The ability to exclude subjects of other continental ancestry in admixed populations was also examined (Supplementary Table S4). For AFA, nearly all individuals of non-West African or European ancestry could be excluded at the 15% exclusion criteria while maintaining nearly all of the subjects of self-identified AFA ancestry using 64 or more In4 AIMs. However, for the MAM/MXN subjects much looser criteria (>30% non-Amerindian or European ancestry) were necessary to include >90% of self-identified MAM/MXN even with 96 In4 AIMs. This is probably due to the small West African contribution present in the MAM/MXN populations requiring a larger number of AIMs to enable good definition of this admixture component.
