Genotype data from appropriate reference population samples can improve ancestry inference in samples from admixed populations, and three contributions [Thornton et al., 2013; Chen et al., 2013; Yorgov et al., 2013] used populations samples from HapMap and HGDP as surrogates for European, African, Native American, and Asian ancestry for proportional ancestry estimation of the GAW18 sample individuals. Thornton et al. [2013] showed that in the absence of reference population samples, individual ancestry estimates with the ADMIXTURE software can be seriously confounded in the presence of relatedness, but that reliable estimates can be obtained in related admixed samples when appropriate surrogates for ancestry are included in the analysis.
