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Skin pigmentation, biogeographical ancestry and admixture mapping
Mark D. Shriver et al.
Hum Genet (2003) 112: 387-399
Abstract Ancestry informative markers (AIMs) are genetic loci showing alleles with large frequency differences between populations. AIMs can be used to estimate biogeographical ancestry at the level of the population, subgroup (e.g. cases and controls) and individual. Ancestry estimates at both the subgroup and individual level can be directly instructive regarding the genetics of the phenotypes that differ qualitatively or in frequency between populations. These estimates can provide a compelling foundation for the use of admixture mapping (AM) methods to identify the genes underlying these traits. We present details of a panel of 34 AIMs and demonstrate how such studies can proceed, by using skin pigmentation as a model phenotype. We have genotyped these markers in two population samples with primarily African ancestry, viz. African Americans from Washington D.C. and an African Caribbean sample from Britain, and in a sample of European Americans from Pennsylvania. In the two African population samples, we observed significant correlations between estimates of individual ancestry and skin pigmentation as measured by reflectometry (R2=0.21, P<0.0001 for the African-American sample and R2=0.16, P<0.0001 for the British African-Caribbean sample). These correlations confirm the validity of the ancestry estimates and also indicate the high level of population structure related to admixture, a level that characterizes these populations and that is detectable by using other tests to identify genetic structure. We have also applied two methods of admixture mapping to test for the effects of three candidate genes (TYR, OCA2, MC1R) on pigmentation. We show that TYR and OCA2 have measurable effects on skin pigmentation differences between the west African and west European parental populations. This work indicates that it is possible to estimate the individual ancestry of a person based on DNA analysis with a reasonable number of well-defined genetic markers. The implications and applications of ancestry estimates in biomedical research are discussed.
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The sample of African Americans from Washington D.C. shows a significantly higher European contribution than the African Caribbean sample from Britain (18.6%±1.5% vs 10.2%±1.4%). In both samples, the native American contribution is small, with the 95% confidence intervals overlapping 0.0 (Washington, D.C.: 2.7%; African Caribbeans: 1.9%). In European Americans from State College, the west African and native American genetic contribution are low (0.7% and 3.2%, respectively).
Posted by Dienekes at March 26, 2003 11:18 PM | PermaLinkFor a few years I had read that U.S. Negroes were estimated to be about 30 percent white. Steve Sailer said current opinion held that the figure was lower, around 17 or 18 percent. This abstract conforms with Steve's figure.
Posted by: Unadorned at March 30, 2003 08:57 PMYes, in fact there is a study of Parra et. al. that says that:
http://www.journals.uchicago.edu/AJHG/journal/issues/v63n6/980409/980409.html
Estimating African American Admixture Proportions by Use of Population-Specific Alleles
Esteban J. Parra,1, Amy Marcini,1 Joshua Akey,1 Jeremy Martinson,2 Mark A. Batzer,3 Richard Cooper,4 Terrence Forrester,5 David B. Allison,6 Ranjan Deka,7 Robert E. Ferrell,2 Mark D. Shriver1,
1Department of Human Genetics, Allegheny University of the Health Sciences, and 2Department of Human Genetics, University of Pittsburgh, Pittsburgh; 3Department of Pathology, Stanley S. Scott Cancer Center, Louisiana State University Medical Center, New Orleans; 4Department of Preventive Medicine and Epidemiology, Loyola University Stritch School of Medicine, Maywood, Illinois; 5Tropical Metabolism Research Unit, University of the West Indies, Mona, Jamaica; 6Obesity Research Center, St. Luke'sRoosevelt Hospital, Columbia University College of Physicians and Surgeons, New York; and 7Department of Environmental Health, University of Cincinnati, Cincinnati
Received May 22, 1998; accepted for publication September 18, 1998; electronically published November 25, 1998.
Summary
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.
*Present affiliation: Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania.
Posted by: J. A. at April 2, 2003 10:18 AMTo Whom It May Concern,
I have a dilemna that I hope you might be able to assist me in sorting out.
I have NMR Lipoprofile performed with results of:
LDL-218
HDL-41
VLDL-119
Giving me a total of 279 total cholersterol counts.
The screening was performed by
LipoScience, Inc.
3009 New Bern Ave.
Raleigh, NC 27610
(877) 547-6837
www.liposcience.com
However, my LDL cholersterol is Pattern A, meaning I have large particle LDL, of which I have been instructed that this is not a risk factor.
This is genetic in my family. My father and brothers are also high and there is no coronary heart disease in my present family. My father is 91 and his cholesterol count is 300. Same with my brothers, two in their 60's, and one late 50's.
All of us enjoy vigorous health. We are all type O+ blood.
My paternal grandmother was from Suriname, South America, and the child of a Dutch landholder and an emancipated slave and it is only family hearsay that her lineage was Amerindian. I have check with the Archives of Holland, and they have exhaused their database for this colony to assist me in discovering solid evidence of her ethnicity only have nothing except records of emancipation.
In those times, all ethnicities of slaves were ignored and slaves were catagorized as one with no distinctions made.
All of our ethnic characteristics are that of Amerindian people.
Is there a way to discover, though our blood, the true nature of our ethnicity?
I understand there are genetic testing facilities that are very expensive, and it has been mentioned to me that there are other ways to screen for certain antigens that would identify phenotypes, and are affordable.
We, as a family, would like to investigate this to further understand our physical health and, of course, our genetic health.
Thank you for your attention in this manner.
Sincerely,
Marie Wilcox
Indiana
Recently I read that there have been MTA DNA studies done in Puerto Rico by Juan Martinez Crusado of the University of Mayaguez.The results for Native American Haplogroups was 61%. Have studies like this one been done In Haiti, Dominican Republic, Cuba, Jamaica? If so what were the results? I just cant figure how an island such as Puerto Rico can have such high Amerindian descent, when historically it is said that the Natives of the Caribbean were all wiped out.
John