Chunk #65 — Materials and Methods — There were three phases to this study — Assessment of population stratification using ancestry informative markers (AIMS)
The Plains Indian and U.S. Caucasian samples were genotyped for 186 ancestry markers that were on the addiction array described above [56]. The AIMs were also genotyped in 1051 individuals from 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 “anchored” approach showed that a seven factor solution was optimal. To evaluate the potential impact of ethnic substructure on our association results, individual alpha power was correlated with individual ethnic factor scores using the Spearman ρ correlation. There were no significant correlations with any of the seven ethnic factors (U.S. Caucasians p = 0.21–0.99; Plains Indians p = 0.3–0.94). These results indicate that ethnic substructure is unlikely to have an impact on the association analyses.
