Examination of ancestry and ethnic affiliation using highly informative diallelic DNA markers: application to diverse and admixed populations and implications for clinical epidemiology and forensic medicine
- 816 Downloads
We and others have identified several hundred ancestry informative markers (AIMs) with large allele frequency differences between different major ancestral groups. For this study, a panel of 199 widely distributed AIMs was used to examine a diverse set of 796 DNA samples including self-identified European Americans, West Africans, East Asians, Amerindians, African Americans, Mexicans, Mexican Americans, Puerto Ricans and South Asians. Analysis using a Bayesian clustering algorithm (STRUCTURE) showed grouping of individuals with similar ethnic identity without any identifier other than the AIMs genotyping and showed admixture proportions that clearly distinguished different individuals of mixed ancestry. Additional analyses showed that, for the majority of samples, the predicted ethnic identity corresponded with the self-identified ethnicity at high probability (P > 0.99). Overall, the study demonstrates that AIMs can provide a useful adjunct to forensic medicine, pharmacogenomics and disease studies in which major ancestry or ethnic affiliation might be linked to specific outcomes.
KeywordsFamilial Mediterranean Fever Admixture Model Admix Population Allele Frequency Difference Ethnic Grouping
Support for this research was provided by National Institute of Health grants U01-DK57249, AR44804, AR50267 and AR20684.
- Begovich AB, Carlton VEH, Honigberg LA, Schrodi SJ, Chokkalingam AP, Alexander HC, Ardlie KG, Huang Q, Smith AM, Spoerke JM, Conn MT, Chang M, Chang YP, Saiki RK, Catanese JJ, Leong DU, Garcia VE, McAllister LB, Jeffery DA, Lee AT, Batliwalla F, Remmers E, Criswell LA, Seldin MF, Kastner DL, Amos CI, Sninsky JJ, Gregersen PK (2004) A missense SNP in the protein tyrosine phosphatase PTPN22 is associated with rheumatoid arthritis. Am J Hum Genet 75:330–337PubMedCrossRefGoogle Scholar
- Cavalli-Sforza L, Menozzi P, Piazza A.(1994) The history and geography of human genes. Princeton University PressGoogle Scholar
- Collins-Schramm HE, Chima B, Morii T, Wah K, Figueroa Y, Criswell LA, Hanson RL, Knowler WC, Silva G, Belmont JW, Seldin MF (2004) Mexican American Ancestry-Informative Markers: examination of population structure and marker characteristics in European Americans, Mexican Americans, Amerindians and Asians. Human Genetics 114:263–271PubMedCrossRefGoogle Scholar
- Fstat (2002) A program to estimate and test gene diversities and fixation indices. Version 2.9.3, Lausanne, SwitzerlandGoogle Scholar
- Lewontin R (1972) The apportionment of human diversity. Evol Biol 6:381–398Google Scholar
- Maindonald J, Braun J (2003) Data analysis and graphics using R. Cambridge University Press, CambridgeGoogle Scholar
- Smith MW, Patterson N, Lautenberger JA, Truelove AL, McDonald GJ, Waliszewska A, Kesing BD, Malasky MJ, Scafe C, Le E, De Jager PL, Mignault AA, Yi Z, de The G, Essex M, Sankale JL, Moore JH, Poku K, Phair JP, Goedert JJ, Vlahov D, Williams SM, Tishkoff SA, Winkler CA, De La Vega FM, Woodage T, Sninky JJ, Hafler DA, Altshuler D, Gilbert DA, O’Brien SJ, Reich D (2004) A high-density admixture map for disease gene discovery in African Americans. Am J Hum Genet 74:1001–1013PubMedCrossRefGoogle Scholar