When testing for GxE (including G×I), it is important to account for differences in genotype and allele frequency distributions across geographic ancestry populations, known as population stratification. If these differences are not accounted for, spurious associations between alleles and phenotypes can result in false positives (Cardon & Palmer, 2003). We used 34 AIMs to identify geographic ancestry in a Principal Coordinate Analyses (PCoA) in which allele-sharing distances are used to extract principal coordinates (PCs) that describe the genetic ancestry of the sample (Halder et al., 2008). Based on PCoA’s of 1,922 participants (94.59% of samples from whom DNA was collected), PC1 provided an index of non-European ancestry that complemented information from self-reported ethnicity; high PC1 scores indicated less European ancestry.
