Estimating African American admixture proportions by use of population-specific alleles.
paper
Cited
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- Authors
- Parra, E J; Marcini, A; Akey, J; Martinson, J; Batzer, M A; Cooper, R; Forrester, T; Allison, D B; Deka, R; Ferrell, R E; Shriver, M D
- Year
- 1998
- Journal
- American journal of human genetics
- PMID
- 9837836
- DOI
- 10.1086/302148
- PMCID
- PMC1377655
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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| Genetic approaches to identify disease genes for birth defects with cleft lip/palate as a model. | Lidral AC et al. | β | 2004 | β |
| Genetic signatures of strong recent positive selection at the lactase gene. | Bersaglieri T et al. | β | 2004 | β |
| Implications of biogeography of human populations for 'race' and medicine. | Tishkoff SA et al. | β | 2004 | β |
| Implications of correlations between skin color and genetic ancestry for biomedical research. | Parra EJ et al. | β | 2004 | β |
| Information on ancestry from genetic markers. | Pfaff CL et al. | β | 2004 | β |
| Mapping multiple sclerosis susceptibility to the HLA-DR locus in African Americans. | Oksenberg JR et al. | β | 2004 | β |
| Maximum-likelihood estimation of demographic parameters using the frequency spectrum of unlinked single-nucleotide polymorphisms. | Adams AM et al. | β | 2004 | β |
| Methods for high-density admixture mapping of disease genes. | Patterson N et al. | β | 2004 | β |
| Mexican American ancestry-informative markers: examination of population structure and marker characteristics in European Americans, Mexican Americans, Amerindians and Asians. | Collins-Schramm HE et al. | β | 2004 | β |
| New approaches to gene hunting in IBD. | Daly MJ et al. | β | 2004 | β |
| NOTCH4 gene haplotype is associated with schizophrenia in African Americans. | Luo X et al. | β | 2004 | β |
| Nutritional genomics: the next frontier in the postgenomic era. | Kaput J et al. | β | 2004 | β |
| Polymorphic Alu insertions in six Brazilian African-derived populations. | Cotrim NH et al. | β | 2004 | β |
| Population history and natural selection shape patterns of genetic variation in 132 genes. | Akey JM et al. | β | 2004 | β |
| Population-specific alleles: the polymorphism (K121Q) of the human glycoprotein PC-1 gene is strongly associated with race but not with insulin resistance in black and white children. | Morrison JA et al. | β | 2004 | β |
| Preconception and prenatal cystic fibrosis carrier screening of African Americans reveals unanticipated frequencies for specific mutations. | Monaghan KG et al. | β | 2004 | β |
| Recent developments in genetic data analysis: what can they tell us about human demographic history? | Beaumont MA | β | 2004 | β |
| Simultaneous detection of linkage disequilibrium and genetic differentiation of subdivided populations. | Kitada S et al. | β | 2004 | β |
| Statistical tests for admixture mapping with case-control and cases-only data. | Montana G et al. | β | 2004 | β |
| The African diaspora: mitochondrial DNA and the Atlantic slave trade. | Salas A et al. | β | 2004 | β |
| The genomic distribution of population substructure in four populations using 8,525 autosomal SNPs. | Shriver MD et al. | β | 2004 | β |
| The T allele of a single-nucleotide polymorphism 13.9 kb upstream of the lactase gene (LCT) (C-13.9kbT) does not predict or cause the lactase-persistence phenotype in Africans. | Mulcare CA et al. | β | 2004 | β |
| Using genetic admixture to study the biology of obesity traits and to map genes in admixed populations. | FernΓ‘ndez JR et al. | β | 2004 | β |
| Admixture analysis of South Asian cattle. | Kumar P et al. | β | 2003 | β |
| Admixture mapping using interval transmission/disequilibrium tests. | Lee WC et al. | β | 2003 | β |
| "Are we there yet?": Deciding when one has demonstrated specific genetic causation in complex diseases and quantitative traits. | Page GP et al. | β | 2003 | β |
| Association of interleukin-6 promoter variant with bone mineral density in pre-menopausal women. | Chung HW et al. | β | 2003 | β |
| Carrier frequency of the RSH/Smith-Lemli-Opitz IVS8-1G>C mutation in African Americans. | Wright BS et al. | β | 2003 | β |
| Color and genomic ancestry in Brazilians. | Parra FC et al. | β | 2003 | β |
| Comparison of polymorphisms in the alpha7 nicotinic receptor gene and its partial duplication in schizophrenic and control subjects. | Gault J et al. | β | 2003 | β |
| Control of confounding of genetic associations in stratified populations. | Hoggart CJ et al. | β | 2003 | β |
| Ethnic differences in markers of thrombophilia: implications for the investigation of ischemic stroke in multiethnic populations: the South London Ethnicity and Stroke Study. | Jerrard-Dunne P et al. | β | 2003 | β |
| Genome-wide linkage scan for the metabolic syndrome in the HERITAGE Family Study. | Loos RJ et al. | β | 2003 | β |
| Genotype-phenotype analysis for the polymorphic CA repeat in the insulin-like growth factor-I (IGF-I) gene. | Kato I et al. | β | 2003 | β |
| Human population structure and genetic association studies. | Ziv E et al. | β | 2003 | β |
| Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. | Falush D et al. | β | 2003 | β |
| Large-scale genotyping of complex DNA. | Kennedy GC et al. | β | 2003 | β |
| Locus-specific genetic diversity between human populations: an analysis of the literature. | Garte S | β | 2003 | β |
| Markers informative for ancestry demonstrate consistent megabase-length linkage disequilibrium in the African American population. | Collins-Schramm HE et al. | β | 2003 | β |
| Maximum-likelihood estimation of admixture proportions from genetic data. | Wang J | β | 2003 | β |
| Measuring and using admixture to study the genetics of complex diseases. | Halder I et al. | β | 2003 | β |
| Patterns of human genetic diversity: implications for human evolutionary history and disease. | Tishkoff SA et al. | β | 2003 | β |
| Race, ancestry, and genes: implications for defining disease risk. | Kittles RA et al. | β | 2003 | β |
| Sarcoidosis susceptibility and resistance HLA-DQB1 alleles in African Americans. | Iannuzzi MC et al. | β | 2003 | β |
| Sequence diversity and haplotype structure in the human ABCB1 (MDR1, multidrug resistance transporter) gene. | Kroetz DL et al. | β | 2003 | β |
| Skin pigmentation, biogeographical ancestry and admixture mapping. | Shriver MD et al. | β | 2003 | β |
| The agouti-related protein and body fatness in humans. | Argyropoulos G et al. | β | 2003 | β |
| The importance of race and ethnic background in biomedical research and clinical practice. | Burchard EG et al. | β | 2003 | β |
| Using genetic admixture to explain racial differences in insulin-related phenotypes. | Gower BA et al. | β | 2003 | β |
| Y chromosome STR haplotypes and the genetic structure of U.S. populations of African, European, and Hispanic ancestry. | Kayser M et al. | β | 2003 | β |
| A comparison of HLA-DR and -DQ allele and haplotype frequencies in Trinidadian populations of African, South Asian, and mixed ancestry. | Carrington CV et al. | β | 2002 | β |
| Adjusting for population structure in admixed populations. | Pfaff CL et al. | β | 2002 | β |
| Categorization of humans in biomedical research: genes, race and disease. | Risch N et al. | β | 2002 | β |
| Ethnic-difference markers for use in mapping by admixture linkage disequilibrium. | Collins-Schramm HE et al. | β | 2002 | β |
| Genetic influences on rheumatoid arthritis in African Americans. | Hughes LB et al. | β | 2002 | β |
| Genetic mapping in hybrid zones. | Rieseberg LH et al. | β | 2002 | β |
| Genetic origins in a South American clefting population. | Vieira AR et al. | β | 2002 | β |
| Genetic polymorphisms in lung disease: bandwagon or breakthrough? | Iannuzzi MC et al. | β | 2002 | β |
| Geographic and haplotype structure of candidate type 2 diabetes susceptibility variants at the calpain-10 locus. | Fullerton SM et al. | β | 2002 | β |
| Interrogating a high-density SNP map for signatures of natural selection. | Akey JM et al. | β | 2002 | β |
| Melting curve SNP (McSNP) genotyping: a useful approach for diallelic genotyping in forensic science. | Ye J et al. | β | 2002 | β |
| Potentially functional polymorphism in the promoter region of prodynorphin gene may be associated with protection against cocaine dependence or abuse. | Chen AC et al. | β | 2002 | β |
| PROGINS Alu insertion and human genomic diversity. | Donaldson CJ et al. | β | 2002 | β |
| Prospects of admixture linkage disequilibrium mapping in the African-American genome. | Rybicki BA et al. | β | 2002 | β |
| Testing for population subdivision and association in four case-control studies. | Ardlie KG et al. | β | 2002 | β |
| The changing face of epidemiology in the genomics era. | Millikan R | β | 2002 | β |
| The design, execution, and interpretation of genetic association studies to decipher complex diseases. | Romero R et al. | β | 2002 | β |
| The distribution of long range admixture linkage disequilibrium in an African-American population. | Rybicki BA et al. | β | 2002 | β |
| Uncoupling proteins and thermoregulation. | Argyropoulos G et al. | β | 2002 | β |
| Unequal contributions of male and female gene pools from parental populations in the African descendants of the city of Melo, Uruguay. | Sans M et al. | β | 2002 | β |
| Accounting for unmeasured population substructure in case-control studies of genetic association using a novel latent-class model. | Satten GA et al. | β | 2001 | β |
| Analysis of the CYP2D6 gene polymorphism and enzyme activity in African-Americans in southern California. | Wan YJ et al. | β | 2001 | β |
| Ancestral proportions and admixture dynamics in geographically defined African Americans living in South Carolina. | Parra EJ et al. | β | 2001 | β |
| A role for the Agouti-Related Protein promoter in obesity and type 2 diabetes. | Mayfield DK et al. | β | 2001 | β |
| Clustering of pedigrees using marker allele frequencies: impact on linkage analysis. | Grigull J et al. | β | 2001 | β |
| Effects of fasting on muscle mitochondrial energetics and fatty acid metabolism in Ucp3(-/-) and wild-type mice. | BΓ©zaire V et al. | β | 2001 | β |
| Estimation of admixture proportions: a likelihood-based approach using Markov chain Monte Carlo. | Chikhi L et al. | β | 2001 | β |
| Heritability of obesity-related traits among Nigerians, Jamaicans and US black people. | Luke A et al. | β | 2001 | β |
| Inferring admixture proportions from molecular data: extension to any number of parental populations. | Dupanloup I et al. | β | 2001 | β |
| Markers for mapping by admixture linkage disequilibrium in African American and Hispanic populations. | Smith MW et al. | β | 2001 | β |
| Pharmacogenetics, race, and ethnicity: social identities and individualized medical care. | Foster MW et al. | β | 2001 | β |
| Population structure in admixed populations: effect of admixture dynamics on the pattern of linkage disequilibrium. | Pfaff CL et al. | β | 2001 | β |
| Risk ratios for obesity in families of obese African-American and Caucasian women. | Price RA et al. | β | 2001 | β |
| Association mapping in structured populations. | Pritchard JK et al. | β | 2000 | β |
| Consistent long-range linkage disequilibrium generated by admixture in a Bantu-Semitic hybrid population. | Wilson JF et al. | β | 2000 | β |
| Genetic inheritance of body mass index in African-American and African families. | Colilla S et al. | β | 2000 | β |
| Heritage characteristics reported by a group of African-Americans who exhibit the pigment dispersion syndrome: a case-control study. | Roberts DK et al. | β | 2000 | β |
| Human genomic variation. | Disotell TR | β | 2000 | β |
| Inference of population structure using multilocus genotype data. | Pritchard JK et al. | β | 2000 | β |
| Significant admixture linkage disequilibrium across 30 cM around the FY locus in African Americans. | Lautenberger JA et al. | β | 2000 | β |
| Survey of the fragile X syndrome CGG repeat and the short-tandem-repeat and single-nucleotide-polymorphism haplotypes in an African American population. | Crawford DC et al. | β | 2000 | β |
| Transthyretin isoleucine-122 mutation in African and American blacks. | Afolabi I et al. | β | 2000 | β |
| Endogenous mutations in human uncoupling protein 3 alter its functional properties. | Brown AM et al. | β | 1999 | β |
| Nativity and race. | Gleiberman L | β | 1999 | β |
| The influence of T cell receptor and cytokine genes on sarcoidosis susceptibility in African Americans. | Rybicki BA et al. | β | 1999 | β |
| A DNA polymorphism discovery resource for research on human genetic variation. | Collins FS et al. | β | 1998 | β |
| Trinucleotide repeat length variation in the human ribosomal protein L14 gene (RPL14): localization to 3p21.3 and loss of heterozygosity in lung and oral cancers. | Shriver SP et al. | β | 1998 | β |