The distribution of long range admixture linkage disequilibrium in an African-American population

Elevated Linkage Disequilibrium and Signatures of Soft Sweeps Are Common in Drosophila melanogaster

The extent to which selection and demography impact patterns of genetic diversity in natural populations of Drosophila melanogaster is yet to be fully understood. We previously observed that linkage disequilibrium (LD) at scales of ∼10 kb in the Drosophila Genetic Reference Panel (DGRP), consisting of 145 inbred strains from Raleigh, North Carolina, measured both between pairs of sites and as haplotype homozygosity, is elevated above neutral demographic expectations. We also demonstrated that signatures of strong and recent soft sweeps are abundant. However, the extent to which these patterns are specific to this derived and admixed population is unknown. It is also unclear whether these patterns are a consequence of the extensive inbreeding performed to generate the DGRP data. Here we analyze LD statistics in a sample of >100 fully-sequenced strains from Zambia; an ancestral population to the Raleigh population that has experienced little to no admixture and was generated by sequencing haploid embryos rather than inbred strains. We find an elevation in long-range LD and haplotype homozygosity compared to neutral expectations in the Zambian sample, thus showing the elevation in LD is not specific to the DGRP data set. This elevation in LD and haplotype structure remains even after controlling for possible confounders including genomic inversions, admixture, population substructure, close relatedness of individual strains, and recombination rate variation. Furthermore, signatures of partial soft sweeps similar to those found in the DGRP as well as partial hard sweeps are common in Zambia. These results suggest that while the selective forces and sources of adaptive mutations may differ in Zambia and Raleigh, elevated long-range LD and signatures of soft sweeps are generic in D. melanogaster.

Human population admixture in Asia

Genetic admixture in human, the result of inter-marriage among people from different well-differentiated populations, has been extensively studied in the New World, where European colonization brought contact between peoples of Europe, Africa, and Asia and the Amerindian populations. In Asia, genetic admixing has been also prevalent among previously separated human populations. However, studies on admixed populations in Asia have been largely underrepresented in similar efforts in the New World. Here, I will provide an overview of population genomic studies that have been published to date on human admixture in Asia, focusing on population structure and population history.

Characterization of genome-wide association-identified variants for atrial fibrillation in African Americans

BACKGROUND

Despite a greater burden of risk factors, atrial fibrillation (AF) is less common among African Americans than European-descent populations. Genome-wide association studies (GWAS) for AF in European-descent populations have identified three predominant genomic regions associated with increased risk (1q21, 4q25, and 16q22). The contribution of these loci to AF risk in African American is unknown.

METHODOLOGY/PRINCIPAL FINDINGS

We studied 73 African Americans with AF from the Vanderbilt-Meharry AF registry and 71 African American controls, with no history of AF including after cardiac surgery. Tests of association were performed for 148 SNPs across the three regions associated with AF, and 22 SNPs were significantly associated with AF (P<0.05). The SNPs with the strongest associations in African Americans were both different from the index SNPs identified in European-descent populations and independent from the index European-descent population SNPs (r(2)<0.40 in HapMap CEU): 1q21 rs4845396 (odds ratio [OR] 0.30, 95% confidence interval [CI] 0.13-0.67, P = 0.003), 4q25 rs4631108 (OR 3.43, 95% CI 1.59-7.42, P = 0.002), and 16q22 rs16971547 (OR 8.1, 95% CI 1.46-45.4, P = 0.016). Estimates of European ancestry were similar among cases (23.6%) and controls (23.8%). Accordingly, the probability of having two copies of the European derived chromosomes at each region did not differ between cases and controls.

CONCLUSIONS/SIGNIFICANCE

Variable European admixture at known AF loci does not explain decreased AF susceptibility in African Americans. These data support the role of 1q21, 4q25, and 16q22 variants in AF risk for African Americans, although the index SNPs differ from those identified in European-descent populations.

Global prostate cancer incidence and the migration, settlement, and admixture history of the Northern Europeans

The most salient feature of prostate cancer is its striking ethnic disparity. High incidences of the disease are documented in two ethnic groups: descendents of the Northern Europeans and African Americans. Other groups, including native Africans, are much less susceptible to the disease. Given that many risk factors may contribute to carcinogenesis, an etiological cause for the ethnic disparity remains to be defined. By analyzing the global prostate cancer incidence data, we found that distribution of prostate cancer incidence coincides with the migration and settlement history of Northern Europeans. The incidences in other ethnic groups correlate to the settlement history and extent of admixture of the Europeans. This study suggests that prostate cancer has been spread by the transmission of a genetic susceptibility that resides in the Northern European genome.

Meta-analysis of genome-wide linkage scans for renal function traits

BACKGROUND

Several genome scans have explored the linkage of chronic kidney disease phenotypes to chromosomic regions with disparate results. Genome scan meta-analysis (GSMA) is a quantitative method to synthesize linkage results from independent studies and assess their concordance.

METHODS

We searched PubMed to identify genome linkage analyses of renal function traits in humans, such as estimated glomerular filtration rate (GFR), albuminuria, serum creatinine concentration and creatinine clearance. We contacted authors for numerical data and extracted information from individual studies. We applied the GSMA nonparametric approach to combine results across 14 linkage studies for GFR, 11 linkage studies for albumin creatinine ratio, 11 linkage studies for serum creatinine and 4 linkage studies for creatinine clearance.

RESULTS

No chromosomal region reached genome-wide statistical significance in the main analysis which included all scans under each phenotype; however, regions on Chromosomes 7, 10 and 16 reached suggestive significance for linkage to two or more phenotypes. Subgroup analyses by disease status or ethnicity did not yield additional information.

CONCLUSIONS

While heterogeneity across populations, methodologies and study designs likely explain this lack of agreement, it is possible that linkage scan methodologies lack the resolution for investigating complex traits. Combining family-based linkage studies with genome-wide association studies may be a powerful approach to detect private mutations contributing to complex renal phenotypes.

The admixture linkage disequilibrium and genetic linkage inference on the gradual admixture population

Through the theoretical analysis of the admixture linkage disequilibrium (ALD) in the gradual admixture (GA) model, in which admixture occurs in every generation, the ALD is found to be proportional to the difference in marker allele frequencies, P1 - P2, between two subpopulations. Based on this property, we can employ a strict monotonic function (delta(ker) = delta/(P1-P2), where delta denotes the linkage disequilibrium (LD)) of the recombination fraction between the marker locus and the disease locus to infer the true genetic linkage. We construct a quasi likelihood ratio test (LRT) for the case-only data utilizing the information of unlinked markers in the human genome. The simulation results show that our tests can be used to fine map a disease locus. The effects of parameter values in the ALD mapping are also discussed.

Analysis of genomic admixture in Uyghur and its implication in mapping strategy

The Uyghur (UIG) population, settled in Xinjiang, China, is a population presenting a typical admixture of Eastern and Western anthropometric traits. We dissected its genomic structure at population level, individual level, and chromosome level by using 20,177 SNPs spanning nearly the entire chromosome 21. Our results showed that UIG was formed by two-way admixture, with 60% European ancestry and 40% East Asian ancestry. Overall linkage disequilibrium (LD) in UIG was similar to that in its parental populations represented in East Asia and Europe with regard to common alleles, and UIG manifested elevation of LD only within 500 kb and at a level of 0.1 <r(2) < 0.8 when ancestry-informative markers (AIMs) were used. The size of chromosomal segments that were derived from East Asian and European ancestries averaged 2.4 cM and 4.1 cM, respectively. Both the magnitude of LD and fragmentary ancestral chromosome segments indicated a long history of Uyghur. Under the assumption of a hybrid isolation (HI) model, we estimated that the admixture event of UIG occurred about 126 [107 approximately 146] generations ago, or 2520 [2140 approximately 2920] years ago assuming 20 years per generation. In spite of the long history and short LD of Uyghur compared with recent admixture populations such as the African-American population, we suggest that mapping by admixture LD (MALD) is still applicable in the Uyghur population but approximately 10-fold AIMs are necessary for a whole-genome scan.

Complex phenotypes and complex genetics: an introduction to genetic studies of complex traits

There is currently intense interest in the genetic factors contributing to many diseases with cardiovascular complications. Diseases like atherosclerosis, diabetes, and hypertension are referred to as complex traits because multiple genes contribute to the phenotype either individually or through interactions with each other or the environment. Enabled and energized by the striking successes over the past 20 years in identifying genes that are responsible for single gene traits, many geneticists have turned to the investigation of methods that will allow for the dissection of complex traits. There have already been some successes, so there is no reason to consider the problem as inherently intractable. However, it is important to reflect on what conditions are necessary for the identification of genes that operate in complex traits. A recurring theme in this research area has been difficulty in repeating and validating research findings, and this most often can be attributed to limitations in study design. It is also important to consider that any particular research strategy can only hope to describe a portion of factors that contribute to variation in the population; therefore, the genetic approach cannot be a panacea. New efficient technologies for genotyping and public databases describing the fine structure of genetic correlations in the genome should aid many aspects of the gene discovery process.

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.

Measuring and using admixture to study the genetics of complex diseases

Admixture is an important evolutionary force that can and should be used in efforts to apply genomic data and technology to the study of complex disease genetics. Admixture linkage disequilibrium (ALD) is created by the process of admixture and, in recently admixed populations, extends for substantial distances (of the order of 10 to 20 cM). The amount of ALD generated depends on the level of admixture, ancestry information content of markers and the admixture dynamics of the population, and thus influences admixture mapping (AM). The authors discuss different models of admixture and how these can have an impact on the success of AM studies. Selection of markers is important, since markers informative for parental population ancestry are required and these are uncommon. Rarely does the process of admixture result in a population that is uniform for individual admixture levels, but instead there is substantial population stratification. This stratification can be understood as variation in individual admixtures and can be both a source of statistical power for ancestry-phenotype correlation studies as well as a confounder in causing false-positives in gene association studies. Methods to detect and control for stratification in case/control and AM studies are reviewed, along with recent studies showing individual ancestry-phenotype correlations. Using skin pigmentation as a model phenotype, implications of AM in complex disease gene mapping studies are discussed. Finally, the article discusses some limitations of this approach that should be considered when designing an effective AM study.

Implications of correlations between skin color and genetic ancestry for biomedical research

Skin pigmentation is a central element of most discussions on 'race' and genetics. Research on the genetic basis of population variation in this phenotype, which is important in mediating both social experiences and environmental exposures, is sparse. We studied the relationship between pigmentation and ancestry in five populations of mixed ancestry with a wide range of pigmentation and ancestral proportions (African Americans from Washington, DC; African Caribbeans living in England; Puerto Ricans from New York; Mexicans from Guerrero; and Hispanics from San Luis Valley). The strength of the relationship between skin color and ancestry was quite variable, with the correlations ranging in intensity from moderately strong (Puerto Rico, rho = 0.633) to weak (Mexico, rho = 0.212). These results demonstrate the utility of ancestry-informative genetic markers and admixture methods and emphasize the need to be cautious when using pigmentation as a proxy of ancestry or when extrapolating the results from one admixed population to another.

The allele frequency spectrum in genome-wide human variation data reveals signals of differential demographic history in three large world populations

We have studied a genome-wide set of single-nucleotide polymorphism (SNP) allele frequency measures for African-American, East Asian, and European-American samples. For this analysis we derived a simple, closed mathematical formulation for the spectrum of expected allele frequencies when the sampled populations have experienced nonstationary demographic histories. The direct calculation generates the spectrum orders of magnitude faster than coalescent simulations do and allows us to generate spectra for a large number of alternative histories on a multidimensional parameter grid. Model-fitting experiments using this grid reveal significant population-specific differences among the demographic histories that best describe the observed allele frequency spectra. European and Asian spectra show a bottleneck-shaped history: a reduction of effective population size in the past followed by a recent phase of size recovery. In contrast, the African-American spectrum shows a history of moderate but uninterrupted population expansion. These differences are expected to have profound consequences for the design of medical association studies. The analytical methods developed for this study, i.e., a closed mathematical formulation for the allele frequency spectrum, correcting the ascertainment bias introduced by shallow SNP sampling, and dealing with variable sample sizes provide a general framework for the analysis of public variation data.

Putative ancestral origins of chromosomal segments in individual african americans: implications for admixture mapping

Theoretically, markers that distinguish European from West African ancestry can be used to examine the origin of chromosomal segments in individual African Americans. In this study, putative ancestral origin was examined by using haplotypes estimated from genotyping 268 African Americans for 29 ancestry informative markers spaced over a 60-cM segment of chromosome 5. Analyses using a Bayesian algorithm (STRUCTURE) provided evidence that blocks of individual chromosomes derive from one or the other parental population. In addition, modeling studies were performed by using hidden real marker data to simulate patient and control populations under different genotypic risk ratios. Ancestry analysis showed significant results for a genotypic risk ratio of 2.5 in the African American population for modeled susceptibility genes derived from either putative parental population. These studies suggest that admixture mapping in the African American population can provide a powerful approach to defining genetic factors for some disease phenotypes.

Mexican American ancestry-informative markers: examination of population structure and marker characteristics in European Americans, Mexican Americans, Amerindians and Asians

Markers with large differences in allele frequencies between ethnicities provide ancestry information that can be applied to genetic studies. We identified over 100 biallelic ancestry informative markers (AIMs) with large allele frequency differences between European Americans (EA) and Pima Amerindians from laboratory and database screens. For 35 of these markers, Mayan, Yavapai and Quechuan Amerindians were genotyped and compared with EA and Pima allele frequencies. Markers with large allele frequency differences between EA and one Amerindian tribe showed only small differences between the Amerindian tribes. Examination of structure in individuals demonstrated a clear separation of subjects of European from those of Amerindian ancestry, and similarity between individuals from disparate Amerindian populations. The AIMs demonstrated the variation in ancestral composition of individual Mexican Americans, providing evidence of applicability in admixture mapping and in controlling for structure in association tests. In addition, a high percentage of single-nucleotide polymorphisms (SNPs) selected on the basis of large frequency differences between EA and Asian populations had large allele frequency differences between EA and Amerindians, suggesting an efficient method for greatly expanding AIMs for use in admixture mapping/structure analysis in Mexican Americans. Together, these data provide additional support for the practical application of admixture mapping in the Mexican American population.

Approaches to identify genes for complex human diseases: lessons from Mendelian disorders

The focus of most molecular genetics research is the identification of genes involved in human disease. In the 20th century, genetics progressed from the rediscovery of Mendel's Laws to the identification of nearly every Mendelian genetic disease. At this pace, the genetic component of all complex human diseases could be identified by the end of the 21st century, and rational therapies could be developed. However, it is clear that no one approach will identify the genes for all diseases with a genetic component, because multiple mechanisms are involved in altering human phenotypes, including common alleles with small to moderate effects, rare alleles with moderate to large effects, complex gene-gene and gene-environment interactions, genomic alterations, and noninherited genetic effects. The knowledge gained from the study of Mendelian diseases may be applied to future research that combines linkage-based, association-based, and sequence-based approaches to detect most disease alleles. The technology to complete these studies is at hand and requires that modest improvements be applied on a wide scale. Improved analytical tools, phenotypic characterizations, and functional analyses will enable complete understanding of the genetic basis of complex diseases.

Markers informative for ancestry demonstrate consistent megabase-length linkage disequilibrium in the African American population

Admixture mapping is a potentially powerful tool for mapping complex genetic diseases. For application of this method, admixed individuals must have genomes composed of large segments derived intact from each founding population. Such segments are thought to be present in African Americans (AA) and should be demonstrable by examination of linkage disequilibrium (LD). Previous studies using a variety of polymorphic markers have variably reported long-range LD or rapid decay of LD. To further define the extent and characteristics of LD caused by admixture in the AA population, the current study utilized a set of 52 diallelic markers that were selected for large standard variances between putative representatives of the founder populations. LD was examined in over 250 marker-pairs, including linked markers from four different chromosomal regions and an equal number of matched unlinked comparisons. In the representative founder populations, strong LD was not observed for markers separated by more than 10 kb. In contrast, results indicated significant LD ( P<0.001, D'>0.3) in AA over large genomic segments exceeding 10 centiMorgans (cM) and 15 megabases (Mb). Only marginally significant LD was present between unlinked markers in this population, suggesting that choosing appropriate levels of significance for admixture mapping can minimize false positive results. The ability to detect LD for extended chromosomal segments in AA decayed not only as a function of the distance between markers, but also as a function of the standard variance of the markers. This examination of several genomic segments provides strong evidence that appropriate selection of informative markers is a crucial prerequisite for the application of admixture mapping to the AA population.

Sarcoidosis susceptibility and resistance HLA-DQB1 alleles in African Americans

Sarcoidosis, in the United States, more commonly and severely affects African Americans. HLA associations with sarcoidosis have been reported, but most studies used case-control designs, which may produce biased results because of population stratification. We examined transmission of HLA-DQB1 alleles in 225 African American families with at least one offspring with sarcoidosis. Of five low-resolution HLA-DQB1 alleles, *02 and *06 showed significant deviation in transmission patterns to affected offspring. High-resolution typing of these allelic subsets revealed that HLA-DQB1*0201 was transmitted to affected offspring half as often as expected (p = 0.001), whereas DQB1*0602 was transmitted to affected offspring about 20% more often than expected (p = 0.029). Examining interactions between *0201 and *0602 alleles and environmental exposures showed that *0602 varied little with respect to exposure, but sarcoidosis risk associated with *0201 often depended on exposure status. Alternatively, the *0602 allele in affected probands was associated with radiographic disease progression, but the *0201 allele showed no significant correlation with phenotype. Major differences in the amino acid sequences encoded by *0201 and *0602 alleles exist, which may explain the differential effects these alleles have on sarcoidosis susceptibility and progression in African Americans.