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T H Beaty

Publications and source records attributed to T H Beaty.

At least 37 records · Page 2Linked to original sources
PubMed2001

Profiling of differential gene expression in activated, allergen-specific human Th2 cells.

Th2 cells play a pivotal role in the pathogenesis of allergic diseases, including asthma, but the molecular basis of the Th1/Th2 dichotomy and the precise molecular pathways leading to Th2-dominant immune responses are still unclear. To this end, we have combined suppression subtractive hybridization (SSH) and high throughput analysis of cDNA arrays spotted with IMAGE clones to determine the profile of differential gene expression in human allergen-specific Th2 cells. Allergen-stimulated Th2 cells were used as the tester, and either resting Th2 cells or stimulated Th1 cells were used as the driver. SSH was used to equalize different mRNA levels and remove common sequences between the tester and the driver. Comparison of cDNA arrays probed with subtracted tester and non-subtracted driver provided a profile of Th2-selective gene expression. Analysis of 77 sequence-confirmed and differentially expressed genes in Th2 cells showed predominant EST sequences, representing 80% of sequences analyzed. The pattern of gene expression in 19 selected sequences was further analyzed in additional Th1 and Th2 clones. A total of 15 sequences showed predominant expression in Th2 cells, while the remaining four EST sequences showed no detectable amplification signal. The database containing Th2-selective genes will further our understanding of Th2 cell function and the genetic basis of allergic diseases.

Allergens↗
PubMed2001

A robust identity-by-descent procedure using affected sib pairs: multipoint mapping for complex diseases.

Multipoint linkage analysis is a powerful tool to localize susceptibility genes for complex diseases. However, the conventional lod score method relies critically on the correct specification of mode of inheritance for accurate estimation of gene position. On the other hand, allele-sharing methods, as currently practiced, are designed to test the null hypothesis of no linkage rather than estimate the location of the susceptibility gene(s). In this paper, we propose an identity-by-descent (IBD)-based procedure to estimate the location of an unobserved susceptibility gene within a chromosomal region framed by multiple markers. Here we deal with the practical situation where some of the markers might not be fully informative. Rather the IBD statistic at an arbitrary within the region is imputed using the multipoint marker information. The method is robust in that no assumption about the genetic mechanism is required other than that the region contains no more than one susceptibility gene. In particular, this approach builds upon a simple representation for the expected IBD at any arbitrary locus within the region using data from affected sib pairs. With this representation, one can carry out a parametric inference procedure to locate an unobserved susceptibility gene. In addition, here we derive a sample size formula for the number of affected sib pairs needed to detect linkage with multiple markers. Throughout, the proposed method is illustrated through simulated data. We have implemented this method including exploratory and formal model-fitting procedures to locate susceptibility genes, plus sample size and power calculations in a program, GENEFINDER, which will be made available shortly.

Chromosome Mapping↗
PubMed2000

Complex segregation analysis provides compelling evidence for a major gene underlying obsessive-compulsive disorder and for heterogeneity by sex.

Evidence from twin and family studies supports a genetic etiology for obsessive-compulsive disorder (OCD). The purpose of this study was to test whether a major gene is implicated in a proportion of families with OCD. Complex segregation analyses of 153 families (80 case and 73 control), ascertained in the Johns Hopkins OCD Family Study, provided strong evidence for a major gene. A Mendelian-dominant model, with significant sex effects and with residual familial effects, best explained the observed data. Stratification of the sample by the sex of probands provided further evidence of heterogeneity with respect to familial aggregation. Segregation analyses of 86 families with a female proband and of the 67 families with a male proband suggested that a Mendelian-dominant model with familial residual effects was the most parsimonious model explaining the inheritance of OCD in both subgroups.

Adolescent↗
PubMed2000

A unified sampling approach for multipoint analysis of qualitative and quantitative traits in sib pairs.

Recent advances in molecular biology have enhanced the opportunity to conduct multipoint mapping for complex diseases. Concurrently, one sees a growing interest in the use of quantitative traits in linkage studies. Here, we present a multipoint sib-pair approach to locate the map position (tau) of a trait locus that controls the observed phenotype (qualitative or quantitative), along with a measure of statistical uncertainty. This method builds on a parametric representation for the expected identical-by-descent statistic at an arbitrary locus, conditional on an event reflecting the sampling scheme, such as affected sib pairs, for qualitative traits, or extreme discordant (ED) sib pairs, for quantitative traits. Our results suggest that the variance about tau&d4;, the estimator of tau, can be reduced by as much as 60%-70% by reducing the length of intervals between markers by one half. For quantitative traits, we examine the precision gain (measured by the variance reduction in tau&d4;) by genotyping extremely concordant (EC) sib pairs and including them along with ED sib pairs in the statistical analysis. The precision gain depends heavily on the residual correlation of the quantitative trait for sib pairs but considerably less on the allele frequency and exact genetic mechanism. Since complex traits involve multiple loci and, hence, the residual correlation cannot be ignored, our finding strongly suggests that one should incorporate EC sib pairs along with ED sib pairs, in both design and analysis. Finally, we empirically establish a simple linear relationship between the magnitude of precision gain and the ratio of the number of ED pairs to the number of EC pairs. This relationship allows investigators to address issues of cost effectiveness that are due to the need for phenotyping and genotyping subjects.

Alleles↗
PubMed2000

Atopic dermatitis is associated with a functional mutation in the promoter of the C-C chemokine RANTES.

Up-regulation of C-C chemokine expression characterizes allergic inflammation and atopic diseases. A functional mutation in the proximal promoter of the RANTES gene has been identified, which results in a new consensus binding site for the GATA transcription factor family. A higher frequency of this allele was observed in individuals of African descent compared with Caucasian subjects (p < 0.00001). The mutant allele was associated with atopic dermatitis in children of the German Multicenter Allergy Study (MAS-90; p < 0.037), but not with asthma. Transient transfections of the human mast cell line HMC-1 and the T cell line Jurkat with reporter vectors driven by either the mutant or wild-type RANTES promoter showed an up to 8-fold higher constitutive transcriptional activity of the mutant promoter. This is the first report to our knowledge of a functional mutation in a chemokine gene promoter. Our findings suggest that the mutation contributes to the development of atopic dermatitis. Its potential role in other inflammatory and infectious disorders, particularly among individuals of African ancestry, remains to be determined.

Alleles↗
PubMed2000

A study of contemporary levels and temporal trends in inbreeding in the Tangier Island, Virginia, population using pedigree data and isonymy.

In this study we describe inbreeding in a large pedigree from Tangier Island, Virginia, in which we compare two commonly used methods to estimate inbreeding in humans: pedigree and isonymy (identical surnames of spouses). Genealogical data on 3,512 individuals dating back to 1722 were used. Using the pedigree method, we determined an average inbreeding coefficient (F) of 0.00873 for the community as a whole, and 0.018 for inbred individuals. Analysis of temporal trends showed that inbreeding began around 1800 and peaked at 0.0109 in 1824-1849 and 1875-1899. Thereafter, inbreeding steadily declined to 0.00565 in 1975-1997. Analysis of pedigree structure complexity over time showed that close consanguinity contributes to inbreeding in the earlier cohorts, and remote consanguinity accounts for much of the inbreeding in the later cohorts. The number of common ancestors increases over time, as does the number of paths connecting inbred individuals to these common ancestors. Inbreeding estimates based on the isonymy approach yielded a 2.2-fold higher value of F (0.01945) compared to the pedigree method. Total isonymy estimates over 25-year cohorts overestimated inbreeding values from pedigree data between 1. 5-8-fold. We speculate that the overestimation is probably due to the inability of our data to satisfy the method's assumption of monophyletic origin of each surname. In conclusion, inbreeding in the Tangier Island population is consistent with the isolated nature of its population, and temporal trends reflect patterns in emigration and a breakdown in isolation over time.

Adolescent↗
PubMed2000

Genetic epidemiology of breast cancer: segregation analysis of 389 Icelandic pedigrees.

A genetic epidemiologic investigation of breast cancer involving 389 breast cancer pedigrees including information on 14,721 individuals from the Icelandic population-based cancer registry is presented. Probands were women born in or after 1920 and reported to have breast cancer in the cancer registry. The average age of the 389 probands was 45.5 years (SD 8.92). Segregation analyses was performed evaluating residual maternal effects, a dichotomous cohort effect, and assuming the age at diagnosis followed a logistic distribution after log-transformation. Familial aggregation could be best explained by the inheritance of a high-risk allele leading to early onset breast cancer among the homozygotes, which represent approximately 2.6% of the population. A Mendelian codominant model was selected as the best fitting model, with an estimated age at diagnosis of 51.8 years among these high-risk homozygotes, 64.0 years for heterozygotes and 76.3 years for the low-risk genotype. The predicted cumulative risk for homozygote carriers of the high-risk allele is 32.2% by age 60, compared to 16.4% for heterozygotes and 5.0% for non-carriers of the same age. These predicted age profiles in the current study complement recent reports from Iceland of a majority of BRCA2 mutation carriers being diagnosed with breast cancer below the age of 50 years, and 60 years being the mean age at diagnosis for non-carriers. This model also predicted a high background risk of breast cancer for women in this population (estimated susceptibility gamma = 0.44 +/- 0.08). This implies that if carriers and non-carriers did not die of competing causes, the estimated risk of being diagnosed with breast cancer by age 80 years irrespective of carrier status is 11.4%.

Age of Onset↗
PubMed2000

A case-control study of tobacco and alcohol consumption in Leber hereditary optic neuropathy.

PURPOSE: To determine if tobacco or alcohol consumption is associated with vision loss among sibships harboring pathogenic mitochondrial mutations associated with Leber hereditary optic neuropathy. METHODS: Retrospective case-control study with questionnaires obtained from both affected and unaffected siblings from 80 sibships with Leber hereditary optic neuropathy. Sibships harbored molecularly confirmed mitochondrial DNA mutations at nucleotide positions 11778 (63), 14484 (10), and 3460 (7). Exposure in affected individuals was calculated based on reported consumption before vision loss. RESULTS: For male probands (67 sibships), the recurrence risk within a sibship was 10.3% (eight of 78) for males and 3.1% (three of 98) for females. For female probands (13 sibships), the recurrence risk within a sibship was 17.6% (three of 17) for males and 0% (zero of 22) for females. Greater risk of vision loss was associated with male sex (odds ratio [OR] = 6.63; 95% confidence interval [CI] = 2.96 to 14.84; P =.00001) and harboring a 3460 or 14484 in comparison with the 11778 mutation (OR = 2.071; 95% CI = 1.19 to 3.58; P =.0095). No significant association of maximal intensity of smoking or cumulative smoking, whether light or heavy, with vision loss was observed. Light (OR = 0. 31; 95% CI = 0.17 to 0.56; P =.0001) and heavy alcohol consumers (OR = 0.25; 95% CI = 0.11 to 0.58; P =.0011) were less likely to be affected than individuals who did not consume alcohol after adjusting for age, sex, and mutation. In a categorical analysis of sibships with the 3460 or 14484 mutation, no relationship of vision loss with tobacco or alcohol consumption was observed. CONCLUSION: Unlike previous studies, the present study calculated exposure based on self-reported consumption of tobacco or alcohol before vision loss. No significant deleterious association between tobacco or alcohol consumption and vision loss among individuals harboring Leber hereditary optic neuropathy mutations was observed. Tobacco and alcohol do not appear to promote vision loss in Leber hereditary optic neuropathy.

Adolescent↗
PubMed2000

The methylenetetrahydrofolate reductase gene is associated with increased cardiovascular risk in Japan, but not in other populations.

The methylenetetrahydrofolate reductase (MTHFR) gene has been associated with increased risk for cardiovascular disease in some, but not all studies. Our data sources included a MEDLINE search of the literature published before December 1998, a bibliography review, and expert consultation. Of 23 studies initially identified, 18 (9855 persons) met the inclusion criteria. Information on sample size, study design, Hardy-Weinberg equilibrium, method of genotype determination, plasma folate and homocysteine were abstracted by two reviewers using a standardized protocol. The overall odds ratio of the MTHFR gene on cardiovascular disease was estimated using the Mantel-Haenzel method. From 12 studies with angiographically-confirmed coronary artery disease (CAD), the overall odds ratio (OR) for CAD among those with heterozygous (V/A) was 1.3 (95% CI, 1.1-1.5), while it was 1.4 (1.2-1.6) for the homozygous mutant (V/V) compared to those with homozygous normal (A/A). However, the overall odds ratio for CAD among those with the V/V genotype versus A/A genotype was not statistically significant (OR: 1.1; 95% CI: 0.9-1.3) after excluding three Japanese studies. The corresponding OR for the three Japanese studies was 2.0 (1.6-2.7). For six studies with myocardial infarction (MI), the overall OR of MI was 1.0 (0.8-1.1) for those with the V/A genotype and 0.9 (0.7-1.1) for those with the V/V genotype, respectively; none of these ORs for MI was statistically significant. The MTHFR gene is associated with increased risk for CAD in Japan, but not in other populations.

Asian People↗
PubMed2000

Association study of proposed candidate genes/regions in a population of Spanish asthmatics.

A number of genes/regions have recently been reported to be linked to asthma or its related phenotypes (i.e. atopy and bronchial hyperresponsiveness), by genetic linkage and allele-sharing methods. We have performed a case-control study comparing the allelic distribution of nine microsatellite markers and two genetic variants in a group of patients attended at emergency room departments because of an acute attack of asthma with respect to an external healthy population of controls. A total of 146 asthmatic subjects and 50 population controls from Barcelona, Spain, were genotyped for nine microsatellite markers from some asthma/atopy candidate genes/regions: the beta-subunit of the high-affinity IgE receptor (Fc epsilonRI-beta) located on chromosome 11; the 5q31-32 candidate region; the T-cell receptor genes, TCR-alpha on chromosome 14 and TCR-beta on chromosome 7. Two genetic variants of the beta-subunit of the high-affinity IgE receptor (Fc epsilonRI-beta) gene were also analyzed. None of the asthmatic or control individuals carried the Ile181Leu variant. There were no significant differences between asthmatic and control subjects neither for the polymorphic markers nor for the other variant of the beta-subunit of the high-affinity IgE receptor (Fc epsilonRI-beta) gene. No association could be observed in this sample of Spanish asthmatics with the genes/regions studied.

Adult↗
PubMed2000

Association and linkage of atopic dermatitis with chromosome 13q12-14 and 5q31-33 markers.

Atopic dermatitis is a chronic inflammatory skin disease that affects 10-20% of the population. Linkage of atopy, asthma, allergic rhinitis, and total serum IgE levels to several different chromosomal regions have been described extensively, but little is known about the genetic control of atopic dermatitis. We tested for the association and linkage between atopic dermatitis and five chromosomal regions: 5q31-33, 6p21.3, 12q15-24.1, 13q12-31, and 14q11.2/14q32.1-32.3. Marker analysis was performed in two Caucasian populations: (i) 192 unrelated German children with atopic dermatitis and 59 non-atopic children from a German birth cohort study (MAS'90), parental DNA was tested in 77 of 192 children with atopic dermatitis; (ii) 40 Swedish families with at least one family member with atopic dermatitis selected from the International Study of Asthma and Allergy in Children. Evidence for linkage and allelic association for atopic dermatitis was observed for markers on chromosome 13q12-14 and 5q31-33.

Child↗
PubMed2000

An IL13 coding region variant is associated with a high total serum IgE level and atopic dermatitis in the German multicenter atopy study (MAS-90).

BACKGROUND: Allergic diseases are one of the major causes of morbidity in the developed countries today, and the prevalence of these diseases is increasing steadily. Study of total serum gE level is important in understanding the genetics of allergic iseases because IgE levels are considered to be a crucial pathogenic component. IL-13 plays an important role in the induction of IgE synthesis and in the pathogenesis of allergic diseases. OBJECTIVE: We sought to examine potential variation at the IL13 gene and estimate its effect on elevated IgE level and atopic dermatitis (AD). METHODS: We conducted mutational analyses of the IL13 gene by using single-stranded conformation polymorphism and DNA sequencing. Case control studies for high-IgE phenotype and AD were performed by using subjects from the German MAS-90 cohort. RESULTS: A novel IL13 coding region variant at 4257 bp (G to A, fourth exon) was identified. Case control studies of a German sample from the MAS-90 cohort showed significant associations between the presence of the A allele and two atopic phenotypes: high IgE (odds ratio, 2.38; 95% confidence interval, 1.35-4.21; P =.0026) and AD (odds ratio, 1.77; 95% confidence interval, 1.06-2.96; P =.03). CONCLUSION: This IL13 coding region variant may be involved in the pathogenesis of AD and high total serum IgE level in a study population of white subjects.

Chromosomes, Human, Pair 5↗
PubMed2000

Statistical designs for familial aggregation.

In the past two decades, it has become increasingly clear that genetic factors contribute to the aetiology of many common diseases including cancers, coronary disease, allergy and psychiatric disorders. While one goal of genetic epidemiological studies is to locate susceptibility genes for these complex diseases, it is important that strong evidence of familial aggregation be established at an early stage of research. In this paper, we discuss several study designs useful to address some issues such as (1) detecting familial aggregation, (2) testing for gene-environment interaction, (3) identifying homogeneous subgroups and (4) measuring magnitude and patterns of familial correlations. These designs include the conventional case-control design and the family case-control design. For each of these two study designs, we discuss analytical strategies as well as their strengths and weaknesses. Throughout, several examples from real studies are used for illustrative purposes.

Case-Control Studies↗
PubMed1999

Mild association between the A/G polymorphism in the promoter of the apolipoprotein A-I gene and apolipoprotein A-I levels: a meta-analysis.

A polymorphism caused by a G-to-A substitution in the promoter area (-75 bp) of the apolipoprotein AI (apo A-I) bene is common in the general population. Several studies have investigated its association with apo A-I levels, but the results were conflicting. Here, we undertook meta-analyses to increase the statistical power to further detect this association. Meta-analyses were first performed for each gender and then on the combined data. The overall sample in this meta-analysis included over 3,000 healthy individuals. Results from healthy individuals suggest that the rare allele A is associated with mildly increased apo A-I levels by about 5 mg/dl (95% CI 2.84 - 6.94). This association is weaker among healthy females than males. The present study cannot determine whether this small but significant association was due to a small genetic effect of the A/G polymorphism, or whether the A/G polymorphism is in linkage disequilibrium with a true mutant allele at a quantitative trait locus controlling apo A-I levels. Although smoking status may interact with genotypes, only three studies investigated this interaction and thus no conclusion could be drawn in this regard.

Adolescent↗
PubMed1999

No common major gene for apolipoprotein A-I and HDL3-C levels: evidence from bivariate segregation analysis.

Apolipoprotein A-I (apo A-I) is the most abundant protein in high-density lipoprotein (HDL) particles, and it plays an important role in HDL metabolism. Both apo A-I and HDL cholesterol (HDL-C) levels are inversely associated with risk of cardiovascular disease. Segregation analyses suggest apo A-I levels are under the control of one or more major loci. Since HDL particles are heterogeneous in their composition and size, genetic influence on its subfractions (i.e., HDL2 and HDL3) could vary. A previous report showed evidence of a major locus controlling HDL3-C levels in a subset of the current study population. Because quantitative trait loci involved in complex diseases are likely to have pleiotropic effects on several related traits, it is possible to have a common major gene involved in regulating apo A-I and HDL3-C levels. We performed a bivariate segregation analysis of apo A-I and HDL3-C levels in 1,006 individuals from 137 families ascertained through probands undergoing elective, diagnostic coronary angiography at the Johns Hopkins Hospital. The results showed significant genetic correlation between these two traits, but the hypothesis of a common major gene was rejected. Bivariate segregation analysis favored a model with two genes controlling apo A-I and a third gene independently controlling HDL3-C, and the genetic correlation between these two traits is due to residual additive polygenes. Overall, results from this study suggest that there are distinct genetic mechanisms for apo A-I and HDL3-C levels. Future studies, especially linkage analysis, should consider distinct genetic mechanisms and multiple major gene loci.

Adult↗
PubMed1999

Physician-derived asthma diagnoses made on the basis of questionnaire data are in good agreement with interview-based diagnoses and are not affected by objective tests.

BACKGROUND: Defining the phenotype is critical for investigating the genetic etiology of asthma. As part of the Collaborative Study on the Genetics of Asthma (CSGA), the primary objective of which is to identify asthma susceptibility loci, an algorithm was designed to determine diagnoses of definite asthma, probable asthma, less than probable asthma, or no asthma. A respiratory questionnaire was designed to assist in the process of characterizing the asthma phenotype. OBJECTIVE: This study was designed to determine the validity of the CSGA algorithm for the diagnosis of asthma, to determine agreement in assessing an asthma diagnosis between the information obtained by the CSGA questionnaire versus a patient interview by a panel of specialist physicians, and to determine the degree to which objective tests would alter the questionnaire-based certainty of asthma diagnosis. METHODS: An expert panel of asthma clinicians (n = 4) indicated to what degree they were certain that a subject (n = 48) had asthma as determined by using a 6-point Likert scale based on a 20-minute interview (phase I), a review of the CSGA questionnaire (phase II), a review of the questionnaire plus skin test and peripheral blood eosinophilia data (phase III), and a review of phase III information plus pulmonary data (spirometry and methacholine-reversibility testing; IV). Intraclass correlation coefficients (ICCs) were calculated between the physicians' interpretation of the likelihood of asthma based on the information they received during each of the phases and between the CSGA algorithm and each of the phases. RESULTS: Interjudge reliability with regard to the degree of certainty with which an asthma diagnosis could be made by interview was excellent (ICC, 98; 95% confidence intervals [95% CIs], 0.87-0.99). We also found that the agreement between the physicians' interview with the patients (phase I) and the CSGA algorithm was good and at least as good with the addition of the CSGA questionnaire data and objective data (ICC, 0. 65-0.75). Good agreement was also observed between the average certainty score from the interview and the CSGA questionnaire (ICC, 92; 95% CI, 0.76-0.93), and ICCs determining the agreement on asthma diagnosis between phase I and phases III and IV, in which objective data were introduced, did not change from the ICCs comparing phase I with phase II (ICC of 0.93 [95% CI, 0.79-0.96] and ICC of 0.91 [95% CI 0.73-0.95], respectively). CONCLUSION: We conclude that the CSGA algorithm is a valid tool for which the diagnosis of asthma can be made at an acceptable level of certainty and that the CSGA questionnaire, interpreted by an asthma specialist, is a useful tool for the diagnosis of asthma in clinical or epidemiologic studies.

Algorithms↗
PubMed1999

Dense mapping of chromosome 12q13.12-q23.3 and linkage to asthma and atopy.

BACKGROUND: Asthma is a complex disease characterized by a high prevalence of allergic diathesis and the almost ubiquitous presence of upper airway disease (eg, rhinitis). Previously, we observed linkage of asthma among Afro-Caribbean families to markers in chromosome 12q, which contains a number of genes encoding for products closely related to allergic airway inflammation and disease. OBJECTIVE: To identify susceptibility loci in chromosome 12q contributing to the genetics of upper and lower airway diseases and to expand the region to include genes encoding IFN-gamma (IFNG ) and one of the signal transducers and activators of transcription (STAT6 ), we conducted further linkage studies among 33 multiplex families. METHODS: We characterized 528 subjects from Barbados for asthma; 82% were characterized for allergic rhinitis. Two-point and multipoint linkage analysis of 22 microsatellite markers (spanning approximately 79 centimorgan) was performed. RESULTS: Affected sib-pair analysis revealed significant evidence for linkage to asthma over approximately 30 cM (P <.05 to.002), with the best evidence for linkage at a CA repeat polymorphism in the first intron of IFNG in 12q21.1 (P =.002). Evidence of linkage to allergic rhinitis was observed in the same region (D12S313, P = 0.006, and IFNGCA, P =.01, respectively). Multipoint linkage analysis also provided evidence for linkage to asthma, with the best nonparametric linkage analysis score at D12S326 (nonparametric linkage score = 3.8, P =.0008). Modest evidence for linkage to allergic rhinitis was observed next to D12S326 at D12S1052 (P =.036). CONCLUSIONS: Our findings suggest that (1) one or more loci in the chromosome 12q13. 12-q23.3 region are contributing to the expression of the clinical phenotype asthma and the strongest evidence for linkage is in a region near the gene encoding IFNG and (2) a susceptibility locus for both asthma and allergic rhinitis maps to this region.

Adult↗