting for population genetic structure in association testing. The latter is particularly important since differences in population genetic structure between cases and controls can confound SNP-disease associations leading to false positive or negative findings (Campbell, et al., 2005; Clayton, et al., 2005; Freedman, et al., 2004; Helgason, et al., 2005; Marchini, et al., 2004). Methods to measure, and therefore address differences in population structure in association testing have been developed (Epstein, et al., 2007; Hoggart, et al., 2003; Price, et al., 2006; Pritchard, et al., 2000b; Purcell,
