ANCESTRYMAP finds skews in ancestry that are potentially associated with disease genes in recently mixed populations like African Americans. Admixture mapping is a method for localizing disease causing genetic variants that differ in frequency across populations. It is most advantageous to apply this approach to populations that have descended from a recent mix of two ancestral groups that have been geographically isolated for many tens of thousands of years: for example, African Americans have both West African and European American ancestry. The approach assumes that near a disease causing gene there will be enhanced ancestry from the population that has greater risk of getting the disease. Thus if one can calculate the ancestry along the genome for an admixed sample set, one could use that to identify disease causing gene variants. The figure below shows a schematic of how a disease locus would appear in an admixture scan of patients and controls.
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Patterson et al. 2004
Methods for High-Density Admixture Mapping of Disease Genes
Am. J. Hum. Genet. 74:000–000, 2004