Estimating African American admixture proportions by use of population-specific alleles.
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...Further, a regression of the correlations have been chosen specifically to have large frequency differences between the putative parental populations (Parra et al. 1998), these loci may be more informative for studying admixture than microsatellites were here....
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...Since the admixture is quite recent (primar-information provided by linkage, it is also possible to ily in the last 200 years or so; Parra et al. 1998; Pfaffreconstruct ancestral populations in the absence of pure et al. 2001), it is likely that admixture LD extends overindividuals, using the…...
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...…asestimate of 17.8% European ancestry is very similar to long as the chromosome chunks are typically larger thanthe estimate of 18.8% obtained by Parra et al. (1998) the intermarker distances, then even highly inaccuratefor their sample from this population. maps do not lead to biases in r.The…...
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...Indeed, Parra et al. (1998) de- tected admixture LD across 22 cM between two markers that have extremely large frequency differences between Africans and Europeans, in several African-American populations....
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...These data are intended to approximate a population of African Americans, with an average of 20% European admixture (this is consistent with estimates given by Parra et al. [1998])....
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...For example, in a sample of African Americans, a typical individual might have 5%–20% European admixture (Parra et al. 1998), whereas some individuals may have substantially more or less. Such a sample could be modeled using subpopulations (African and K = 2 European), with typical individuals having q1 in the range and q2 in the range , but with some (.05,.2) (.8,.95) individuals having more extreme values. The challenge is to infer this kind of pattern using genetic data. Pritchard et al. (2000) provide a method of performing such inference, even when little is known about either the number of subpopulations that have contributed to the sample or the allele frequencies in these putative subpopulations....
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...For example, in a sample of African Americans, a typical individual might have 5%–20% European admixture (Parra et al. 1998), whereas some individuals may have substantially more or less....
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...For example, in a sample of African Americans, a typical individual might have 5%–20% European admixture (Parra et al. 1998), whereas some individuals may have substantially more or less. Such a sample could be modeled using subpopulations (African and K = 2 European), with typical individuals having q1 in the range and q2 in the range , but with some (.05,.2) (.8,.95) individuals having more extreme values. The challenge is to infer this kind of pattern using genetic data. Pritchard et al. (2000) provide a method of performing such inference, even when little is known about either the number of subpopulations that have contributed to the sample or the allele frequencies in these putative subpopulations. They use a Markov chain Monte Carlo method to estimate the number of subpopulations, the allele frequencies in each subpopulation, and the value of q for each sampled individual. The method can be applied to most of the commonly used genetic markers, including microsatellites and SNPs, and can produce accurate results using modest numbers of loci, even when popular clustering algorithms such as Neighbor-Joining are relatively uninformative. The accuracy of the inference depends on the sample size, the number of loci used, and on the magnitude of allele-frequency differences between the subpopulations. Examples of applications of this method are given later. See Pritchard et al. (2000) for further details....
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"Estimating African American admixtu..." refers background in this paper
...…also been proposed by McKeigue (1997) and Kaplan et al. (1997) that the linkage disequilibrium that results from recent admixture could also be used to detect disease genes for qualitative or quantitative traits by means of the transmission disequilibrium test (Spielman et al. 1993; Allison 1997)....
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...(1997) that the linkage disequilibrium that results from recent admixture could also be used to detect disease genes for qualitative or quantitative traits by means of the transmission disequilibrium test (Spielman et al. 1993; Allison 1997)....
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1,913 citations
"Estimating African American admixtu..." refers background or methods in this paper
...…regions were Senegambia (Gambia and Senegal), Sierra Leone (Guinea and Sierra Leone), Windward Coast (Ivory Coast and Liberia), Gold Coast (Ghana), Bight of Benin (from the Volta River to the Benin River), Bight of Biafra (east of the Benin River to Gabon), and Angola (southwest Africa,…...
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...D′ coefficients, in which the gametic disequilibrium (D) is standardized by the theoretical maximum disequilibrium (Dmax), were calculated on the basis of the estimated haplotype frequencies (Lewontin 1964, 1988; Thomson et al. 1988)....
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"Estimating African American admixtu..." refers background in this paper
...L and H are the most common haplogroups that are unique to African and European populations, respectively (Torroni et al. 1994, 1996; Chen et al. 1995), and can be used to test the relative African and European maternal contribution to African Americans and Jamaicans....
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