Mapping genes that underlie ethnic differences in disease risk: methods for detecting linkage in admixed populations, by conditioning on parental admixture.

Genes that underlie ethnic differences in disease risk can be mapped in affected individuals of mixed descent if the ancestry of the alleles at each marker locus can be assigned to one of the two founding populations. Linkage can be detected by testing for association of the disease with the ancestry of alleles at the marker locus, by conditioning on the admixture (defined as the proportion of genes that have ancestry from the high-risk population) of both parents. With regard to exploiting the effects of admixture, this test is more flexible and powerful than the transmission-disequilibrium test. Under the assumption of a multiplicative model, the statistical power for a given sample size depends only on parental admixture and the risk ratio r between populations that is generated by the locus. The most informative families are those in which mean parental admixture is .2-.7 and in which admixture is similar in both parents. The number of markers required for a genome search depends on the number of generations since admixture and on the information content for ancestry (f) of the markers, defined as a function of allele frequencies in the two founding populations. Simulations using a hidden Markov model suggest that, when admixture has occurred 2-10 generations earlier, a multipoint analysis using 2,000 biallelic markers, with f values of 30%, can extract 70%-90% of the ancestry information for each locus. Sets of such markers could be selected from libraries of single-nucleotide polymorphisms, when these become available.