Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Genotype Data”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 451 records · Page 25Linked to original sources
PubMed2000

Environmental factor dependent maximum likelihood method for association study targeted to personalized medicine.

The most challenging strategy for analyzing genome-wide polymorphisms and/or expression profiles is to solve multi-factor causal-relationship simultaneously. As the first step, we propose a framework of association study using maximum likelihood method that simultaneously handles genetic polymorphisms and epi-genetic information, e.g. environmental factors. We evaluate the theory by applying it to genotyped data of myocardial infarction (MI) patients.

Algorithms↗
PubMed2002

HapScope: a software system for automated and visual analysis of functionally annotated haplotypes.

We have developed a software analysis package, HapScope, which includes a comprehensive analysis pipeline and a sophisticated visualization tool for analyzing functionally annotated haplotypes. The HapScope analysis pipeline supports: (i) computational haplotype construction with an expectation-maximization or Bayesian statistical algorithm; (ii) SNP classification by protein coding change, homology to model organisms or putative regulatory regions; and (iii) minimum SNP subset selection by either a Brute Force Algorithm or a Greedy Partition Algorithm. The HapScope viewer displays genomic structure with haplotype information in an integrated environment, providing eight alternative views for assessing genetic and functional correlation. It has a user-friendly interface for: (i) haplotype block visualization; (ii) SNP subset selection; (iii) haplotype consolidation with subset SNP markers; (iv) incorporation of both experimentally determined haplotypes and computational results; and (v) data export for additional analysis. Comparison of haplotypes constructed by the statistical algorithms with those determined experimentally shows variation in haplotype prediction accuracies in genomic regions with different levels of nucleotide diversity. We have applied HapScope in analyzing haplotypes for candidate genes and genomic regions with extensive SNP and genotype data. We envision that the systematic approach of integrating functional genomic analysis with population haplotypes, supported by HapScope, will greatly facilitate current genetic disease research.

Algorithms↗
PubMed2005

Linkage mapping reveals sex-dimorphic map distances in a passerine bird.

Linkage maps are lacking for many highly influential model organisms in evolutionary research, including all passerine birds. Consequently, their full potential as research models is severely hampered. Here, we provide a partial linkage map and give novel estimates of sex-specific recombination rates in a passerine bird, the great reed warbler (Acrocephalus arundinaceus). Linkage analysis of genotypic data at 51 autosomal microsatellites and seven markers on the Z-chromosome (one of the sex chromosomes) from an extended pedigree resulted in 12 linkage groups with 2-8 loci. A striking feature of the map was the pronounced sex-dimorphism: males had a substantially lower recombination rate than females, which resulted in a suppressed autosomal map in males (sum of linkage groups: 110.2 cM) compared to females (237.2 cM; female/male map ratio: 2.15). The sex-specific recombination rates will facilitate the building of a denser linkage map and cast light on hypotheses about sex-specific recombination rates.

Animals↗
PubMed2006

Estimating haplotype relative risks in complex disease from unphased SNPs data in families using a likelihood adjusted for ascertainment.

The understanding of complex diseases and insights to improve their medical management may be achieved through the deduction of how specific haplotypes may play a joint effect to change relative risk information. In this paper we describe an ascertainment adjusted likelihood-based method to estimate haplotype relative risks using pooled family data coming from association and/or linkage studies that were used to identify specific haplotypes. Haplotype-based analysis tends to require a large amount of parameters to capture all the information that leads to efficiency problems. An adaptation of the Stochastic Expectation Maximization algorithm is used for haplotypes inference from genotypic data and to reduce the number of nuisance parameters for risk estimation. Using different simulations, we show that this method provides unbiased relative risk estimates even in case of departure from Hardy-Weinberg equilibrium.

Algorithms↗
PubMed2001

GAW12: simulated genome scan, sequence, and family data for a common disease.

The Genetic Analysis Workshop (GAW) 12 simulated data involves a common disease defined by imposing a threshold on a quantitative liability distribution. Associated with the disease are five quantitative risk factors, a quantitative environmental exposure, and a dichotomous environmental variable. Age at disease onset and household membership were also simulated. Genotype data, including 2,855 microsatellites on 22 autosomes, were simulated for 1,497 individuals in 23 families. Phenotype data and sequence data for seven candidate genes were provided for 1,000 of these individuals who were "living" and available for study. Data were simulated for 50 replicate samples in each of two populations, a general population and a population isolate formed from a small group of founders.

Adolescent↗
PubMed1997

Apolipoprotein E genotypes in a neuropathological series from the Consortium to Establish a Registry for Alzheimer's Disease.

We evaluated the sensitivity, specificity, and predictive value of the apolipoprotein E (ApoE) epsilon4 allele for the neuropathological diagnosis of Alzheimer disease (AD) in a clinical series of well-characterized AD patients and controls followed longitudinally in the multicenter study of the Consortium to Establish a Registry for Alzheimer's Disease (CERAD). In the 162 patients for whom autopsy and ApoE genotype data were available, the clinical diagnosis of AD was verified as the primary cause of dementia in 139 cases (139 of 162, or 86%). The sensitivity and specificity of the epsilon4 allele for AD were both 83%. The positive predictive value of the epsilon4 allele was very high at 97% (115 of 119); whereas, the negative predictive value was 44% (19 of 43), providing no useful information for diagnosis of AD when the epsilon4 allele is not present. Of the cases where AD was not considered the primary or sole cause of dementia (n = 23), 6 cases exhibited concomitant neuropathological findings of definite or probable AD and 2 of these 6 cases had at least one epsilon4 allele. These multicenter data extend previous observations reported from smaller case series of single laboratories and demonstrate that once the clinical diagnosis of AD is established, the presence of an epsilon4 allele reliably predicts the ultimate CERAD neuropathological diagnosis of AD. The findings also suggest that ApoE genotype information is useful clinically in bolstering diagnostic confidence when an epsilon4 allele is present and in identifying a group of patients for whom additional diagnostic evaluations may be warranted when the epsilon4 allele is absent.

Aged↗
PubMed1999

Cytogenetic effects from exposure to mixed pesticides and the influence from genetic susceptibility.

Exposure to pesticides remains a major environmental health problem. Health risk from such exposure needs to be more precisely understood. We conducted three different cytogenetic assays to elucidate the biological effects of exposure to mixed pesticides in 20 Costa Rica farmers (all nonsmokers) compared with 20 matched controls. The farmers were also exposed to dibromochloropropane during the early employment years, and most of them experienced sterility/fertility problems. Our data show that the farmers had consistently higher frequencies of chromosome aberrations, as determined by the standard chromosome aberration assay, and significantly abnormal DNA repair responses (p < 0.05), as determined by the challenge assay, but no statistically significant differences in the tandem-probe fluorescence in situ hybridization (FISH) assay (p > 0.05). Genotype analysis indicates that farmers with certain "unfavorable" versions of polymorphic metabolizing genes (cytochrome P4502E1, the glutathione S-transferases mu and theta, and the paraoxonase genes) had significantly more biological effects, as determined by all three cytogenetic assays, than both the farmers with the "favorable" alleles and the matched controls. A unique observation is that, in individuals who had inherited any of the mentioned "unfavorable" alleles, farmers were consistently underrepresented. In conclusion, the Costa Rican farmers were exposed to genotoxic agents, most likely pesticides, which expressed the induction of biological and adverse health effects. The farmers who had inherited "unfavorable" metabolizing alleles were more susceptible to genotoxic effects than those with "favorable" alleles. Our genotype data suggest that the well-recognized "healthy worker effect" may be influenced by unrecognized occupational selection pressure against genetically susceptible individuals.

Adult↗
PubMed1994

Integrated mapping analysis of the Werner syndrome region of chromosome 8.

The Werner syndrome locus (WRN) is located at 8p11-p12. To facilitate eventual cloning of the WRN gene, a 10,000-rad radiation-reduced hybrid (RH) cell panel was generated to map genetic markers, sequence-tagged sites (STSs), and genes in this region. A hamster cell line carrying an intact human chromosome 8 was fused with another hamster cell line. Two sets of hybrid cell panels from 2 separate fusions were generated; each panel consisted of 50 independent clones; 33 and 34 cell lines from the 2 fusions retained human chromsome material as determined by inter-Alu PCR. The combined panel was genotyped for 52 markers spanning the entire chromosome, including 10 genes, 29 anonymous polymorphic loci, and 13 STSs. Seventeen of these markers have not been previously described. Markers near the centromere were retained at a higher frequency than more distal markers. Fluorescence in situ hybridization was also used to localize and order a subset of the markers. A RH map of the WRN region was constructed using a maximum likelihood method, giving the following most likely order: D8S131-D8S339 (GSR)-D8S124-D8S278-D8S259-(D8S71)-D8S283- D8S87-D8S105-D8S135 (FGFR1)-D8S135PB-D8S255-ANK1. A genetic map of 15 short tandem repeat polymorphic loci in the WRN region was also constructed. The marker orders from the genetic and RH maps were consistent. In addition, an integrated map of 24 loci in the WRN region was generated using information from both genetic and RH mapping methods. A 1000:1 framework map for 6 loci (LPL-D8S136-D8S137-D8S87-FGFR1-ANK1) was determined by genetic mapping, and the resulting locus order was fixed during analysis of the RH genotype data. The resulting integrated map contained more markers than could confidently be ordered by either genetic or RH mapping alone.

Base Sequence↗
PubMed2006

Dipsogenic genes associated with weight changes during Ironman Triathlons.

Thirst is regulated by a complex interaction of signalling pathways within the central nervous system, including components of the renin-angiotensin and kalikrein kinin systems, as well as the serotonergic pathways. The aim of this study was to determine whether there were any associations between polymorphisms within the ACE, BDKRB2, NOS3 and/or 5-HTT genes with weight changes during the 2000 and 2001 226 km South African Ironman Triathlons. Pre- and post-race serum [Na(+)] and body weights, as well as genotype data, were collected from 428 (61.1%) Caucasian male triathletes who were divided into three groups according to their relative weight loss during the triathlon (0-3, 3-5 and >5%). There was a significant linear trend for the distribution of both the BDKRB2 +9/+9 genotype and the 5-HTT SS genotype between the three weight loss groups, with the >5% group having the highest percentage of athletes with the +9/+9 genotype (chi(2)=5.3, P=0.021) and the highest percentage of athletes with the SS genotype (chi(2)=5.8, P=0.016). Likewise, the >5% group had the highest percentage of athletes with the combined SS 5-HTT and/or +9/+9 BDKRB2 genotypes (chi(2)=7.4, P=0.007). In conclusion, the functional SS genotype of the serotonin transporter-linked polymorphic region (5-HTTLPR) within the 5-HTT gene and the functional +9/+9 genotype of the BDKBR2 gene were associated with larger weight losses during the Ironman Triathlons. These findings suggest the involvement of the serotonergic pathways in the control of thirst and drinking behaviour and provide further evidence for the dipsogenic effect of circulating bradykinin.

Adult↗
PubMedDate not supplied

Analytical bayesian approach for assigning individuals to populations.

We propose a general formulation of the Bayesian method for assigning individuals to a population among a predetermined set of reference populations using molecular marker information. Compared to previously published methods, ours allows us to consider different types of prior information about allele frequencies by using a Dirichlet prior probability distribution. It also makes it possible to assign a set of individuals assumed to belong to the same population with increased accuracy using their pooled genotype data. The efficiency of the method is illustrated by application to a group of closely related coconut populations. An interesting feature of the Bayesian procedure is the way it handles imprecise information. With a poor or even incomplete dataset, assignment is still be possible and gives valid results: poor data quality is reflected in an ambiguous result rather than in a false conclusion.

Bayes Theorem↗
PubMed1997

Apolipoprotein E-associated risk for Alzheimer's disease in the African-American population is genotype dependent.

As a part of our ongoing study on Alzheimer's disease (AD) in elderly African Americans, we obtained clinical assessment and apolipoprotein E (ApoE) genotype data on 288 individuals (including 60 with AD). The ApoE epsilon4 allele frequency was significantly increased in AD patients compared with controls. The age-adjusted odds ratio (OR) for AD in epsilon4 homozygotes was 4.83 (95% confidence interval [CI], 1.71-13.64) compared with the epsilon3/epsilon3 genotype, but the OR for AD with the epsilon3/epsilon4 genotype did not reach significance (1.20; 95% CI, 0.58-2.45). These findings suggest that the association between ApoE epsilon4 and AD is weaker in African Americans than in whites.

Aged↗
PubMed2006

Association of transforming growth factor-beta1 gene polymorphisms with myocardial infarction in patients with angiographically proven coronary heart disease.

OBJECTIVE: Transforming growth factor (TGF)-beta1 (TGF-beta1) is a multifunctional cytokine that exhibits vasculoprotective properties. Production and plasma levels of TGF-beta1 are influenced by polymorphisms in the TGF-beta1 gene (TGFB1). We investigated whether the -509C/T (rs1800469), 868T/C (rs1982073), 913G/C (rs1800471), and 11929C/T (rs1800472) polymorphisms of TGFB1 are associated with myocardial infarction. METHODS AND RESULTS: The study population consisted of 3657 patients with myocardial infarction (885 women and 2772 men) and 1211 control individuals (598 women and 613 men) with angiographically normal coronary arteries and without signs or symptoms of myocardial infarction. Polymorphism-related genotypes were determined with TaqMan assays and haplotypes were estimated from the genotype data. The -509C/T polymorphism and -509C/868T/913G/11929C (CTGC) haplotype were associated with myocardial infarction in men, independently from the potentially confounding factors age, arterial hypertension, hypercholesterolemia, cigarette smoking, and diabetes mellitus. Lower risks of myocardial infarction were observed among the carriers of the -509CC genotype (adjusted odds ratio [OR], 0.49; 95% confidence interval [CI], 0.27 to 0.87; P=0.014) and homozygous carriers of the CTGC haplotype (adjusted OR, 0.61; 95% CI, 0.38 to 0.98; P=0.042) than among the noncarriers of this genotype or haplotype. None of the genotypes (P> or =0.37) or haplotypes (P> or =0.35) was associated with myocardial infarction in women. CONCLUSIONS: Positive association findings in this study suggest that TGFB1 is a susceptibility locus for myocardial infarction.

Adult↗
PubMed1993

Testing the Hardy-Weinberg law across strata.

The problem of testing the Hardy-Weinberg law when data are sampled from several populations with different allele frequencies is considered. An odds-ratio representation of disequilibrium is proposed. This ratio is assumed to be constant across strata, an assumption that seems more reasonable than that of previous authors of a constant difference in true and expected (under equilibrium) heterozygote proportions. A score-type test which optimally combines information from the separate strata is then derived using the theory of unbiased estimating equations. Simulations show that the new test has greater power than previously proposed tests when the disequilibrium ratio is constant across strata. The method is applied to glyoxalase genotype data from populations in India.

Alleles↗
PubMed2002

CYP1A1*2 and CYP1A1*3 polymorphisms cosegregate in the Indian population.

Several ethnic groups have been genotyped for polymorphisms at the CYP1A1 gene locus that encodes the enzyme that catalyzes the initial step in the metabolism of polycyclic aromatic hydrocarbons. Two of the CYP1A1 polymorphisms, namely, CYP1A1*2 and CYP1A1*3 are reported to cosegregate among the Japanese and to a lesser extent in Caucasians, but not in people of African descent. In the absence of such information in the Indian population, the frequency of the CYP1A1*2 polymorphism was determined in this study, using DNA samples from 649 ethnic Indians who had been earlier genotyped for the CYP1A1*3 polymorphism. Analysis of the combined genotype data revealed that the two polymorphisms cosegregate in the Indian population.

Africa↗
PubMed2002

Enhanced pedigree error detection.

Accurate information on the relationships among individuals in a study is critical for valid linkage analysis. We extend the MLLR, EIBD, AIBS and IBS tests for detection of misspecified relationships to a broader range of relative pairs, and we improve the two-stage screening procedure for analyzing large data sets. We have developed software, PREST, which calculates the test statistics and performs the corresponding hypothesis tests for relationship misclassification in general outbred pedigrees. When a potential pedigree error is detected, our companion program, ALTERTEST, can be used to determine which relationships are compatible with the genotype data. Both programs are now freely available on the web.

Computer Simulation↗
PubMed2006

Linkage disequilibrium and haplotype homozygosity in population samples genotyped at a high marker density.

OBJECTIVE: Analyze the information contained in homozygous haplotypes detected with high density genotyping. METHODS: We analyze the genotypes of approximately 2,500 markers on chr 22 in 12 population samples, each including 200 individuals. We develop a measure of disequilibrium based on haplotype homozygosity and an algorithm to identify genomic segments characterized by non-random homozygosity (NRH), taking into account allele frequencies, missing data, genotyping error, and linkage disequilibrium. RESULTS: We show how our measure of linkage disequilibrium based on homozygosity leads to results comparable to those of R(2), as well as the importance of correcting for small sample variation when evaluating D'. We observe that the regions that harbor NRH segments tend to be consistent across populations, are gene rich, and are characterized by lower recombination. CONCLUSIONS: It is crucial to take into account LD patterns when interpreting long stretches of homozygous markers.

Chromosomes, Human, Pair 22↗
PubMed2004

Manganese superoxide dismutase polymorphism, plasma antioxidants, cigarette smoking, and risk of breast cancer.

Oxidative stress may be involved in the development of breast cancer. Manganese superoxide dismutase (MnSOD) is one of the primary enzymes that directly scavenge potential harmful oxidizing species. A valine (Val) to alanine (Ala) substitution at amino acid 16, occurring in the mitochondrial targeting sequence of the MnSOD gene, has been associated with an increase in breast cancer risk. We conducted a nested case-control study within the Nurses' Health Study cohort to examine the role of this polymorphism and its interaction with environmental factors with breast cancer risk. MnSOD genotype data are available from 968 incident cases of breast cancer diagnosed after blood collection in 1989 and 1990, but before June 1, 1998 and 1,205 matched controls. Compared with women homozygous for the Val allele, women homozygous for the Ala allele were not at an increased risk of breast cancer (multivariate odds ratio, 0.96; 95% confidence interval, 0.74-1.24). We did not observe any significant interactions between MnSOD genotype with alcohol consumption, postmenopausal hormone use, plasma antioxidant levels, or dietary sources of antioxidants. We did observe evidence that the MnSOD Ala allele may modify the relation of cigarette smoking with breast cancer risk. A nonsignificant increased risk of breast cancer among current smokers was limited to women homozygous for the Ala alleles compared with Val/Val never smokers (multivariate odds ratio, 1.41; 95% confidence interval 0.77-2.60; P for interaction = 0.03). These data suggest that the Ala allele of MnSOD may modify breast cancer risk among current smokers, but is not an independent risk factor for breast cancer.

Adult↗
PubMed2006

The neuropeptide genes TAC1, TAC3, TAC4, VIP and PACAP(ADCYAP1), and susceptibility to multiple sclerosis.

The related immunomodulatory neuropeptides vasoactive intestinal peptide (VIP) and pituitary adenylyl cyclase activating peptide (PACAP; gene symbol ADCYAP1) have recently been proposed as novel therapeutics for the treatment of multiple sclerosis (MS). These neuropeptides, as well as those belonging to the tachykinin family exert pleiotropic effects, many of which are of relevance to central nervous system inflammation. In the present study, we have analysed 14 single nucleotide polymorphisms (SNPs) and 4 microsatellite markers in the VIP, ADCYAP1, TAC3 and TAC4 genes for susceptibility to MS in a case-control collection from Northern Ireland. Following correction for multiple comparisons, we did not find any significant associations between single polymorphic markers or multiple-marker haplotypes and susceptibility to MS. Furthermore, we analysed 2 SNPs in the TAC1 gene in a set of Sardinian trio MS families, based on our previous observation of association of these SNPs with MS in the Northern Irish (Genes Immun. 2005, 6, 265-270). Analysis of these SNPs in the Sardinians was not significant though a similar trend to that originally observed in the Northern Irish was present. Meta-analysis of the Sardinian and Northern Irish TAC1 SNP genotype data revealed a Mantel-Haenszel Common OR Estimate for the TAC1 intron 1 SNP rs2072100 of 0.76 (95% CI 0.63-0.92; P=0.005; A allele) and for the TAC1 promoter SNP rs7793277 of 0.76 (95% CI 0.615-0.95; P=0.014; C allele). Our data advocate a need for further exploration of the TAC1 gene region in MS.

Disease Susceptibility↗