Mexican American ancestry-informative markers: examination of population structure and marker characteristics in European Americans, Mexican Americans, Amerindians and Asians
Heather E. Collins-Schramm1, Bill Chima1, Takanobu Morii1, Kimberly Wah1, Yolanda Figueroa1, Lindsey A. Criswell2, Robert L. Hanson3, William C. Knowler3, Gabriel Silva4, John W. Belmont5 and Michael F. Seldin1
(1) Rowe Program in Human Genetics, Departments of Biological Chemistry and Medicine, University of California at Davis, One Shields Avenue, Davis, CA 95616-8669, USA
(2) Rosalind Russell Medical Research Center for Arthritis, University of California, San Francisco, San Francisco, CA 94143, USA
(3) National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, AZ 85014, USA
(4) Obras Sociales Del Hermano Pedro, Antigua, Guatemala
(5) Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
Abstract
Markers with large differences in allele frequencies between ethnicities provide ancestry information that can be applied to genetic studies. We identified over 100 biallelic ancestry informative markers (AIMs) with large allele frequency differences between European Americans (EA) and Pima Amerindians from laboratory and database screens. For 35 of these markers, Mayan, Yavapai and Quechuan Amerindians were genotyped and compared with EA and Pima allele frequencies. Markers with large allele frequency differences between EA and one Amerindian tribe showed only small differences between the Amerindian tribes. Examination of structure in individuals demonstrated a clear separation of subjects of European from those of Amerindian ancestry, and similarity between individuals from disparate Amerindian populations. The AIMs demonstrated the variation in ancestral composition of individual Mexican Americans, providing evidence of applicability in admixture mapping and in controlling for structure in association tests. In addition, a high percentage of single-nucleotide polymorphisms (SNPs) selected on the basis of large frequency differences between EA and Asian populations had large allele frequency differences between EA and Amerindians, suggesting an efficient method for greatly expanding AIMs for use in admixture mapping/structure analysis in Mexican Americans. Together, these data provide additional support for the practical application of admixture mapping in the Mexican American population.
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