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.     

GM allotypes in Native Americans: evidence for three distinct migrations across the Bering land bridge

We report the results of typings, for immunoglobulin G allotypes, of 5392 Native Americans from ten samples, the typings having been performed over the last 20 years. Four cultural groups are represented: the Pimans-Pima and Papago; the Puebloans-Zuni and Hopi; the Pai-Walapai; and the Athabascans-Apache and Navajo. The haplotype Gm1;21 has the highest frequency in each population while Gm1,2;21 is polymorphic in all except the Hopi. The Mongoloid marker Gm1;11,13 is found primarily in the Athabascans. The Caucasian haplotype Gm3;5,11,13 is found at polymorphic frequencies in several of the populations but its frequency is very low or absent among nonadmixed individuals. Although Nei's standard genetic distance analysis demonstrates genetic similarity at the Gm and Km loci, the heterogeneity that does exist is consistent both with what is known about the prehistory of Native Americans and traditional cultural categories. When the current Gm distributions are analyzed with respect to the three-migration hypothesis, there are three distinct Gm distributions for the postulated migrants: Gm1;21 and Gm1,2;21 for the Paleo-Indians 16,000 to 40,000 years ago; Gm1;21, Gm1,2;21, and Gm1;11,13 for the second wave of Na-Dene hunters 12,000 to 14,000 years ago; and Gm1;21 and Gm1;11,13 for the Eskimo-Aleut migration 9,000 years ago. The Pimans, Puebloans, and the Pai are descendents of the Paleo-Indians while the Apache and Navajo are the contemporary populations related to the Na-Dene. Finally, the Gm distribution in Amerindians is found to be consistent with a hypothesis of one migration of Paleo-Indians to South American, while the most likely homeland for the three ancestral populations is found to be in northeastern Asia.     

中国人免疫球蛋白同种异型的研究:中华民族起源的一个假说

调查了我国24个民族、74个群体的免疫球蛋白同种异型Gm、Km分布。测定了9560例个体的Gm(1,2,3,5,21)因子和9611例个体的Km(1)因子。根据Gm单体型频率计算了遗传距离并绘制了系统树。结果支持作者早前提出的有关中华民族起源于古代两个不同群体的假说。这两个群体大致以北纬30度为界,分别居栖在黄河和长江流域。本文数据和其他主要人种的Gm分布资料相比较,作者认为在人类进化中,尼格鲁人种首先和高加索-蒙古人种分离;然后高加索人种和蒙古人种分离。不同人种间的差异,大于同一人种内不同群体间的差异。蒙古人种明显地被分为南、北两大类型,分别以具有高频率的Gm~(1;21)和Gm~(1,3;5)单体型作为种族的标记。与高加索人种关联的Gm~(3;5)单体型存在于中国西北地区的少数民族中,提示混有高加索人种血缘。很可能来源于中亚地区的高加索人,通过“丝绸之路”进入中国。Km因子在所调查的74个群体中呈随机分布。     

Analysis of DNA polymorphism haplotypes linked to the cystic fibrosis locus in North American black and Caucasian families supports the existence of multiple mutations of the cystic fibrosis gene.

Strong linkage disequilibrium (LD) was found between DNA marker XV2c and the cystic fibrosis (CF) locus (delta = 0.46) and between DNA marker KM19 and CF (delta = 0.67) in 157 CF and 138 normal chromosomes from U.S. Caucasians. DNA haplotypes with nine polymorphic sites were created in 54 Caucasian families. There is a strong LD between the haplotypes and the presence of the mutant CF genes. This implies that the DNA polymorphisms examined are close to the CF gene and that one mutation of the CF gene predominates in the Caucasian population. Haplotype analysis can also be used to refine estimates of CF carrier risk in Caucasians. Data for XV2c and MET markers in 16 American black patients and their families revealed a different haplotype distribution and LD pattern with the CF locus. These data suggest that racial admixture alone does not explain the occurrence of CF in American blacks and that multiple alleles of the CF gene may exist in this population.     

Population genetic studies of the Philippine Negritos. II. gm and km allotypes of three population groups.

Serum samples of the three tribal Negrito populations in the Philippine Islands (127 from Zambales, 87 from Bataan, and 93 from Agusan) were tested for Glm(1,2,3 and 17), and G3m(5,6,11,13,14,15,16, and 21), and Km(1). The GMpatterm of the Negritos is characterized by three haplotypes, Gm1,17;21, Gm1,2,17;21, and Gm1,3;5,11,13,14, which is also characteristic of Mongoloid-related populations, especially with high incidence of the latter haplotype. They also have the haplotype, Gm1,17;5,13,14, prevalent in Africa, New Guinea, and northern Australia, suggesting an ancient link between the Negritos and the New Guinean-Australian group. Two unusual samples of G3m(15) positive without G3m(16) observed in Zambales Negritos suggest the presence of Gm1,17;5,11,13,14,15 haplotype in the population. This appears to be unique to Zambales Negritos and the first such samples to be found.     

Robust testing of haplotype/disease association

Haplotypes, the combination of closely linked alleles that fall on the same chromosome, show great promise for studying the genetic components of complex diseases. However, when only multilocus genotype data are available, statistical approaches need to be employed to resolve haplotype phase ambiguity. Recently, we have proposed an approach to testing and estimating haplotype/disease association that is invariant to any existing genetic structure in the population. Here we evaluate this approach by applying it to the Genetic Analysis Workshop 14 simulated data.     

Gm and Km allotypes in 74 Chinese populations: a hypothesis of the origin of the Chinese nation

Summary This paper reports the distribution of immunoglobulin Gm and Km allotypes in 74 Chinese geographical populations. These populations are derived from 24 nationalities comprising 96.6% of the total population of China. A total of 9,560 individuals were phenotyped for Gm(1,2,3,5,21) factors, and 9,611 were phenotyped for Km(1). Phylogenetic trees were constructed on the basis of Gm haplotype frequencies and genetic distances. The results of cluster analysis show the heterogeneity of the Chinese nation, and confirm the hypothesis that the modern Chinese nation originated from two distinct populations, one population originating in the Yellow River valley and the other originating in the Yangtze River valley during early neolithic times (3,000–7,000 years ago). Frequencies of the Gm haplotype of 74 Chinese populations were compared with those of 33 populations from major racial groups. The results suggest that during human evolution, the Negroid group and Caucasoid-Mongoloid group diverged first, followed by a divergence between the Caucasoid and Mongoloid. Interrace divergence is high in comparison with intrarace divergence. There appear to be two distinct subgroups of Mongoloid, northern and southern Mongoloid. The northern and southern Mongoloid have Gm^1;21 and Gm^1,3;5 haplotypes as race-associate markers, respectively. Furthermore, the Caucasian-associated haplotype Gm^3;5 was found in several of the minorities living in the northwest part of China. The presence of the Gm^3;5 haplotype is attributed to the Caucasians living in Central Asia throughout the Silk Road. The amount of Caucasian admixture has been estimated. In contrast to the Gm haplotype distribution, Km¹ gene frequencies showed a random distribution in the populations studied.     

Mapping disease genes: family-based association studies.

With recent rapid advances in mapping of the human genome, including highly polymorphic and closely linked markers, studies of marker associations with disease are increasingly relevant for mapping disease genes. The use of nuclear-family data in association studies was initially developed to avoid possible ethnic mismatching between patients and randomly ascertained controls. The parental marker alleles not transmitted to an affected child or never transmitted to an affected sib pair form the so-called AFBAC (affected family-based controls) population. In this paper, the theoretical foundation of the AFBAC method is proved for any single-locus model of disease and for any nuclear family-based ascertainment scheme. In a random-mating population, when there is a marker association with disease, the AFBAC population provides an unbiased estimate of the overall population (control) marker alleles when the recombination fraction (theta) between the marker and disease genes is sufficiently small that it can be taken as zero (theta = 0). With population stratification, only marker associations present in the subpopulations will be detected with family-based analyses. Of more importance, however, is the fact that, when theta not equal to 0, differences between transmitted parental (patient) marker allele frequencies and non- or never-transmitted parental marker allele frequencies (implying a marker association with disease) can only be observed for marker genes linked to a disease gene (theta < 1/2). Thus, associations of unlinked marker loci with disease at the population level, caused by population stratification, migration, or admixture, are eliminated. This validates the use of family-based association tests as an appropriate strategy for mapping disease genes.     

The transmission/disequilibrium test: history, subdivision, and admixture.

Disease association with a genetic marker is often taken as a preliminary indication of linkage with disease susceptibility. However, population subdivision and admixture may lead to disease association even in the absence of linkage. In a previous paper, we described a test for linkage (and linkage disequilibrium) between a genetic marker and disease susceptibility; linkage is detected by this test only if association is also present. This transmission/disequilibrium test (TDT) is carried out with data on transmission of marker alleles from parents heterozygous for the marker to affected offspring. The TDT is a valid test for linkage and association, even when the association is caused by population subdivision and admixture. In the previous paper, we did not explicitly consider the effect of recent history on population structure. Here we extend the previous results by examining in detail the effects of subdivision and admixture, viewed as processes in population history. We describe two models for these processes. For both models, we analyze the properties of (a) the TDT as a test for linkage (and association) between marker and disease and (b) the conventional contingency statistic used with family data to test for population association. We show that the contingency test statistic does not have a chi 2 distribution if subdivision or admixture is present. In contrast, the TDT remains a valid chi 2 statistic for the linkage hypothesis, regardless of population history.     

African ancestry and its correlation to type 2 diabetes in African Americans: a genetic admixture analysis in three U.S. population cohorts

The risk of type 2 diabetes is approximately 2-fold higher in African Americans than in European Americans even after adjusting for known environmental risk factors, including socioeconomic status (SES), suggesting that genetic factors may explain some of this population difference in disease risk. However, relatively few genetic studies have examined this hypothesis in a large sample of African Americans with and without diabetes. Therefore, we performed an admixture analysis using 2,189 ancestry-informative markers in 7,021 African Americans (2,373 with type 2 diabetes and 4,648 without) from the Atherosclerosis Risk in Communities Study, the Jackson Heart Study, and the Multiethnic Cohort to 1) determine the association of type 2 diabetes and its related quantitative traits with African ancestry controlling for measures of SES and 2) identify genetic loci for type 2 diabetes through a genome-wide admixture mapping scan. The median percentage of African ancestry of diabetic participants was slightly greater than that of non-diabetic participants (study-adjusted difference = 1.6%, P<0.001). The odds ratio for diabetes comparing participants in the highest vs. lowest tertile of African ancestry was 1.33 (95% confidence interval 1.13-1.55), after adjustment for age, sex, study, body mass index (BMI), and SES. Admixture scans identified two potential loci for diabetes at 12p13.31 (LOD = 4.0) and 13q14.3 (Z score = 4.5, P = 6.6 × 10(-6)). In conclusion, genetic ancestry has a significant association with type 2 diabetes above and beyond its association with non-genetic risk factors for type 2 diabetes in African Americans, but no single gene with a major effect is sufficient to explain a large portion of the observed population difference in risk of diabetes. There undoubtedly is a complex interplay among specific genetic loci and non-genetic factors, which may both be associated with overall admixture, leading to the observed ethnic differences in diabetes risk.     

Relative predispositional effects (RPEs) of marker alleles with disease: HLA-DR alleles and Graves disease.

A method is described to reveal the relative predispositional effects (RPEs) (predisposing, protective, or neutral) of the HLA alleles or of any other marker system that is associated with a disease. When the disease is associated with two or more alleles of a locus, the RPE method identifies the associations sequentially according to their strength; thus the problem that a strong association with one allele can create misleading deviations in the frequencies of other alleles is alleviated. Using this method, we have examined the relative effects of HLA-DR alleles in susceptibility to Graves disease in the Caucasian population. The well-established positive association with DR3 was confirmed as the strongest effect. In addition, a negative association was found between DR5 and Graves disease. The reduced frequency of DR5 among patients is statistically significant and is not a result of the increase in DR3. Finally, when patients were divided according to the presence or absence of eye disease, the latter showed a significant increase in the frequency of DR4. With family data, linkage to HLA of Graves disease was established in both Caucasian and Chinese families by the sib-pair method.     

Testing for association based on excess allele sharing in a sample of related cases and controls

Samples consisting of a mix of unrelated cases and controls, small pedigrees, and much larger pedigrees present a unique challenge for association studies. Few methods are available for efficient analysis of such a broad spectrum of data structures. In this paper we introduce a new matching statistic that is well suited to complex data structures and compare it with frequency-based methods available in the literature. To investigate and compare the power of these methods we simulate datasets based on complex pedigrees. We examine the influence of various levels of linkage disequilibrium (LD) of the disease allele with a marker allele (or equivalently a haplotype). For low frequency marker alleles/haplotypes, frequency-based statistics are more powerful in detecting association. In contrast, for high frequency marker alleles, the matching statistic has greater power. The highest power for frequency-based statistics occurs when the disease allele frequency closely matches the frequency of the linked marker allele. In contrast maximum power of the matching statistic always occurs for intermediate marker allele frequency regardless of the disease allele frequency. Moreover, the matching and frequency-based statistics exhibit little correlation. We conclude that these two approaches can be viewed as complementary in finding possible association between a disease and a marker for many different situations.     

Pima Indians as a model to study the genetics of NIDDM.

More than half the Pima Indians over 35 years of age have non-insulin dependent diabetes mellitus (NIDDM). They have been the focus of prospective epidemiologic and metabolic studies for over two decades and the data collected during these studies are now proving invaluable in efforts to find genetic markers for NIDDM in humans. The Pima Indian model of this disease affords two major advantages. The population is genetically homogeneous compared to Caucasian populations, and therefore the causes of NIDDM are less heterogeneous, simplifying genetic linkage studies. Equally important, based on results from metabolic studies, two pre-diabetic phenotypes have been identified in the Pimas: insulin resistance and a low metabolic rate. Use of these phenotypes in genetic linkage analyses should greatly improve chances of finding genetic markers for NIDDM since these phenotypes may be more closely related to the putative abnormal gene products, and actual disease genes, than is the hyperglycemia of the fully developed phenotype of NIDDM.     

Assessing the role of HLA-linked and unlinked determinants of disease.

The relationship between increased risk in relatives over population prevalence (lambda R = KR/K) and probability of sharing zero marker alleles identical by descent (ibd) at a linked locus (such as HLA) by an affected relative pair is examined. For a model assuming a single disease-susceptibility locus or group of loci tightly linked to a marker locus, the relationship is remarkably simple and general. Namely, if phi R is the prior probability for the relative pair to share zero marker alleles identical by descent, then P (sharing 0 markers/both relatives are affected) is just phi R/lambda R. Alternatively, lambda AR, the increased risk over population prevalence to a relative R due to a disease locus tightly linked to marker locus A, equals the prior probability that the relative pair share zero A alleles ibd divided by the posterior probability that they share zero alleles ibd, given that they are both affected. For example, for affected sib pairs, P (sharing 0 markers/both sibs are affected) = .25/lambda S. This formula holds true for any number of alleles at the disease locus and for their frequencies, penetrances, and population prevalence. Similar formulas are derived for sharing one and two markers. Application of these formulas to several well-studied HLA-associated diseases yields the following results: For multiple sclerosis, insulin-dependent diabetes mellitus, and coeliac disease, a single-locus model of disease susceptibility is rejected, implying the existence of additional unlinked familial determinants. For all three diseases, the effect of the HLA-linked locus on familiality is minor: for multiple sclerosis, it accounts for only a 2.5-fold increased risk to sibs over the population prevalence, compared to an observed value of 20; for coeliac disease, it accounts for approximately a 5.25-fold increased risk to sibs, while the observed value is on the order of 60; for insulin-dependent diabetes mellitus, it accounts for a 3.42-fold increased risk in sibs, while the observed value is 15. In all cases, the secondary determinants must be outside the HLA region. For tuberculoid leprosy, an unlinked familial determinant is also implicated (increased risk to sibs due to HLA = 1.49; observed value = 2.38). For hemochromatosis and Hodgkin's disease, there is little evidence for HLA-unlinked familial determinants. With this formula, it is also possible to examine the hypothesis of pleiotropy versus linkage dis-equilibrium by comparing lambda AS with the increased risk to sibs due to the associated allele(s).(ABSTRACT TRUNCATED AT 400 WORDS)     

HLA-DQ primarily confers protection and HLA-DR susceptibility in type I (insulin-dependent) diabetes studied in population-based affected families and controls.

The association between HLA-DR and -DQ and insulin-dependent diabetes mellitus (IDDM) in a defined high-incidence area was analyzed in a total of 58 population-based patients, representing 77% of IDDM patients with age at onset below 16 years, and in 92 unrelated parents in control families without IDDM. HLA haplotypes were confirmed by analyzing first-degree relatives in both groups. Seven different methods were used to analyze risk: (1) odds ratio, (2) absolute risk, (3) haplotype relative risk, (4) transcomplementation relative risk, (5) relative predisposing effects, (6) stratification analysis, and (7) test of predisposing allele on haplotype. DQB1*0302 indicated somewhat higher risk than did DR4, while DR3 had a higher risk than DQB1*0201; however, the 95% confidence intervals of the risk estimates overlapped. The positive association between IDDM and the DQB1*0201-DQA1*0501-DR3 haplotype seems to be due to DR3 or to an unknown linked gene. More important, DQA1*0301 was present among 93% of the patients, and this allele in various transcomplementation combinations with DQB1 alleles showed closer association to IDDM than did any other alleles. The strong negative association of the DQB1*0602 allele also in the presence of either DR4 or DQB1*0302 or both suggests that, in a high-risk population for IDDM, HLA-DQ primarily confers protection, perhaps by induction of tolerance. Consistent with known functions, HLA-DR may primarily confer susceptibility, perhaps by induction of autoreactive T lymphocytes.     

Application and interpretation of transmission/disequilibrium tests: transmission of HLA-DQ haplotypes to unaffected siblings in 526 families with type 1 diabetes

It is widely believed that, if a genetic marker shows a transmission distortion in patients by the transmission/disequilibrium test (TDT), then a transmission distortion in healthy siblings would be seen in the opposite direction. This is also the case in a complex disease. Furthermore, it has been suggested that replacing the McNemar statistics of the TDT with a test of heterogeneity between transmissions to affected and unaffected children could increase the power to detect disease association. To test these two hypotheses empirically, we analyzed the transmission of HLA-DQA1-DQB1 haplotypes in 526 Norwegian families with type 1 diabetic children and healthy siblings, since some DQA1-DQB1 haplotypes represent major genetic risk factors for type 1 diabetes. Despite the strong positive and negative disease associations with particular DQ haplotypes, we observed no significant deviation from 50% for transmission to healthy siblings. This could be explained by the low penetrance of susceptibility alleles, together with the fact that IDDM loci also harbor strongly protective alleles that can override the risk contributed by other loci. Our results suggest that, in genetically complex diseases, detectable distortion in transmission to healthy siblings should not be expected. Furthermore, the original TDT seems more powerful than a heterogeneity test.     

An exact test for the association between the disease and alleles at highly polymorphic loci with particular interest in the haplotype analysis

The association analysis between the disease and genetic alleles is one of the simple methods for localizing the susceptibility locus in the genes. For revealing the association, several statistical tests have been proposed without discussing explicitly the alternative hypotheses. We therefore specify two types of alternative hypotheses (i.e., there is only one susceptibility allele in the locus, and there is an extension or shortening of alleles associated with the disease) and derive exact tests for the respective hypotheses. We also propose to combine these two tests when the prior knowledge is not sufficient enough to specify one of these two hypotheses. In particular, these ideas are extended to the haplotype analysis of three-way association between the disease and bivariate allele frequencies at two closely linked loci. As a by-product, a factorization of the probability distribution of the three-way cell frequencies under the null hypothesis of no three-way interaction is obtained.     

Genetic polymorphisms at the human liver/islet glucose transporter (GLUT2) gene locus in Caucasian and West Indian subjects with type 2 (non-insulin-dependent) diabetes mellitus.

The liver/islet glucose transporter (GLUT2) is mainly expressed in the hepatocytes of the liver and the beta-cells of the pancreatic islets and a defect in this transporter could lead to diabetic phenotypes, such as relative hypoinsulinaemia and reduced uptake and metabolism of glucose in the liver. DNA from unrelated individuals was digested with the restriction endonucleases Bgl-I and Taq-I followed by blotting and hybridisation with a 32P-labelled GLUT2 cDNA which revealed three restriction fragment length polymorphisms (RFLPs) (B1, T1 and T2) in both Caucasian and West Indian populations. Linkage analysis between these variant sites demonstrated that the alleles of these polymorphisms were in strong linkage disequilibrium. Disease association of genetic variants at the GLUT2 locus with type 2 diabetes was examined with these RFLPs in both Caucasian (n = 54) and West Indian (n = 46) populations with type 2 diabetes. There were no significant differences in the frequency of alleles, genotypes or haplotypes between diabetic patients and non-diabetic controls. However, there were significant differences in the allele frequencies of all these three polymorphisms between Caucasian and West Indian populations.     

Score tests of genetic association in the presence of linkage based on the additive genetic gamma frailty model

Nuclear families with multiple affected sibs are often collected for genetic linkage analysis of complex diseases. Once linkage evidence is established, dense markers are often typed in the linked region for genetic association analysis based on linkage disequilibrium (LD). Detection of association in the presence of linkage localizes disease genes more accurately than the methods that rely on linkage alone. However, test of association due to LD in the linked region needs to account for dependency of the allele transmissions to different sibs within a family. In this paper, we define a joint model for genetic linkage and association and derive the corresponding joint survival function of age of onset for the sibs within a sibship. The joint survival function is a function of both the inheritance vector and the genotypes at the candidate marker locus. Based on this joint survival function, we derive score tests for genetic association. The proposed methods utilize the phenotype data of all the sibs and have the advantages of family-based designs which can avoid the potential spurious association caused by population admixture. In addition, the methods can account for variable age of onset or age at censoring and possible covariate effects, and therefore provide important tools for modelling disease heterogeneity. Simulation studies and application to the data sets from the 12th Genetic Analysis Workshop indicate that the proposed methods have correct type 1 error rates and increased power over other existing methods for testing allelic association.     

The predisposition to type 1 diabetes linked to the human leukocyte antigen complex includes at least one non-class II gene

The human leukocyte antigen (HLA) complex, encompassing 3.5 Mb of DNA from the centromeric HLA-DPB2 locus to the telomeric HLA-F locus on chromosome 6p21, encodes a major part of the genetic predisposition to develop type 1 diabetes, designated "IDDM1." A primary role for allelic variation of the class II HLA-DRB1, HLA-DQA1, and HLA-DQB1 loci has been established. However, studies of animals and humans have indicated that other, unmapped, major histocompatibility complex (MHC)-linked genes are participating in IDDM1. The strong linkage disequilibrium between genes in this complex makes mapping a difficult task. In the present paper, we report on the approach we have devised to circumvent the confounding effects of disequilibrium between class II alleles and alleles at other MHC loci. We have scanned 12 Mb of the MHC and flanking chromosome regions with microsatellite polymorphisms and analyzed the transmission of these marker alleles to diabetic probands from parents who were homozygous for the alleles of the HLA-DRB1, HLA-DQA1, and HLA-DQB1 genes. Our analysis, using three independent family sets, suggests the presence of an additional type I diabetes gene (or genes). This approach is useful for the analysis of other loci linked to common diseases, to verify if a candidate polymorphism can explain all of the association of a region or if the association is due to two or more loci in linkage disequilibrium with each other.