American Journal of Human Genetics (in press)
A Genome-Wide SNP panel for Mexican American Admixture Mapping
Chao Tian et al.
For admixture mapping studies in Mexican Americans (MAM) we define a genome-wide SNP panel that can distinguish between chromosomal segments of Amerindian (AMI) or European (EUR) ancestry. These studies used genotypes for > 400K SNPs defined in EUR and both Pima and Mayan AMI to define a set of ancestry informative markers (AIMs). The use of two AMI populations was necessary to remove a subset of SNPs that distinguished genotypes of only one AMI subgroup from EUR genotypes. The AIMs set contained 8144 SNPs separated by a minimum of 50 kb with only three intermarker intervals >1 Mb and had EUR/AMI Fst values > 0.30 (mean Fst = 0.48), and Mayan/Pima Fst values < 0.05 (mean Fst < 0.01). Analysis of a subset of these SNP AIMs suggested that this panel may also distinguish ancestry between EUR and other disparate AMI groups including Quechuan from South America. We show, using realistic simulation parameters which are based on our analyses of MAM genotyping results, that this panel of SNP AIMs provides good power for detecting disease-associated chromosomal segments for genes with modest ethnicity risk ratios. A reduced set of 5287 SNP AIMs captured almost the same admixture mapping information but smaller SNP sets show substantial drop-off in admixture mapping information and power. The results will enable studies of type 2 diabetes, rheumatoid arthritis and other diseases where epidemiological studies suggest differences in the distribution of ancestry associated susceptibility.