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At least 613 records · Page 34Linked to original sources
PubMed2005

A population association study of angiotensinogen polymorphisms and haplotypes with left ventricular phenotypes.

Several studies have shown an association between single nucleotide polymorphisms (SNPs) in the angiotensinogen (AGT) gene and hypertension. Because hypertension is a risk factor for left ventricular (LV) hypertrophy and because evidence from animal models suggests that AGT may play a role in the growth and hypertrophy of the heart, we chose to conduct a population association study examining the relationship of 10 SNPs in the AGT gene with 7 different LV phenotypes measured by echocardiography. Participants (336 whites and 441 blacks) were drawn from the Hypertension Genetic Epidemiology Network (HyperGEN) study. Individuals were genotyped for 10 previously identified SNPs within the AGT gene. SNP genotype results were regressed against continuous LV phenotypes to test associations separately in each race. Using a cutoff of P<0.005 to account for multiple testing, we found 1 SNP (rs943580) significantly associated with transmitral early peak filling velocity (MVE) in the black population. We also used Phase 2.0.2 to reconstruct haplotypes from genotype data. Using the same cutoff of P<0.005, we found no haplotypes to be significantly associated with the LV phenotypes. To better understand the association between rs943580 and MVE, we examined AGT haplotype associations with MVE. The single SNP association was driven by a large group of SNPs in high linkage disequilibrium that includes the promoter SNP rs5051.

Aged↗
PubMed2006

CYP2C19 genetic polymorphism in Thai, Burmese and Karen populations.

The genetic polymorphism of CYP2C19 was examined in three Southeast Asian populations. This study was conducted in 774 Thais, 127 Burmeses and 131 Karens. Genomic DNA was extracted from leucocytes and analyzed by the PCR-RFLP technique. Genotype analysis revealed that the allele frequencies of CYP2C19*1, CYP2C19*2 and CYP2C19*3 in the Thais were 0.68, 0.29 and 0.03, respectively, and those of the Burmese population were 0.66, 0.30 and 0.04, respectively. For Karens, the minority ethnic in Mynmar, the allele frequencies of CYP2C19*1, CYP2C19*2 and CYP2C19*3 were 0.71, 0.28 and 0.01, respectively. The prevalence of PM estimated from genotype data among these three ethnic populations were 9.2%, 11.0%, and 8.4%, respectively. The PM phenotype and the frequencies of CYP2C19 defective alleles, particularly CYP2C19*3 among these three Southeast Asian ethnics appeared to be lower than other Asian populations. Lower prevalence of CYP2C19 PM suggests that these ethnics may have different capacity to metabolize drugs that are substrates of CYP2C19. Certain drug dosage regiments should be considered differently for Asian populations.

Adult↗
PubMed2002

A drosophila model for attention deficit hyperactivity disorder (ADHD): No evidence of association with PRKG1 gene.

Attention deficit hyperactivity disorder (ADHD) is a prevalent psychiatric condition in children and follow up studies have indicated that 22-33% of patients continue to suffer from ADHD during late adolescence and adulthood. The action of psychostimulant drugs may be determined by additional mechanisms beyond the dopamine transporter and receptors. We are exploring new methodology for discovering these mechanisms. For example, in Drosophila, such an additional determinant of psychostimulant action could be protein kinase G (PKG) that affects food-search behavior. Here we initiated studies with the human homologue of PKG, the PRKG1 gene. The aim of this study was to investigate for the presence of linkage disequilibrium between the protein kinase G gene (PRKG1) and adult ADHD in a sample of nuclear families. Genotyping data for the C2276T polymorphism were analyzed using the Transmission Disequilibrium Test (TDT). Sixty three nuclear families were informative for the TDT on C2276T polymorphism, which showed no preferential transmission of either allele (chi-square = 0.778, df = 1, p = 0.316). These findings exclude a direct involvement of this genetic marker of the Protein kinase G gene in the pathogenesis of ADHD.

Animals↗
PubMed2001

Case-control studies of association in structured or admixed populations.

Case-control tests for association are an important tool for mapping complex-trait genes. But population structure can invalidate this approach, leading to apparent associations at markers that are unlinked to disease loci. Family-based tests of association can avoid this problem, but such studies are often more expensive and in some cases--particularly for late-onset diseases--are impractical. In this review article we describe a series of approaches published over the past 2 years which use multilocus genotype data to enable valid case-control tests of association, even in the presence of population structure. These tests can be classified into two categories. "Genomic control" methods use the independent marker loci to adjust the distribution of a standard test statistic, while "structured association" methods infer the details of population structure en route to testing for association. We discuss the statistical issues involved in the different approaches and present results from simulations comparing the relative performance of the methods under a range of models.

Alleles↗
PubMed2003

Genome-wide linkage screen of a consanguineous multiple sclerosis kinship.

Multiple sclerosis (MS), like Alzheimer's disease (AD) and Parkinson's disease (PD), is a common neurological disorder thought to be caused by the interaction of several genes with unknown environmental factors. In both AD and PD the identification of disease forms inherited in a classic Mendelian fashion has helped investigators elucidate pathogenetic mechanisms. In this study a whole-genome screen, with an average of 608 successful genotypes per person, was performed on nine members of a consanguineous family: the index case, three of her siblings and her daughter, all of whom have been diagnosed with definite MS; as well as the parents of the index case (first cousins), one of her five healthy siblings and her husband (who is also her first cousin). Nonparametric linkage analysis was performed on genotyping data. Based on the presence of consanguinity, the a priori hypothesis was that the disease is transmitted in an autosomal recessive fashion in the pedigree. Linkage analysis revealed a suggestive logarithm of odds (LOD) score of 2.29 on the long arm of chromosome 9. Four of five affected family members were identically homozygous for a haplotype under this peak, spanning approximately 43 cM, while the fifth affected subject and all unaffected family members were heterozygous for the haplotype.

Adolescent↗
PubMed2002

A novel locus for autosomal dominant nuclear cataract mapped to chromosome 2p12 in a Pakistani family.

PURPOSE: To map the disease locus in a four-generation, consanguineous Pakistani family affected by autosomal dominant congenital nuclear cataract (adNCat). All affected individuals had early onset of bilateral nuclear cataract. METHODS: Genomic DNA from family members was typed for alleles at more than 300 known polymorphic genetic markers by polymerase chain reaction. The lod scores were calculated by using two-point linkage analysis of the genotyping data. RESULTS: The maximum lod score, 4.05, was obtained for the marker D2S2333. Proximal and distal crossovers were observed with markers D2S286 and D2S1790, respectively. These crossovers define the critical disease locus to an interval of approximately 9 centimorgans (cM). CONCLUSIONS: Linkage analysis identified a novel locus for adNCat on chromosome 2p12 in a Pakistani family. A genome database analysis of the target interval is being undertaken to identify candidate gene(s) for the disease.

Adult↗
PubMed2001

Genetic polymorphisms of microsomal and soluble epoxide hydrolase and the risk of Parkinson's disease.

Oxidative stress is hypothesized to play a major role in the destruction of dopaminergic neurons, which is associated with Parkinson's disease. Epoxides are potentially reactive intermediates formed through the oxidative metabolism of both exogenous and endogenous substances that contribute to cytotoxic damage mediated by oxidative stress. The microsomal (EPHX1) and soluble (EPHX2) epoxide hydrolases function to regulate the oxidation status of a wide range of xenobiotic- and lipid-derived substrates; therefore, interindividual variation in these pathways may mitigate epoxide-related cellular injury. In this investigation, we examined the potential association between the risk of Parkinson's disease and genetic variation within the EPHX1 and EPHX2 genes. Fluorescent 5' nuclease-based assays were developed to identify the allelic status of individuals with respect to specific single nucleotide polymorphisms in exons 3 and 4 of the EPHX1 gene and exons 8 and 13 of the EPHX2 gene. EPHX1 and EPHX2 genotype data were obtained from 133 idiopathic Parkinson's disease patients and 212 control subjects matched on age, gender and ethnicity. No statistically significant differences were found in the distribution of the reference and variant alleles between Parkinson's disease and control subjects, or when results were stratified by gender. Therefore, common polymorphisms within EPHX1 and EPHX2 do not appear to be important risk factors for Parkinson's disease.

Adult↗
PubMed2005

Hybrid Vibrio vulnificus.

The recent emergence of the human-pathogenic Vibrio vulnificus in Israel was investigated by using multilocus genotype data and modern molecular evolutionary analysis tools. We show that this pathogen is a hybrid organism that evolved by the hybridization of the genomes from 2 distinct and independent populations. These findings provide clear evidence of how hybridization between 2 existing and nonpathogenic forms has apparently led to the emergence of an epidemic infectious disease caused by this pathogenic variant. This novel observation shows yet another way in which epidemic organisms arise.

Animals↗
PubMed2002

Linkage disequilibrium between dopamine D1 receptor gene (DRD1) and bipolar disorder.

BACKGROUND: Based on the dopamine hypothesis, the dopamine D1 receptor gene (DRD1) is considered to be a good candidate gene for bipolar disorder (BP). METHODS: In our study, three polymorphisms of the DRD1 gene, -800T/C, -48A/G, and 1403T/C, were analyzed in 286 BP trios. Both the transmission disequilibrium test (TDT) and haplotype TDT were performed on the genotype data to test for the presence of linkage disequilibrium between DRD1 and bipolar disorder. With the extended transmission disequilibrium test (ETDT), we also calculated the maternal transmission and paternal transmission for each allele. RESULTS: Although no association was found for each individual polymorphism, there is a significant association between DRD1 and BP for haplotype TDT analysis (chi(2) = 16.068, df = 3, p =.0011). CONCLUSIONS: These results indicate that DRD1 may play a role in the etiology of bipolar disorder.

Adult↗
PubMed2005

Temporal genetic structure of a drone congregation area of the giant Asian honeybee (Apis dorsata).

The giant Asian honeybee (Apis dorsata), like all other members of the genus Apis, has a complex mating system in which the queens and males (drones) mate at spatially defined drone congregation areas (DCAs). Here, we studied the temporal genetic structure of a DCA of A. dorsata over an 8-day time window by the genotyping of sampled drones with microsatellite markers. Analysis of the genotypic data revealed a significant genetic differentiation between 3 sampling days and indicated that the DCA was used by at least two subpopulations at all days in varying proportions. The estimation of the number of colonies which used the DCA ranged between 20 and 40 colonies per subpopulation, depending on the estimation procedure and population. The overall effective population size was estimated as high as N (e)=140. The DCA seems to counteract known tendencies of A. dorsata for inbreeding within colony aggregations by facilitating gene flow among subpopulations and increasing the effective population size.

Animals↗
PubMed2003

A meta-analysis of whole genome linkage screens in multiple sclerosis.

Linkage studies in complex diseases like multiple sclerosis, where the effects attributable to individual loci are modest, are critically dependent upon the number of families included. We have combined the raw genotyping data from all published genome linkage screens in multiple sclerosis and thereby performed a linkage analysis including 719 families studied with a weighted average of 359 microsatellite markers per family (range 257-453) providing an average marker separation of 10.2 cM. Linkage with genome-wide significance is confirmed in the HLA region on chromosome 6p21. In addition, two novel regions suggestive of linkage are seen (17q21 and 22q13). Our simulations would imply that the number of peaks with NPL scores >/=2.1 exceeds the number expected by chance alone.

Alleles↗
PubMed1999

Typing for the human lewis blood group system by quantitative fluorescence-activated flow cytometry: large differences in antigen presentation on erythrocytes between A(1), A(2), B, O phenotypes.

BACKGROUND: Lewis phenotyping by hemagglutination is an unreliable routine method for Lewis antigen designation. Now genomic typing of the Lewis gene is available. Additionally, flow cytometry has been used for typing. We wanted to compare the results of Lewis typing in healthy individuals using the three methods. MATERIALS AND METHODS: Ninety-three randomly selected plasma donors were genotyped for inactivating Secretor (FUT2) G428A and Lewis (FUT3) T59G, T202C, C314T, G508A and T1067A point mutations. All Le(a+b-) individuals (nonsecretors) were homozygous for the FUT2 G428A mutation and all Le(a-b-) individuals had inactivating mutations on both FUT3 alleles. Fixed erythrocytes were analyzed by fluorescence-activated flow cytometry and the results were compared with hem- agglutination and genotypic data. Antigen availability was expressed as median fluorescence intensity and as percentage positive cells with fluorescence intensities > or =10(2). RESULTS: Using an anti-Le(a) reagent a mean of 99% of erythrocytes from Le(a+b-) individuals and 1% of erythrocytes from Le(a-b-) or Le(a-b+) individuals were stained positive. Using an anti-Le(b) reagent, a mean of 71% of erythrocytes from A(1), 95% from B and 99% from O and A(2) Le(a-b+) individuals and less than 10% of erythrocytes from Le(a-b-) or Le(a+b-) individuals were stained positive. After papain treatment 100% of the erythrocytes from A(1) and A(1)B Le(a-b+) individuals stained positive without increase in background staining. The flow cytometric technique revealed large differences in staining intensities, within each ABO Le(a-b+) subgroup which was not directly correlated to plasma donation frequencies nor to Secretor or Lewis genotypes. CONCLUSION: Flow cytometry may prove valuable as a Lewis blood group typing technique but also as a research tool when investigating Lewis phenotypes of human erythrocytes.

ABO Blood-Group System↗
PubMed2004

Does linkage disequilibrium generate heterozygosity-fitness correlations in great reed warblers?

Heterozygosity-fitness correlations (HFCs) at noncoding genetic markers are commonly assumed to reflect fitness effects of heterozygosity at genomewide distributed genes in partially inbred populations. However, in populations with much linkage disequilibrium (LD), HFCs may arise also as a consequence of selection on fitness loci in the local chromosomal vicinity of the markers. Recent data suggest that relatively high levels of LD may prevail in many ecological situations. Consequently, LD may be an important factor, together with partial inbreeding, in causing HFCs in natural populations. In the present study, we evaluate whether LD can generate HFCs in a small and newly founded population of great reed warblers (Acrocephalus arundinaceus). For this purpose dyads of full siblings of which only one individual survived to adult age (i.e., returned to breed at the study area) were scored at 19 microsatellite loci, and at a gene region of hypothesized importance for survival, the major histocompatibility complex (MHC). By examining siblings, we controlled for variation in the inbreeding coefficient and thus excluded genome-wide fitness effects in our analyses. We found that recruited individuals had significantly higher multilocus heterozygosity (MLH), and mean d2 (a microsatellite-specific variable), than their nonrecruited siblings. There was a tendency for the survivors to have a more diverse MHC than the nonsurvivors. Single-locus analyses showed that the strength of the genotype-survival association was especially pronounced at four microsatellite loci. By using genotype data from the entire breeding population, we detected significant LD between five of 162 pairs of microsatellite loci after accounting for multiple tests. Our present finding of a significant within-family multilocus heterozygosity-survival association in a nonequilibrium population supports the view that LD generates HFCs in natural populations.

Animals↗
PubMed2004

Ex situ population management in the absence of pedigree information.

For captive breeding to play a significant role in conservation, ex situ populations must be scientifically managed to meet objective goals for retaining representative genetic variation. Imperfect genealogical information requires fundamental assumptions to be made that may bias downstream measures of genetic importance, upon which management decisions are based. The impacts of such assumptions are most pronounced within breeding programmes characterized by a high proportion of individuals of unknown ancestry, as exemplified by the large captive population of the St Vincent parrot (Amazona guildingii). The degree to which microsatellite-based estimates of relatedness may improve upon the assumptions of conventional pedigree-based management was investigated using genotypic data collected at eight microsatellite loci and two marker-based relatedness estimators. The measure, rxyLR, was found to explain the highest amount of variation in true relatedness. Integration of pairwise estimates of founder relatedness with studbook data transformed current understanding of the relatedness structure of the A. guildingii population from two subgroups characterized by a high and low degree of relatedness, respectively, to a situation where all 72 individuals are prioritized for breeding according to their estimated mean kinships. Furthermore, the discovery of opposing, directional bias exhibited by rxyLR and rxyQG in assigning dyads to a given relationship category suggests that an approach that utilizes a combination of pairwise relatedness estimators may provide the most genetic information for balancing the dual considerations of maximizing gene diversity and minimizing inbreeding in developing breeding recommendations.

Animals↗
PubMed2000

Characterization of human crossover interference.

We present an analysis of crossover interference over the entire human genome, on the basis of genotype data from more than 8,000 polymorphisms in eight CEPH families. Overwhelming evidence was found for strong positive crossover interference, with average strength lying between the levels of interference implied by the Kosambi and Carter-Falconer map functions. Five mathematical models of interference were evaluated: the gamma model and four versions of the count-location model. The gamma model fit the data far better than did any of the other four models. Analysis of intercrossover distances was greatly superior to the analysis of crossover counts, in both demonstrating interference and distinguishing between the five models. In contrast to earlier suggestions, interference was found to continue uninterrupted across the centromeres. No convincing differences in the levels of interference were found between the sexes or among chromosomes; however, we did detect possible individual variation in interference among the eight mothers. Finally, we present an equation that provides the probability of the occurrence of a double crossover between two nonrecombinant, informative polymorphisms.

Centromere↗
PubMed1988

Structuring strain data for storage and retrieval of information on fungi and yeasts in MINE, the Microbial Information Network Europe.

A distributed Microbial Information Network Europe (MINE) is being constructed by a number of major microbial culture collections in countries of the European Community, with the support of the Biotechnology Action Programme (BAP) of the Commission of the European Community. The representatives of the collections participating in MINE have agreed to adopt a general format for the computer storage and retrieval of strain data. This uniform format will facilitate the electronic combination and exchange of data from different collections in order to produce integrated catalogues and the use of identical commands to search the different databases. It is recommended to other collections who may wish to contribute data to the MINE network or between themselves. Three kinds of records can be linked to the leading 'species records': strain records, synonym records, and alternative morphonym records. A minimum data set of 30 fields (similar to the fields used for producing catalogues) is defined that facilitates the exchange of data between the national nodes and serves as a directory to strains available at other nodes. It is suggested that the full strain record comprise 99 fields, grouped in 12 blocks: internal administration--name--strain administration--status--environment and history--biological interactions--sexuality--properties (cytology, biomolecular data)--genotype and genetics--growth conditions--chemistry and enzymes--practical applications. Several fields are divided into subfields of different ranks. Delimiters are used either to separate a range of entries that have to be indexed or to divide an entry from the reference to its source or remarks that should not be indexed. The contents and structure of the fields proposed for filamentous fungi and yeasts are described and in some cases illustrated by examples. Uniformity of input is essential for indexed fields and desirable for non-indexed fields. Seven thesaurus files are envisaged to ensure consistency.

Data Collection↗
PubMed2005

The role of pedigree information in combined linkage disequilibrium and linkage mapping of quantitative trait loci in a general complex pedigree.

Combined linkage disequilibrium and linkage (LDL) mapping can exploit historical as well as recent and observed recombinations in a recorded pedigree. We investigated the role of pedigree information in LDL mapping and the performance of LDL mapping in general complex pedigrees. We compared using complete and incomplete genotypic data, spanning 5 or 10 generations of known pedigree, and we used bi- or multiallelic markers that were positioned at 1- or 5-cM intervals. Analyses carried out with or without pedigree information were compared. Results were compared with linkage mapping in some of the data sets. Linkage mapping or LDL mapping with sparse marker spacing ( approximately 5 cM) gave a poorer mapping resolution without considering pedigree information compared to that with considering pedigree information. The difference was bigger in a pedigree of more generations. However, LDL mapping with closely linked markers ( approximately 1 cM) gave a much higher mapping resolution regardless of using pedigree information. This study shows that when marker spacing is dense and there is considerable linkage disequilibrium generated from historical recombinations between flanking markers and QTL, the loss of power due to ignoring pedigree information is negligible and mapping resolution is very high.

Alleles↗
PubMed2004

A family-based association study of the 5-HT-1Dbeta receptor gene in obsessive-compulsive disorder.

Pharmacological studies have shown that sumatriptan, a selective ligand of the serotonin 5-HT-1Dbeta autoreceptor, modifies obsessive-compulsive disorder (OCD) symptoms. The current study analysed the G861C polymorphism of the 5-HT-1Dbeta gene in a sample of 72 trios. Genotyping data were analysed using the Family-Based Association Test (FBAT). We did not replicate the previously reported linkage disequilibrium between the G861 variant and OCD. However, a quantitative trait analysis, assessing severity of OCD symptoms and defined as YBOCS score, confirmed the finding that subjects with a preferential transmission of the G861 variant showed higher YBOCS Obsession scores compared to patients carrying the C861 allele. These preliminary findings may indicate that the 5-HT-1Dbeta receptor gene could be involved in the severity of obsession symptoms in OCD. However, it is important to perform the replication of these findings in larger sample sizes of informative families.

DNA↗