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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Acknowledgements
Support for this research was provided by National Institute of Health grants U01-DK57249 (MFS), RO1-HD39056 (JB). We thank the members of the Gila River Indian Community for participating in the studies of the Pima Indians. We thank Dr. David Smith (University of California, Davis, Dept. of Anthropology) for generously providing Yavapai Amerindian samples and useful discussions on this work.
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URLsfor data in thismanuscript are as follows:
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FSTAT software, http://www.unil.ch/izea/softwares/fstat.html (for documentation for FSTAT software Version 2.9.3.2.
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STRUCTURE software, (http://pritch.bsd.uchicago.edu/software/readme/readme.html (for documentation for STRUCTURE software: Version 2)
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The Marshfield Center for Medical Genetics, http://research.marshfieldclinic.org/genetics (for initial screening information for the indels utilized in this study and Japanese and Amazonian typing results)
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The SNP consortium website, http://snp.cshl.org/ (for initial screening information on the SNPs utilized in this study and Asian typing results)
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UC Davis, Rowe Program, http://roweprogram.ucdavis.edu/cover.htm (for the website tables cited in this manuscript)
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US Census Bureau, http://www.census.gov (for size of the MA population)
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Collins-Schramm, H.E., Chima, B., Morii, T. et al. Mexican American ancestry-informative markers: examination of population structure and marker characteristics in European Americans, Mexican Americans, Amerindians and Asians. Hum Genet 114, 263–271 (2004). https://doi.org/10.1007/s00439-003-1058-6
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DOI: https://doi.org/10.1007/s00439-003-1058-6