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Am J Hum Genet. 1998 Dec; 63(6): 1839–1851.
doi: 10.1086/302148
PMCID: PMC1377655
PMID: 9837836

Estimating African American admixture proportions by use of population-specific alleles.

E J Parra, A Marcini, J Akey, J Martinson, M A Batzer, R Cooper, T Forrester, D B Allison, R Deka, R E Ferrell, and M D Shriver
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Abstract

We analyzed the European genetic contribution to 10 populations of African descent in the United States (Maywood, Illinois; Detroit; New York; Philadelphia; Pittsburgh; Baltimore; Charleston, South Carolina; New Orleans; and Houston) and in Jamaica, using nine autosomal DNA markers. These markers either are population-specific or show frequency differences >45% between the parental populations and are thus especially informative for admixture. European genetic ancestry ranged from 6.8% (Jamaica) to 22.5% (New Orleans). The unique utility of these markers is reflected in the low variance associated with these admixture estimates (SEM 1.3%-2.7%). We also estimated the male and female European contribution to African Americans, on the basis of informative mtDNA (haplogroups H and L) and Y Alu polymorphic markers. Results indicate a sex-biased gene flow from Europeans, the male contribution being substantially greater than the female contribution. mtDNA haplogroups analysis shows no evidence of a significant maternal Amerindian contribution to any of the 10 populations. We detected significant nonrandom association between two markers located 22 cM apart (FY-null and AT3), most likely due to admixture linkage disequilibrium created in the interbreeding of the two parental populations. The strength of this association and the substantial genetic distance between FY and AT3 emphasize the importance of admixed populations as a useful resource for mapping traits with different prevalence in two parental populations.

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Selected References

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  • Adams J, Ward RH. Admixture studies and the detection of selection. Science. 1973 Jun 15;180(4091):1137–1143. [PubMed] [Google Scholar]
  • Allison DB. Transmission-disequilibrium tests for quantitative traits. Am J Hum Genet. 1997 Mar;60(3):676–690. [PMC free article] [PubMed] [Google Scholar]
  • Ataman SL, Cooper R, Rotimi C, McGee D, Osotimehin B, Kadiri S, Kingue S, Muna W, Fraser H, Forrester T, et al. Standardization of blood pressure measurement in an international comparative study. J Clin Epidemiol. 1996 Aug;49(8):869–877. [PubMed] [Google Scholar]
  • Batzer MA, Arcot SS, Phinney JW, Alegria-Hartman M, Kass DH, Milligan SM, Kimpton C, Gill P, Hochmeister M, Ioannou PA, et al. Genetic variation of recent Alu insertions in human populations. J Mol Evol. 1996 Jan;42(1):22–29. [PubMed] [Google Scholar]
  • Bookstein R, Lai CC, To H, Lee WH. PCR-based detection of a polymorphic BamHI site in intron 1 of the human retinoblastoma (RB) gene. Nucleic Acids Res. 1990 Mar 25;18(6):1666–1666. [PMC free article] [PubMed] [Google Scholar]
  • Briscoe D, Stephens JC, O'Brien SJ. Linkage disequilibrium in admixed populations: applications in gene mapping. J Hered. 1994 Jan-Feb;85(1):59–63. [PubMed] [Google Scholar]
  • Chakraborty R. Estimation of race admixture--a new method. Am J Phys Anthropol. 1975 May;42(3):507–511. [PubMed] [Google Scholar]
  • Chakraborty R, Weiss KM. Admixture as a tool for finding linked genes and detecting that difference from allelic association between loci. Proc Natl Acad Sci U S A. 1988 Dec;85(23):9119–9123. [PMC free article] [PubMed] [Google Scholar]
  • Chakraborty R, Kamboh MI, Nwankwo M, Ferrell RE. Caucasian genes in American blacks: new data. Am J Hum Genet. 1992 Jan;50(1):145–155. [PMC free article] [PubMed] [Google Scholar]
  • Chen YS, Torroni A, Excoffier L, Santachiara-Benerecetti AS, Wallace DC. Analysis of mtDNA variation in African populations reveals the most ancient of all human continent-specific haplogroups. Am J Hum Genet. 1995 Jul;57(1):133–149. [PMC free article] [PubMed] [Google Scholar]
  • Cooper R, Rotimi C, Ataman S, McGee D, Osotimehin B, Kadiri S, Muna W, Kingue S, Fraser H, Forrester T, et al. The prevalence of hypertension in seven populations of west African origin. Am J Public Health. 1997 Feb;87(2):160–168. [PMC free article] [PubMed] [Google Scholar]
  • Fernandez-Reyes D, Craig AG, Kyes SA, Peshu N, Snow RW, Berendt AR, Marsh K, Newbold CI. A high frequency African coding polymorphism in the N-terminal domain of ICAM-1 predisposing to cerebral malaria in Kenya. Hum Mol Genet. 1997 Aug;6(8):1357–1360. [PubMed] [Google Scholar]
  • GLASS B. On the unlikelihood of significant admixture of genes from the North American Indians in the present composition of the Negroes of the United States. Am J Hum Genet. 1955 Dec;7(4):368–385. [PMC free article] [PubMed] [Google Scholar]
  • GLASS B, LI CC. The dynamics of racial intermixture; an analysis based on the American Negro. Am J Hum Genet. 1953 Mar;5(1):1–20. [PMC free article] [PubMed] [Google Scholar]
  • Gotoda T, Yamada N, Murase T, Shimano H, Shimada M, Harada K, Kawamura M, Kozaki K, Yazaki Y. Detection of three separate DNA polymorphisms in the human lipoprotein lipase gene by gene amplification and restriction endonuclease digestion. J Lipid Res. 1992 Jul;33(7):1067–1072. [PubMed] [Google Scholar]
  • Guo SW, Thompson EA. Performing the exact test of Hardy-Weinberg proportion for multiple alleles. Biometrics. 1992 Jun;48(2):361–372. [PubMed] [Google Scholar]
  • Hammer MF. A recent insertion of an alu element on the Y chromosome is a useful marker for human population studies. Mol Biol Evol. 1994 Sep;11(5):749–761. [PubMed] [Google Scholar]
  • Hsieh CL, Sutton HE. Mitochondrial and nuclear variants in a U.S. black population: origins of a hybrid population. Ann Hum Genet. 1992 May;56(Pt 2):105–112. [PubMed] [Google Scholar]
  • Lewontin RC. The Interaction of Selection and Linkage. I. General Considerations; Heterotic Models. Genetics. 1964 Jan;49(1):49–67. [PMC free article] [PubMed] [Google Scholar]
  • Liu Y, Saha N, Low PS, Tay JS. Linkage disequilibrium between two loci (5' untranslated exon 1 and intron 5-DdeI) of the antithrombin III gene in three ethnic groups in Singapore. Hum Hered. 1995 Jul-Aug;45(4):192–198. [PubMed] [Google Scholar]
  • Long JC. The genetic structure of admixed populations. Genetics. 1991 Feb;127(2):417–428. [PMC free article] [PubMed] [Google Scholar]
  • Long JC, Williams RC, Urbanek M. An E-M algorithm and testing strategy for multiple-locus haplotypes. Am J Hum Genet. 1995 Mar;56(3):799–810. [PMC free article] [PubMed] [Google Scholar]
  • McKeigue PM. Mapping genes underlying ethnic differences in disease risk by linkage disequilibrium in recently admixed populations. Am J Hum Genet. 1997 Jan;60(1):188–196. [PMC free article] [PubMed] [Google Scholar]
  • Reed TE. Caucasian genes in American Negroes. Science. 1969 Aug 22;165(3895):762–768. [PubMed] [Google Scholar]
  • ROBERTS DF. The dynamics of racial intermixture in the American Negro-some anthropological considerations. Am J Hum Genet. 1955 Dec;7(4):361–367. [PMC free article] [PubMed] [Google Scholar]
  • Shriver MD, Smith MW, Jin L, Marcini A, Akey JM, Deka R, Ferrell RE. Ethnic-affiliation estimation by use of population-specific DNA markers. Am J Hum Genet. 1997 Apr;60(4):957–964. [PMC free article] [PubMed] [Google Scholar]
  • Soodyall H, Vigilant L, Hill AV, Stoneking M, Jenkins T. mtDNA control-region sequence variation suggests multiple independent origins of an "Asian-specific" 9-bp deletion in sub-Saharan Africans. Am J Hum Genet. 1996 Mar;58(3):595–608. [PMC free article] [PubMed] [Google Scholar]
  • Spielman RS, McGinnis RE, Ewens WJ. Transmission test for linkage disequilibrium: the insulin gene region and insulin-dependent diabetes mellitus (IDDM). Am J Hum Genet. 1993 Mar;52(3):506–516. [PMC free article] [PubMed] [Google Scholar]
  • Stephens JC, Briscoe D, O'Brien SJ. Mapping by admixture linkage disequilibrium in human populations: limits and guidelines. Am J Hum Genet. 1994 Oct;55(4):809–824. [PMC free article] [PubMed] [Google Scholar]
  • Torroni A, Lott MT, Cabell MF, Chen YS, Lavergne L, Wallace DC. mtDNA and the origin of Caucasians: identification of ancient Caucasian-specific haplogroups, one of which is prone to a recurrent somatic duplication in the D-loop region. Am J Hum Genet. 1994 Oct;55(4):760–776. [PMC free article] [PubMed] [Google Scholar]
  • Torroni A, Huoponen K, Francalacci P, Petrozzi M, Morelli L, Scozzari R, Obinu D, Savontaus ML, Wallace DC. Classification of European mtDNAs from an analysis of three European populations. Genetics. 1996 Dec;144(4):1835–1850. [PMC free article] [PubMed] [Google Scholar]
  • Tournamille C, Colin Y, Cartron JP, Le Van Kim C. Disruption of a GATA motif in the Duffy gene promoter abolishes erythroid gene expression in Duffy-negative individuals. Nat Genet. 1995 Jun;10(2):224–228. [PubMed] [Google Scholar]
  • Wallace DC, Torroni A. American Indian prehistory as written in the mitochondrial DNA: a review. Hum Biol. 1992 Jun;64(3):403–416. [PubMed] [Google Scholar]
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