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Results for “Haplotype structures”

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PubMed1981

Anti-self receptors. IV. H-2-restricted receptors on thymocytes recognize carbohydrate structures on target cells.

Rosetting between thymocytes and autologous erythrocytes in mediated by receptors on thymocytes that primarily recognize self H-2L molecules on erythrocytes. This paper describes preliminary attempts to chemically characterize the receptor and acceptor molecules involved in this H-2-restricted interaction. On the basis of sugar inhibition studies and the sensitivity of the receptors to protease and glycosidase treatments it appears that a protein receptor on thymocytes recognizes the carbohydrate portion of a glycoprotein on erythrocytes. Furthermore, the thymocyte receptor appears to recognize terminal D-galactose, D-mannose and sialic acid residues on a branched-chain carbohydrate structure on erythrocytes, with mouse strains of different H-2 haplotype expressing carbohydrate structures that differ in the linkage of these three terminal sugars. These findings indicate that H-2-restricted carbohydrate-protein interactions can occur between cells, a conclusion with important theoretical implications.

Animals↗

PubMed1996

Network analysis of human Y microsatellite haplotypes.

To investigate the utility of Y chromosome microsatellites for studying human male-lineage evolution, we typed samples from three populations for five tetranucleotide repeats and an Alu insertion polymorphism. We found very high levels of haplotype diversity and evidence that most mutations involve the gain or loss of only one repeat unit, implying that any given microsatellite haplotype may have arisen independently on two or more Y-chromosome lineages. Together, these factors suggest that interpretation of small sample sizes (< 30) will be problematic. By typing a large sample of individuals (n = 174) from one population, East Anglia, we were able to construct a haplotype network. The network exhibits a well-connected core structure of commoner haplotypes. Computer simulations based on this network estimate the convergence time for African and Caucasian groups may be between 1.4 and 1.8 times as long as the convergence of the East Anglian population. Based on our comparison between large and small sample sizes, we suggest that large sample sizes are necessary in order to interpret Y-microsatellite haplotypes, and that a network analysis of the type we describe may prove informative in future studies.

Base Sequence↗

PubMed2000

The haplotype linkage disequilibrium test for genome-wide screens: its power and study design.

The focus of human genetics continues to shift toward the dissection of complex phenotypes. Integral to these endeavors is the development of powerful analytical tools. To this end, we propose a novel method designated the haplotype linkage disequibrium (LD) test for identifying diseases genes. The basic structure of the haplotype test statistic is a chi-square in which haplotypes, as opposed to individual marker data, are compared between cases and controls. Specifically, we performed power calculations and demonstrate that the use of haplotypes improves the power of mapping disease genes. We show that this approach can be used for initial genome-wide screens in mapping disease genes. Furthermore, we investigated the factors influencing statistical power of the method and discussed basic principals underlying study design. Published data from the Hereditary Hemochromatosis region was used to illustrate the utility of the haplotype test. Also discussed is its relationship with linkage disequibrium.

Alleles↗

PubMed1981

Structural comparisons of TL antigens derived from normal and leukemia cells of Tl+ and TL- strains and relationship to genetically linked H-2 major histocompatibility complex products.

Comparative tryptic peptide analysis was used to probe the structure of the TL products coded for by normally expressed TL alleles (Tlaa and Tlac haplotypes) and the structure of the TL product on ERLD, a TL+ leukemia occurring in a strain that does not normally express TL antigens (Tlab haplotype). In mice that have the Tlaa haplotype, the peptide maps of TL glycoproteins from normal thymocytes and from TL+ leukemias were identical, a finding that is consistent with the indistinguishable serologically defined TL phenotype of these cells. Analysis of the TL product on ERLD leukemia cells (TL phenotype, TL.1,2,4) indicates a single TL glycoprotein species with the TL.4 determinant (restricted to leukemias of Tlab and Tlac haplotypes) coexisting on the same glycoprotein as the Tl.1 determinant (normally expressed by thymocytes of Tlaa haplotype). Comparison of the peptides of the TL product of ERLD and the products of the normally expressed Tlaa and Tlac loci showed a high degree of structural similarity (i.e., 70-80%) of shared peptides. In contrast, the products of the Tlaa, Tlab, and Tlac loci shared relatively few peptides with the products of the K, D, and L loci of the closely linked major histocompatibility complex (15-35%). The TL family, therefore, consists of alleles that are highly homologous. This contrasts with the marked diversity and polymorphism among the alleles of the K, D, and L loci.

Alleles↗

PubMed2006

Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure.

Catechol-O-methyltransferase (COMT) is a key regulator of pain perception, cognitive function, and affective mood. Three common haplotypes of the human COMT gene, divergent in two synonymous and one nonsynonymous position, code for differences in COMT enzymatic activity and are associated with pain sensitivity. Haplotypes divergent in synonymous changes exhibited the largest difference in COMT enzymatic activity, due to a reduced amount of translated protein. The major COMT haplotypes varied with respect to messenger RNA local stem-loop structures, such that the most stable structure was associated with the lowest protein levels and enzymatic activity. Site-directed mutagenesis that eliminated the stable structure restored the amount of translated protein. These data highlight the functional significance of synonymous variations and suggest the importance of haplotypes over single-nucleotide polymorphisms for analysis of genetic variations.

Alleles↗

PubMed2006

Genetic diversity of Triatoma infestans (Hemiptera: Reduviidae) in Chuquisaca, Bolivia based on the mitochondrial cytochrome b gene.

Partial cytochrome b DNA sequences for 62 Triatoma infestans were analyzed to determine the degree of genetic variation present in populations of this insect in the northwest region of Chuquisaca, Bolivia. A total of seven haplotypes were detected in the localities sampled. The phylogenetic relationship and population genetic structure of the haplotypes found in this region, indicate that there is greater variation in this relatively small region of Bolivia than what has been previously reported by studies using the same gene fragment, for more distant geographic areas of this country. In addition, a comparison of rural and peri-urban localities, indicate that there is no difference in the genetic variation of T. infestans between these two environments.

Animals↗

PubMed1993

Mitochondrial DNA variation among red snapper (Lutjanus campechanus) from the Gulf of Mexico.

Variation in mitochondrial DNA (mtDNA) was examined among 86 red snapper (Lutjanus campechanus) from three geographic localities in the northern Gulf of Mexico (Gulf). A total of 29 composite mtDNA genotypes (haplotypes) was found; one haplotype occurred in 39 of 86 (45.3%) individuals assayed, and 20 haplotypes occurred in only one individual each. Tests of heterogeneity in mtDNA haplotype frequencies among localities were not significant, and there was little evidence of phylogeographic structuring of mtDNA haplotypes. These findings are consistent with the hypothesis that red snapper in the northern Gulf comprise a single, panmictic population. The observed genetic homogeneity also indicates considerable gene flow (migration) among red snapper in the northern Gulf. Significant differences in levels of intrapopulational mtDNA variation were found among localities. Levels of intrapopulational mtDNA diversity in red snapper are low relative to other marine fish species studied to date.

Animals↗

PubMed2002

Distribution of recombination crossovers and the origin of haplotype blocks: the interplay of population history, recombination, and mutation.

Recent studies suggest that haplotypes are arranged into discrete blocklike structures throughout the human genome. Here, we present an alternative haplotype block definition that assumes no recombination within each block but allows for recombination between blocks, and we use it to study the combined effects of demographic history and various population genetic parameters on haplotype block characteristics. Through extensive coalescent simulations and analysis of published haplotype data on chromosome 21, we find that (1) the combined effects of population demographic history, recombination, and mutation dictate haplotype block characteristics and (2) haplotype blocks can arise in the absence of recombination hot spots. Finally, we provide practical guidelines for designing and interpreting studies investigating haplotype block structure.

Algorithms↗

PubMed2003

Recent evolutionary history of the bluethroat (Luscinia svecica) across Eurasia.

We analysed mitochondrial DNA (mtDNA) sequences from 154 bluethroats (Luscinia svecica) sampled at 21 sites throughout much of their Eurasian range. A previously reported, single base-pair mtDNA difference between L. s. svecica and L. s. namnetum was inconsistent upon expanded geographical sampling. A significant FST value (0.29) and an isolation-by-distance effect show the existence of geographical differentiation. Phylogenetic analysis of haplotypes revealed northern and southern groups, although lineage sorting is incomplete. There was no geographical structure to the haplotype tree within groups, and currently recognized subspecies were not supported. A minimum evolution tree based on pairwise mtDNA genetic distances among average samples showed the same two broadly distributed northern and southern groups. These groups abut in the centre of the latitudinal range, and were possibly isolated by forest that developed and spread westward over the last 15 000 years. Pairwise FST values averaged 0.16 in the southern group, 0.04 in the northern group, and 0.42 between groups. Mismatch distributions suggested population growth in each group, with that in the south being more recent. In the northern group, the geographical pattern in tau suggested northward and eastward expansion. Analysis of nucleotide diversity suggested westward expansion in the southern group. The northern group had higher nucleotide diversity than the southern group, consistent with a larger current population size in the north. Given the significant FST, incompletely sorted haplotype tree, and broadly patterned minimum evolution tree, L. svevica appears to represent a species at an intermediate stage of differentiation between panmixia and reciprocal monophyly.

Analysis of Variance↗

PubMed2002

Identification and ethnic distribution of major haplotypes in the gene GNB3 encoding the G-protein beta3 subunit.

The 825T-allele of the gene GNB3 encoding the G protein beta3 subunit is associated with hypertension and obesity, and identifies individuals highly responsive to diuretic therapy. Gbeta3s, a Gbeta3 protein variant generated by alternative splicing in carriers of the 825T-allele, is linked to increased signal transduction and is a potential cause for the observed pathophysiology. Here, we searched the entire GNB3 gene for additional polymorphisms and analysed their prevalence in Caucasian, black African and Asian populations. We detected six novel single nucleotide polymorphisms which were termed according to their location as G76A, G1906T, G2906A, A3882C, G5177A, and G5249A. Furthermore, we found a CACA-insertion-deletion polymorphism at position 6496. Genotyping and association studies resulted in the definition of two major GNB3 haplotypes, termed 'C-haplotype' (alleles 825C, 3882A, 5249G, 6496CACA-) and 'T-haplotype' (alleles 825T, 3882C, 5249A, 6496CACA+). Molecular modelling studies revealed that the pre-mRNA structures of both haplotypes exhibit marked differences which may account for the alternative splicing predominantly observed with the T-haplotype. The prevalence of these haplotypes in major ethnic populations differs considerably. Furthermore, we detected additional frequent GNB3 polymorphisms. These variants were restricted to one or two major ethnic populations. Our results will aid future studies on population-specific effects of the GNB3 variants on risk and course of frequent diseases, including hypertension, obesity, stroke and myocardial infarction. Furthermore, they will contribute to the understanding of GNB3-related population-specific pharmacogenetic differences in the response to major drugs, as already shown for diuretics and antidepressants.

Adolescent↗

PubMed2005

Human F7 sequence is split into three deep clades that are related to FVII plasma levels.

It is widely accepted that FVII levels are strongly, consistently, and independently related to cardiovascular risk. These levels are influenced by genetic and environmental factors. Among the genetic factors, only a limited number of polymorphisms in the F7 gene have been reported, and they explain only a small proportion of the genetic variability. Recently, we have accomplished the complete dissection of the F7 quantitative trait locus responsible for all of the genetic variability observed in FVII levels. Now, we present the thorough study of the haplotype organization of F7 DNA sequence variation among individuals and the evolutionary processes that produced this variation, by sequencing 15 kb of genomic DNA sequence from the F7 locus in 40 unrelated individual (80 chromosomes) from the genetic analysis of idiopathic thrombophilia (GAIT) project as well as four non-human primate species. Our study revealed 49 polymorphisms, of which 39 SNPs were further considered. Genotyping of these DNA variations in the whole family-based GAIT sample helped resolve linkage phases, and a total of 37 distinct haplotypes were identified.Tajima's D was significantly positive in this sample, suggesting balancing selection. This parameter was a reflection of the phylogenetic structure of F7 haplotype, which was deeply split into three well-supported clades or haplogroups, suggesting that functional differences among F7 variants do not depend on a few single-site variations. Moreover, haplogroup 2 was associated with high FVII levels and haplogroup 3 with low levels. In this study, we have for the first time established a clear relation between genotypic variability structure and phenotypic variability of a particular quantitative trait involved in a complex disease.

Animals↗

PubMed2001

Y-chromosome variation in a Norwegian population sample.

Y-chromosome DNA profiles are promising tools in population genetics and forensic science. Here we present DNA profiles of 300 unrelated Y-chromosomes of Norwegian origin. The profile is composed of eight short tandem repeats (STRs) and one single nucleotide polymorphism (SNP). In more than 2/3 of the haplotypes the modular structure in the 5' end of the minisatellite locus DYF155S1 was revealed by minisatellite variant repeat PCR (MVR-PCR) These haplotypes were also typed for deletions of fragment 50f2C (DYF155S2). Allele distribution and paternity exclusion parameters are given for each marker. The degree of haplotype diversity and its implication for statistics are evaluated. In the 300 samples 177 different haplotypes were encountered, of which 137 were observed once only. Analysis showed that the main source of variation is within the population. The Fst values were less than 0.015 in general. Haplotype grouping by the SNP demonstrated two haplogroups (Tat/T and Tat/C). Haplogroup Tat/C--found in 5.7% of the present material - is the same haplogroup as encountered in 60% of Finnish males [Am. J. Hum. Genet. 62 (1998) 1171]. Mutation analysis in 150 father/son pairs (a total of 1200 meiotic events) revealed an average mutation frequency of 0.0042 (95% CI 0.0014-0.0097).

Alleles↗

PubMed1987

Defective antigen presentation and novel structural properties of DR1 from an HLA haplotype associated with 21-hydroxylase deficiency.

We have segregated DR1+ individuals into two categories according to whether or not their class II+ cells stimulated T lymphocyte clones specific for or restricted to DR1. In a majority of cases (87%), failure to stimulate was a property of cells having the B14;DR1 haplotype and/or nonclassical 21-hydroxylase deficiency. Absence of clonal proliferation could not be explained by release of an intercellular suppressor factor or by stimulator cell absorption of interleukin 2. Homozygous cells inheriting both stimulatory (DR1n) and nonstimulatory (DR1x) haplotypes did not successfully mediate clonal expansion, implying that a trans acting factor operates intracellularly to modify both DR1 alleles or their products. Other DR alleles did not appear to be affected as evidence by normal proliferative responses of T lymphocyte clones restricted to DR2 or DR7 and stimulated by DR1x,2 and DR1x,7 cells, respectively. By two-dimensional gel analysis, we have further identified a 50-kD surface glycoprotein contained in anti-DR immunoprecipitates of DR1x, but not DR1n or non-DR1 cellular lysates. This 50-kD structure had antigenic and peptide identity to DR alpha and beta chains but was resistant to dissociation under conditions that normally separate DR alpha and beta (8 M urea plus 5% 2-mercaptoethanol); boiling in sodium dodecyl sulfate was required to segregate the component polypeptides of the 50-kD heterodimer. We postulate that a product of a novel combinatorial association between constitutive chains of DR may interfere with or compete for normal T cell receptor recognition of DR1 as both an alloantigen and a restricting element. We further propose that gene abnormalities within the class III region of a haplotype associated with nonclassical 21-hydroxylase deficiency may extend into the DR subregion of the major histocompatibility complex with consequent aberrations in DR1 presentation.

Adrenal Hyperplasia, Congenital↗

PubMed2003

Genetic structure of Mediterranean populations revealed by Y-chromosome haplotype analysis.

The allelic variability at six Y-chromosome-specific polymorphisms (YAP, DYS19, DYS389-I, DYS390, DYS391, and DYS392) was used to generate male-specific haplotypes in 333 males representing 12 population samples from the region around the Mediterranean sea. Extreme interindividual variation was observed, as more than 160 distinct Y-chromosome variants could be defined as six-locus haplotypes. Concomitant with this high variability, low levels of population genetic structure were observed. In particular, a "core" of populations directly facing the north and the east of the Mediterranean basin, from the Middle East to the Italian Peninsula, was found to be genetically undifferentiated. This observation, supported by a reanalysis of Y-specific binary polymorphisms in the same populations, suggests that at least part of the male-specific gene pools of these populations has either a very recent common origin (that could be related with the Neolithic demic diffusion hypothesis), and/or that gene flow has played a significant role in shaping the patterns of genetic variability in this region. In agreement with both hypotheses, we found that the spatial distribution of DYS392 alleles revealed a marked differentiation between the East and the West of the Mediterranean area. Through the analysis of microsatellite variation, the time to the most recent common ancestor (TMRCA) of the YAP(+) sublineage 4 has been estimated. The estimations, based on two different data sets, turn out to be quite recent (7,000-11,000 YBP), suggesting that this lineage may have been first introduced into Southern Europe through Neolithic migrations from the Middle East.

Chromosomes, Human, Y↗

PubMed2000

Chloroplast DNA polymorphism reveals little geographical structure in Castanea sativa Mill. (Fagaceae) throughout southern European countries.

The distribution of haplotypic diversity of 38 European chestnut (Castanea sativa Mill.) populations was investigated by PCR/RFLP analysis of regions of the chloroplast and mitochondrial genomes in order to shed light on the history of this heavily managed species. The rapid expansion of chestnut starting from 3000 years ago is strongly related to human activities such as agricultural practice. This demonstrates the importance of human impact, which lasted some thousands of years, on the present-day distribution of the species. No polymorphism was detected for the single mitochondrial analysed region, while a total of 11 different chloroplast (cp) haplotypes were scored. The distribution of the cpDNA haplotypes revealed low geographical structure of the genetic diversity. The value of population subdivision, as measured by GSTc, is strikingly lower than in the other species of the family Fagaceae investigated. The actual distribution of haplotypic diversity may be explained by the strong human impact on this species, particularly during the Roman civilization of the continent, and to the long period of cultivation experienced during the last thousand years.

Agriculture↗

PubMed2006

Phylogeography, phylogeny and hybridization in trichechid sirenians: implications for manatee conservation.

Abstract The three living species of manatees, West Indian (Trichechus manatus), Amazonian (Trichechus inunguis) and West African (Trichechus senegalensis), are distributed across the shallow tropical and subtropical waters of America and the western coast of Africa. We have sequenced the mitochondrial DNA control region in 330 Trichechus to compare their phylogeographic patterns. In T. manatus we observed a marked population structure with the identification of three haplotype clusters showing a distinct spatial distribution. A geographic barrier represented by the continuity of the Lesser Antilles to Trinidad Island, near the mouth of the Orinoco River in Venezuela, appears to have restricted the gene flow historically in T. manatus. However, for T. inunguis we observed a single expanding population cluster, with a high diversity of very closely related haplotypes. A marked geographic population structure is likely present in T. senegalensis with at least two distinct clusters. Phylogenetic analyses with the mtDNA cytochrome b gene suggest a clade of the marine Trichechus species, with T. inunguis as the most basal trichechid. This is in agreement with previous morphological analyses. Mitochondrial DNA, autosomal microsatellites and cytogenetic analyses revealed the presence of hybrids between the T. manatus and T. inunguis species at the mouth of the Amazon River in Brazil, extending to the Guyanas and probably as far as the mouth of the Orinoco River. Future conservation strategies should consider the distinct population structure of manatee species, as well as the historical barriers to gene flow and the likely occurrence of interspecific hybridization.

Animals↗

PubMed2004

Open reading frame sequencing and structure-based alignment of polypeptides encoded by RT1-Bb, RT1-Ba, RT1-Db, and RT1-Da alleles.

MHC class II genes are major genetic components in rats developing autoimmunity. The majority of rat MHC class II sequencing has focused on exon 2, which forms the first external domain. Sequence of the complete open reading frame for rat MHC class II haplotypes and structure-based alignment is lacking. Herein, the complete open reading frame for RT1-Bbeta, RT1-Balpha, RT1-Dbeta, and RT1-Dalpha was sequenced from ten different rat strains, covering eight serological haplotypes, namely a, b, c, d, k, l, n, and u. Each serological haplotype was unique at the nucleotide level of the sequenced RT1-B/D region. Within individual genes, the number of alleles identified was seven, seven, six, and three and the degree of amino-acid polymorphism between allotypes for each gene was 22%, 16%, 19%, and 0.4% for RT1-Bbeta, RT1-Balpha, RT1-Dbeta, and RT1-Dalpha, respectively. The extent and distribution of amino-acid polymorphism was comparable with mouse and human MHC class II. Structure-based alignment identified the beta65-66 deletion, the beta84a insertion, the alpha9a insertion, and the alpha1a-1c insertion in RT1-B previously described for H2-A. Rat allele-specific deletions were found at RT1-Balpha76 and RT1-Dbeta90-92. The mature RT1-Dbeta polypeptide was one amino acid longer than HLA-DRB1 due to the position of the predicted signal peptide cleavage site. These data are important to a comprehensive understanding of MHC class II structure-function and for mechanistic studies of rat models of autoimmunity.

Alleles↗

PubMed2005

Fine-scale mapping in case-control samples using locus scoring and haplotype-sharing methods.

Both haplotype-based and locus-based methods have been proposed as the most powerful methods to employ when fine mapping by association. Although haplotype-based methods utilize more information, they may lose power as a result of overparameterization, given the large number of haplotypes possible over even a few loci. Recently methods have been developed that cluster haplotypes with similar structure in the hope that this reflects shared genealogical ancestry. The aim is to reduce the number of parameters while retaining the genotype information relating to disease susceptibility. We have compared several haplotype-based methods with locus-based methods. We utilized 2 regions (D2 and D4) simulated to be in linkage disequilibrium and to be associated with disease susceptibility, combining 5 replicates at a time to produce 4 datasets that were analyzed. We found little difference in the performance of the haplotype-based methods and the locus-based methods in this dataset.

Case-Control Studies↗