8.8 years ago by
Boston, MA USA
My colleague has done some extensive work on this with a Puerto Rican population. Individuals originated from three ancestral populations: European settlers, native Taíno Indians, and West Africans. He used two programs: STRUCTURE 2.2 (Falush et al. 2003; Pritchard et al. 2000) and IAE3CI (Tsai et al. 2005; Parra et al. 2001), then the EIGENSTRAT (Price et al. 2006) program was implemented in HelixTree (Golden Helix, Bozeman, MT, USA) to calculate the principal components based on the genotypes of 100 ancestry informative markers in the population.
Added in edit 27 Jan 2012: Keep in mind that these calculations (of admixture) work best when one knows the frequencies of informative markers in each of the ancestral populations.
Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164:1567–1587.[?]
Parra EJ, Kittles RA, Argyropoulos G, et al. (2001) Ancestral proportions and admixture dynamics in geographically defined African Americans living in South Carolina. Am J Phys Anthropol 114:18–29.[?]
Price AL, Patterson NJ, Plenge RM, et al. (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38:904–909.[?]
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959.[?]
Tsai HJ, Choudhry S, Naqvi M, et al. (2005) Comparison of three methods to estimate genetic ancestry and control for stratification in genetic association studies among admixed populations. Hum Genet 118:424–433.[?]