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PubMed1980

Skin colorimetry and admixture measurement: some further considerations.

Several techniques for using skin colorimetric data to measure admixture contributions to a hybrid population have been reviewed by Lees and Relethford ('78), who find this general approach to be useful. This paper extends their evaluation, providing a method for obtaining an error term and considering at greater length certain potential sources of estimate bias. Questions are raised about their discussion of the appropriate employment of distance statistics in this context, and an alternative procedure for obtaining a single estimate of admixture proportions jointly over all reflectance measurements is offered. While it is shown that the hybrid reflectance curves do not support entirely an assumption of unlinked foci contributing equally and additively to skin color, preliminary findings indicate that admixture estimates made from these data are apparently unbiased and reasonably efficient.

Black People↗

PubMed1986

Relationship of prevalence of non-insulin-dependent diabetes mellitus to Amerindian admixture in the Mexican Americans of San Antonio, Texas.

A genetic and epidemiological survey of non-insulin-dependent diabetes mellitus (NIDDM) was conducted among the Mexican Americans residing in three socioeconomically distinct areas of San Antonio, Texas: a low socioeconomic (SES) traditional area (barrio), a middle SES, ethnically balanced area (transitional), and a high SES, predominantly Anglo area (suburb). Seventeen polymorphic markers were used to relate the prevalences of NIDDM with the extent of Amerindian ancestry of 1,237 Mexican Americans of these three residential areas. While only the RH and haptoglobin loci showed evidence of association with NIDDM, an admixture analysis of the combined allele frequency data revealed a pattern of decreasing NIDDM prevalence with increasing socioeconomic status (as approximated by neighborhood of residence) and a parallel decrease in Amerindian ancestry. The rank-order correlation between NIDDM prevalence and Amerindian admixture is 0.943 (P less than .001) for the crude prevalence rate and 0.829 (P less than .02) for the age-adjusted rate. Nested gene diversity analysis revealed that the heterogeneity of allele frequencies is more pronounced when individuals were classified by their NIDDM disease status as compared to the classification by neighborhood. Estimation of Amerindian ancestry of each individual did not reveal any significant change in the shape of the distributions of individual admixture proportions in diabetics as compared to the controls. Nevertheless, the results suggest that genetic factors partially explain the differences in NIDDM prevalence observed between the Mexican American and Anglo populations in the southwestern United States.

Adult↗

PubMed1992

Detection of linkage under heterogeneity: comparison of the two-locus vs. admixture models.

Linkage analysis under the two-locus model and the admixture model was compared on pedigree data for a common disease stimulated under a model of genetic heterogeneity. The ascertainment of families was designed so that the samples had a large proportion of families segregating for both disease loci. The two-locus linkage analysis model did not demonstrate increased power of detecting linkage or more accurate estimates of the recombination fraction, theta than did the admixture model linkage analysis. When a sample was purposely chosen so that all of the families were segregating for both loci, then the two-locus lod score analysis was better. However, the increased power depended on assuming the correct gene frequency for the linked locus. It can be concluded that under the conditions of genetic heterogeneity examined here, testing for linkage under the admixture model is the preferred method of analysis. However, this is not a general conclusion that can apply to all two-locus disease models.

Chromosome Mapping↗

PubMed2004

A hidden Markov modeling approach for admixture mapping based on case-control data.

Admixture mapping is potentially a powerful method for mapping genes for complex human diseases, when the disease frequency due to a particular disease-susceptible gene is different between founding populations of different ethnicity. The method tests for association of the allele ancestry with the disease. Since the markers used to define ancestral populations are not fully informative for the ancestry status, direct test of such association is not possible. In this report, we develop a unified hidden Markov model (HMM) framework for estimating the unobserved ancestry haplotypes across a chromosomal region based on marker haplotype or genotype data. The HMM efficiently utilizes all the marker data to infer the latent ancestry states at the putative disease locus. In this HMM modelling framework, we develop a likelihood test for association of allele ancestry and the disease risk based on case-control data. Existence of such association may imply linkage between the candidate locus and the disease locus. We evaluate by simulations how several factors affect the power of admixture mapping, including sample size, ethnicity relative risk, marker density, and the different admixture dynamics. Our simulation results indicate correct type 1 error rates of the proposed likelihood ratio tests and great impact of marker density on the power. The simulation results also indicate that the methods work well for the admixed populations derived from both hybrid-isolation and continuous gene-flowing models. Finally, we observed that the genotype-based HMM performs very similarly in power as the haplotype-based HMM when the haplotypes are known and the set of markers is highly informative.

Alleles↗

PubMed2005

Estimation of individual admixture: analytical and study design considerations.

The genome of an admixed individual represents a mixture of alleles from different ancestries. In the United States, the two largest minority groups, African-Americans and Hispanics, are both admixed. An understanding of the admixture proportion at an individual level (individual admixture, or IA) is valuable for both population geneticists and epidemiologists who conduct case-control association studies in these groups. Here we present an extension of a previously described frequentist (maximum likelihood or ML) approach to estimate individual admixture that allows for uncertainty in ancestral allele frequencies. We compare this approach both to prior partial likelihood based methods as well as more recently described Bayesian MCMC methods. Our full ML method demonstrates increased robustness when compared to an existing partial ML approach. Simulations also suggest that this frequentist estimator achieves similar efficiency, measured by the mean squared error criterion, as Bayesian methods but requires just a fraction of the computational time to produce point estimates, allowing for extensive analysis (e.g., simulations) not possible by Bayesian methods. Our simulation results demonstrate that inclusion of ancestral populations or their surrogates in the analysis is required by any method of IA estimation to obtain reasonable results.

Black or African American↗

PubMed1999

Chemical and Structural Properties of Jordanian Zeolitic Tuffs and Their Admixtures with Urea and Thiourea: Potential Scavengers for Phenolics in Aqueous Medium.

Native Jordanian zeolitic tuffs, rich in phillipsite, were treated with urea and thiourea. The chemical and structural properties of the tuffs and their urea and thiourea admixtures were studied using SEM, XRF, XRD, and FTIR techniques, and their adsorption capacities were estimated by the methylene blue method. The urea and thiourea treatment has not affected the mineral constitution of the tuffs. The results revealed that urea and thiourea were linked by hydrogen bonding through the NH(2) moiety to the zeolite substrate, with urea showing the strongest effect. Experiments were carried out to investigate the possible use of the prepared materials for the removal of phenol and chlorinated phenols from aqueous solutions. Although thiourea caused a reduction in the relative surface area, both urea and thiourea admixtures were more effective than the free zeolitic tuff in the removal of phenol and chlorinated phenols from water, with urea admixture displaying the largest removal capacity. Copyright 1999 Academic Press.

Journal Article↗

PubMed1987

Diabetes and glucose tolerance in New South Wales coastal Aborigines: possible effects of non-Aboriginal genetic admixture.

A survey of adults living in two predominantly Aboriginal communities in eastern New South Wales revealed a crude prevalence of clinically diagnosed diabetes of 6.7% in Aboriginals. 1.4% of Aboriginal subjects investigated with 75 g oral glucose tolerance tests were found to have previously undiagnosed diabetes, and 2.8% had impaired glucose tolerance. 53% of women and 27% of men were obese as judged by body mass index. The age-sex standardised prevalence of diabetes in Aboriginals (previously diagnosed and newly detected) was 7.8%, which is substantially lower than the 15.6% prevalence found in the Aboriginal population of Bourke (central New South Wales). HLA antigen studies on these same individuals suggest approximately 60% genetic admixture from non-Aboriginal sources. Insulin response to oral glucose and mean body mass index were both related to non-Aboriginal genetic admixture with higher values in Aboriginal subjects than in their non-Aboriginal neighbours, and highest values were found in those with no detectable non-Aboriginal HLA haplotypes. The extent of genetic admixture in these communities may partly explain the lower prevalence of diabetes when compared with that found in the Aboriginal population of Bourke.

Adolescent↗

PubMed2003

Skin pigmentation, biogeographical ancestry and admixture mapping.

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 (R(2)=0.21, P<0.0001 for the African-American sample and R(2)=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.

Africa↗

PubMed1992

HLA class I variation controlled for genetic admixture in the Gila River Indian Community of Arizona: a model for the Paleo-Indians.

The genetic distribution of the HLA class I loci is presented for 619 "full blooded" Pima and Tohono O'odham Native Americans (Pimans) in the Gila River Indian Community. Variation in the Pimans is highly restricted. There are only three polymorphic alleles at the HLA-A locus, *A2, *A24, and *A31, and only 10 alleles with a frequency greater than 0.01 at HLA-B where *Bw48 (0.187), *B35 (0.173), and the new epitope *BN21 (0.143) have the highest frequencies. Two and three locus disequilibria values and haplotype frequencies are presented. Ten three-locus haplotypes account for more than 50% of the class I variation, with *A24 *BN21 *Cw3 (0.085) having the highest frequency. Gm allotypes demonstrate that little admixture from non-Indian populations has entered the Community since the 17th century when Europeans first came to this area. As a consequence many alleles commonly found in Europeans and European Americans are efficient markers for Caucasian admixture, while the "private" Indian alleles, *BN21 and *Bw48, can be used to measure Native American admixture in Caucasian populations. It is suggested that this distribution in "full blooded" Pimans approximates that of the Paleo-Indian migrants who first entered the Americas between 20,000 and 40,000 years ago.

Alleles↗

PubMed1994

Resuscitation of canine hemorrhagic hypotension with large-volume isotonic crystalloid: impact on lung water, venous admixture, and systemic arterial oxygen saturation.

The objective of this study was to test the hypothesis that after hemorrhagic hypotension, reinfusion of the shed blood with threefold that volume of lactated Ringer's (LR) solution will significantly increase lung water and venous admixture and hence decrease systemic arterial oxygen saturation. A prospective, randomized, fixed-volume hemorrhage laboratory study was performed at the Oklahoma University Health Sciences Center on 18 anesthetized mongrel dogs. After 40 mL/kg of blood were withdrawn through a femoral artery catheter, the dogs were randomized either to the control group (n = 9) that received a reinfusion of the shed blood, or to the LR treatment group (n = 9) that received an intravenous mixture of the shed blood with 120 mL/kg of LR. After fluid resuscitation, pulmonary artery occlusion pressure (PAOP) and cardiac output (CO) were significantly increased in the LR group compared with control animals (PAOP, 18.7 +/- 1.1 vs 13.4 +/- 2.9 mm Hg; CO, 8.14 +/- 1.08 vs 4.59 +/- 0.47 L/min; P < .05 each). However, lung water, venous admixture, and systemic arterial PO2 were similar between groups. In this fixed-volume hemorrhage model, hemodiluting the reinfused shed blood with threefold the volume of LR did not significantly influence lung water, venous admixture, or systemic arterial oxygen saturation.

Animals↗

PubMed2026

Large-scale admixture mapping in the All of Us Research Program improves the characterization of cross-population phenotypic differences.

Admixed individuals have been understudied in medical research largely due to their complex genetic ancestries. However, the consideration of admixture can identify ancestry-enriched genetic associations, delineating genetic underpinnings of cross-population phenotypic variation. Here, we performed admixture mapping in individuals with inferred admixture from African and European populations (N = 48,921). Across 22 traits, we identified 71 ancestry-trait associations, including loci where ancestral haplotypes explained phenotypic variation yet were missed by single-variant association testing due to their stricter multiple testing burden. One such locus where inferred local AFR ancestries are associated with increased hemoglobin A1c (HbA1c) was 12q14.3, highlighting its potential role in explaining differences between populations. Together, our results expand upon the phenotypic differences between populations and characterize loci where genetic ancestries play a critical role in the architecture of disease.

Humans↗

PubMed2004

Admixture in the Hispanics of the San Luis Valley, Colorado, and its implications for complex trait gene mapping.

Hispanic populations are a valuable resource that can and should facilitate the identification of complex trait genes by means of admixture mapping (AM). In this paper we focus on a particular Hispanic population living in the San Luis Valley (SLV) in Southern Colorado. We used a set of 22 Ancestry Informative Markers (AIMs) to describe the admixture process and dynamics in this population. AIMs are defined as genetic markers that exhibit allele frequency differences between parental populations >or=30%, and are more informative for studying admixed populations than random markers. The ancestral proportions of the SLV Hispanic population are estimated as 62.7 +/- 2.1% European, 34.1 +/- 1.9% Native American and 3.2 +/- 1.5% West African. We also estimated the ancestral proportions of individuals using these AIMs. Population structure was demonstrated by the excess association of unlinked markers, the correlation between estimates of admixture based on unlinked marker sets, and by a highly significant correlation between individual Native American ancestry and skin pigmentation (R2= 0.082, p < 0.001). We discuss the implications of these findings in disease gene mapping efforts.

Adult↗

PubMed2006

Admixture mapping identifies 8q24 as a prostate cancer risk locus in African-American men.

A whole-genome admixture scan in 1,597 African Americans identified a 3.8 Mb interval on chromosome 8q24 as significantly associated with susceptibility to prostate cancer [logarithm of odds (LOD) = 7.1]. The increased risk because of inheriting African ancestry is greater in men diagnosed before 72 years of age (P < 0.00032) and may contribute to the epidemiological observation that the higher risk for prostate cancer in African Americans is greatest in younger men (and attenuates with older age). The same region was recently identified through linkage analysis of prostate cancer, followed by fine-mapping. We strongly replicated this association (P < 4.2 x 10(-9)) but find that the previously described alleles do not explain more than a fraction of the admixture signal. Thus, admixture mapping indicates a major, still-unidentified risk gene for prostate cancer at 8q24, motivating intense work to find it.

Black or African American↗

PubMedDate not supplied

Genetic structure and admixture in urban populations of the Argentine North-West.

BACKGROUND: From the ethnic point of view, the Argentine North-West (ANW) constitutes one of the most noticeable areas in the country due to the cultural peculiarities that integrate it to the Andean world and the ethno-historical and demographic characteristics of how it became populated. AIM: The study analysed the genetic structure and diversity of the ANW urban populations, and the contribution of parental populations to its genetic pool. SUBJECTS AND METHODS: Previously reported data on allele frequencies of HLA-A and HLA-B loci of 1293 individuals from Jujuy, Salta, Tucumán, Santiago del Estero, Catamarca and La Rioja were used. Our estimates include: (a) genetic intra-population diversity; (b) genetic distances between populations; (c) linkage disequilibrium (LD); (d) admixture rates and genetic distances with respect to three parental populations (European, American Indian and African). RESULTS: Low intra-population genetic differentiation and low genetic distances between populations were found. Differential LD distribution varied according to province, with 60% variance due to intra-population differences. The Spanish contribution (50%) predominated in ANW, followed by the American Indian (40%) and African (10%) contributions, and a marked inter-population heterogeneity of genetic admixture rates was observed. The shortest genetic distance was found in the American Indian parental population, and the longest in the African parental population. CONCLUSION: Five hundred years after the Spanish conquest, urban populations at ANW that have probably been subject to the same evolutionary forces present low genetic diversity and a similar genetic structure. Genetic distances and admixture percentages observed agree with census and ethno-historical data on settlement in the region.

Argentina↗

PubMedDate not supplied

Genealogical and genetical African admixture estimations, blood pressure and hypertension in a Caribbean community.

This study examines the relationships between blood pressure, prevalence of hypertension, and the degree of black African admixture in the population of the Caribbean Island of La Désirade which is homogeneous with respect to the environmental factors and for which the socioeconomical stratification does not match racial origin. The degree of admixture was estimated by using both genealogical information and genetic markers. Blood pressure was repeatedly measured using an automatic sphygmomanometer. After adjustment for age, sex, ponderal index, Na/K urinary ratio, and clinical alcoholism, blood pressure and prevalence of hypertension were found to be significantly higher for the individuals having the largest proportion of genes of black origin. Identical results were obtained when either genetic markers or genealogical information were used as an individual--estimator of admixture.

ABO Blood-Group System↗

PubMed2004

Treatment of murine systemic aspergillosis with polyene-intralipid admixtures.

The objective of this research was the evaluation of the activity of admixtures of amphotericin B (AMB)--intralipid (AMB-IL) and nystatin (Ny)--intralipid (Ny-IL) against experimental systemic aspergillosis in immunocompromised mice. ICR mice were transiently immunosuppressed by intraperitoneal (i.p.) administration of cyclophosphamide (CY). Three days post CY administration the mice were inoculated intravenously (i.v.) with Aspergillus fumigatus conidia. The animals were treated with various doses of AMB-IL or Ny-IL admixtures administered i.v. for 5 consecutive days, starting 2 h after infection. The mean survival rate (MSR) and mean survival time (MST) were evaluated during an observation period of 30 days in comparison to untreated infected mice and to animals treated with conventional formulations of these drugs. These experiments showed that AMB-IL increased significantly the MSR. Specifically, the MSR ranged in dependence of dose, between 48 and 65.7% vs. 0% of the untreated (P < 0.001, anova analysis) and 39.7% of AMB-treated animals (P < 0.01). The MSR of the Ny-IL-treated mice ranged between 16.2 and 40% in comparison to 0% of the untreated group (P < 0.001). Treatment with both admixtures prolonged the MST of the mice (AMB-IL: 17.3-23.07 days; Ny-IL: 8.61-16.8 days) in comparison to either untreated (6.13 days) or AMB treated animals (15.23 days). The data obtained in this study show that both AMB-IL and Ny-IL formulations, particularly AMB-IL at the highest dose, were effective in the treatment of experimental systemic aspergillosis.

Amphotericin B↗

PubMed1998

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

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.

Africa↗

PubMed2000

Individual estimates of European genetic admixture associated with lower body-mass index, plasma glucose, and prevalence of type 2 diabetes in Pima Indians.

Individual genetic admixture estimates (IA) from European Americans (EAs) were computed in 7,996 members of the Gila River Indian Community (Arizona). Parental populations for the analysis were European Americans and full-heritage Pima Indians. A logistic regression was performed on 7,796 persons, to assess association of IA with type 2 diabetes. The odds ratio, comparing diabetes risk in full-heritage EAs with full-heritage Pima Indians, was 0.329 (95% confidence interval [CI] 0.225-0.482). Proportional-hazards analysis was performed on 5,482 persons who were nondiabetic at their first examination and 1,215 subjects who developed diabetes during the study. The hazard risk ratio for IA was 0.455 (95% CI 0.301-0.688). Nondiabetic persons had significantly more European IA. In nondiabetic Pimans, multivariate linear regressions of quantitative predictors of type 2 diabetes mellitus, including fasting plasma glucose, 2-h post-load plasma glucose, and body-mass index, showed significant inverse relations with IA when controlled for sex and age. These results illustrate the ongoing evolution of populations by the mechanism of gene flow and its effect on disease risk in the groups with admixture. When the two parental populations differ in disease prevalence, higher or lower risk is associated with admixture, depending on the origin of the admixed alleles and the relative magnitude of the disease prevalence in the parental populations. These data also illustrate the strong genetic components in type 2 diabetes and are consistent with one susceptibility locus common to obesity and diabetes.

Age Factors↗