Populations with cryptic genetic clusters could contribute differential linkage signals [Lewis et al., 2008; Li et al., 2008; Myles et al., 2008; Lei et al., 2009; Rebbeck et al., 2009] (although not false positive linkage results). We used ancestry informative markers (AIMs) and analyzed them in STRUCTURE, which implements a Bayesian clustering method, to infer genetic ancestry for each subject [Falush et al., 2003, 2007; Pritchard et al., 2000]. A total of 1,574 AIMs were selected from the SNP linkage panel. The selection of AIMs was based on the marker characteristic inferred from the Hapmap CEU (European) and YRI (African) samples. The following criteria were used to select AIMs: (i) the absolute allele-frequency difference (d) between the two HapMap populations > 0.2, (ii) pair-wise SNP r2 < 0.1 within each population, and (iii) HWE testing with P-value > 0.01 within each population. A combination of 10,000 burn-ins and 10,000 collected iterations was implemented in the STRUCTRUE analysis. Individual inferred population was based on >50% estimated ancestry in that population. We identified families as either EA or AA based on the predominant classification for each family.
