The Plains Indian and Finnish Caucasian samples were genotyped for 186 ancestry markers (Hodgkinson et al, 2008). These AIMs were also genotyped in 1051 individuals from the 51 worldwide populations represented in the HGDP-CEPH Human Genome Diversity Cell Line Panel (http://www.cephb.fr/HGDP-CEPH-Panel). PHASE Structure 2.2 (http://pritch.bsd.uchicago.edu/software.html) was run, simultaneously using the AIMS genotypes from our two samples and the 51 CEPH populations to identify population substructure and compute individual ethnic factor scores. This ancestry assessment showed that within the Plains Indian sample there was on average 0.05 admixture with Caucasians (median value = 0.01) and 0.01 with African Americans. In the Finnish Caucasians, the only detectable admixture was with an Asian factor (mean = 0.07, median = 0.02). Since the ethnic factor scores were highly skewed (due to very low admixture) we used a median split in analyses. Ethnic factor scores were initially tested as covariates in the Plains Indian and Finnish Caucasian analyses but their inclusion had no significant effects on any analyses.
