Markers for mapping by admixture linkage disequilibrium in African American and Hispanic populations

Population linkage disequilibrium occurs as a consequence of mutation, sele ction, genetic drift, and population substructure produced by admixture of genetically distinct ethnic populations. African American and Hispanic ethn ic groups have a history of significant gene flow among parent groups, whic h can be of value in affecting genome scans for disease-gene discovery in t he case-control and transmission/disequilibrium test designs. Disease-gene discovery using mapping by admixture linkage disequilibrium (MALD) requires a map of polymorphic markers that differentiate between the founding popul ations, along with differences in disease-gene allele frequencies. We descr ibe markers appropriate for MALD mapping by assessing allele frequencies of 744 short tandem repeats (STRs) in African Americans, Hispanics, European Americans, and Asians, by choosing STR markers that have large differences in composite delta, log-likelihood ratios, and/or I*(2) for MALD. Additiona l markers can be added to this MALD map by utilization of the rapidly growi ng single-nucleotide-polymorphism databases and the literature, to achieve a 3-10-cM scanning scale. The map will be useful for studies of diseases, i ncluding prostate and breast cancer, diabetes, hypertension, and end-stage renal disease, that have large differences in incidence between the foundin g populations of either Hispanics or African Americans.