The samples were genotyped for 186 HapMap derived ancestry informative markers (AIMS) (Hodgkinson et al., 2008). The same 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). Structure 2.2 (http://pritch.bsd.uchicago.edu/software.html) was run simultaneously using the AIMS genotypes from our sample and the 51 CEPH populations to identify population substructure and compute individual ethnic factor scores. This ancestry assessment identifies seven ethnic factors that have been previously described (Hodgkinson et al., 2008). In this sample of African Americans, the mean African factor score was 0.77 (median = 0.81) and the mean European factor score was 0.09 (median value = 0.04). Both a Mid East factor and an Asian factor had a mean score of 0.06 (median 0.04).
