Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “association testing”

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 199 records · Page 11Linked to original sources

Respiratory allergenicity of detergent enzymes in the guinea pig intratracheal test: association with sensitization of occupationally exposed individuals.

A guinea pig intratracheal test was used to set occupational operating guidelines for new enzyme proteins used in the detergent industry. In these studies, animals were intratracheally dosed with different levels of enzyme protein and sera from the animals were titered for allergic antibody to the enzyme. The amount of antibody produced to an enzyme was compared to the amount of antibody produced to the same protein doses of Alcalase, for which effective operating guidelines exist. These comparisons were used to determine if a new enzyme was more potent, less potent, or equivalent to Alcalase; operating guidelines were then established for the new enzyme. Termamyl was about 10-fold more potent than Alcalase and the protease subtilisin B was shown to be less potent. Another protease, Savinase, was shown to be equivalent in potency to Alcalase. The operating guidelines for Termamyl were adjusted lower, whereas the operating guidelines for the proteases were set the same as that of Alcalase. Under these conditions, we would predict that sensitizations to new enzymes would be comparable to or lower than the sensitizations to Alcalase. Prospective evaluation of skin prick test data of factory workers showed that sensitizations to Termamyl and Savinase were similar to sensitizations to Alcalase. The sensitizations to subtilisin B were lower than those to Alcalase. During this time period (7 years), only three respiratory incidents (rhinitis) were reported, demonstrating that employees with positive skin prick tests can continue to work. These comparisons indicate that the guinea pig intratracheal test is a good animal model for evaluating enzymes as respiratory allergens and that the data generated can be used to set operating guidelines for occupational allergens.

Amylases↗

Assessment of apraxia: inter-rater reliability of a new apraxia test, association between apraxia and other cognitive deficits and prevalence of apraxia in a rehabilitation setting.

OBJECTIVE: To investigate the inter-rater reliability of a new apraxia test. Furthermore to examine the association of apraxia with other neuropsychological impairments and the prevalence of apraxia in a rehabilitation setting on the basis of the new test. DESIGN: Cross-sectional cohort study, involving 100 patients with a first stroke admitted to a rehabilitation centre in the Netherlands. MEASURES: General patient characteristics and stroke-related aspects. Cognitive screening involving apraxia, visuospatial scanning, abstract thinking and reasoning, memory, attention, planning and aphasia. RESULTS: The indices for inter-rater agreement range from excellent to poor. Significant correlations are found between apraxia and visuospatial scanning, memory, attention, planning and aphasia. The patients with apraxia perform significantly worse than the patients without apraxia on memory, the time needed to complete the tests for scanning and attention, and aphasia. The prevalence of apraxia is 25.3% in the total group, 51.3% in the left hemisphere stroke patients and 6.0% in the right hemisphere stroke patients. Patients with and without apraxia do not differ significantly concerning age, gender and type of stroke. CONCLUSION: The apraxia test has been shown to be a reliable instrument. Apraxia is often associated with aphasia, memory problems and mental slowness. This study shows that on the basis of the apraxia test, the prevalence of apraxia among patients in the rehabilitation centre is high, especially among patients with left hemisphere lesions.

Apraxias↗

Association testing in a linked region using large pedigrees.

This report describes computer implementation of a scheme for joint linkage and association analysis. The model implemented in the computer package Mendel estimates both recombination and linkage-disequilibrium parameters and conducts likelihood-ratio tests for (1) linkage alone, (2) linkage and association simultaneously, and (3) association in the presence of linkage. Application of the method to data from Finnish pedigrees with familial combined hyperlipidemia illustrates its potential for identification of associated SNP haplotypes in the presence of linkage. For the test results to be valid, good estimates of haplotype frequencies must be used in the analysis.

Female↗

Family-based tests of association in the presence of linkage.

Linkage analysis may not provide the necessary resolution for identification of the genes underlying phenotypic variation. This is especially true for gene-mapping studies that focus on complex diseases that do not exhibit Mendelian inheritance patterns. One positional genomic strategy involves application of association methodology to areas of identified linkage. Detection of association in the presence of linkage localizes the gene(s) of interest to more-refined regions in the genome than is possible through linkage analysis alone. This strategy introduces a statistical complexity when family-based association tests are used: the marker genotypes among siblings are correlated in linked regions. Ignoring this correlation will compromise the size of the statistical hypothesis test, thus clouding the interpretation of test results. We present a method for computing the expectation of a wide range of association test statistics under the null hypothesis that there is linkage but no association. To standardize the test statistic, an empirical variance-covariance estimator that is robust to the sibling marker-genotype correlation is used. This method is widely applicable: any type of phenotypic measure or family configuration can be used. For example, we analyze a deletion in the A2M gene at the 5' splice site of "exon II" of the bait region in Alzheimer disease (AD) discordant sibships. Since the A2M gene lies in a chromosomal region (chromosome 12p) that consistently has been linked to AD, association tests should be conducted under the null hypothesis that there is linkage but no association.

Algorithms↗

Minor alterations in thyroid-function tests associated with diabetes mellitus and obesity in outpatients without known thyroid illness.

Thyroid function tests might be affected by diabetes and obesity. To evaluate the influence of these parameters in routine conditions, 72 diabetic and 53 non-diabetic outpatients without known thyroid diseases or severe chronic illness were recruited over a 7-month period. For each patient, dosages of thyrotropin (TSH), total and free thyroxine (TT4 and FT4, respectively), total and free triiodothyronine (TT3 and FT3) and T3 resin uptake (T3RU) were performed by radioimmunoassays. The simultaneous influence of various parameters known to affect thyroid-function tests was evaluated by multivariate linear regression. The studied variables included gender, age, glucosteroids, estrogens, tobacco habits, iodine contacts, body mass index (BMI) and diabetes mellitus. Tobacco habits and iodine contacts did not influence any tests. As expected, estrogens induced an increase in TT4 and TT3 values (p < 0.001 and 0.020, respectively) associated with a decrease in T3RU (p < 0.001). Consequently, females had lower T3RU than males (p < 0.0001). Corticotherapy was associated with decreased TSH values (p = 0.022). TT3 and FT3 decreased with age (p < 0.001), whereas T3RU and FT4 increased (p = 0.020 and 0.004, respectively). In contrast to an increase in TSH (p = 0.006), TT4 and FT4 decreased at higher BMI levels (p = 0.018 and 0.004, respectively), which is consistent with subclinical hypothyroidism. In diabetic patients, TSH was lower than in nondiabetic subjects (p = 0.039). Thus, the present study indicates that besides known parameters such as age and drugs, thyroid-function tests can also be altered by diabetes mellitus and obesity.

Adolescent↗

Tuberculin test conversion during repeated skin testing, associated with sensitivity to nontuberculous mycobacteria.

To determine whether repeating the tuberculin test after a brief interval might result in tuberculin conversion, we tested 213 healthy volunteers twice, 1 month apart, with 5 TU of tuberculin purified protein derivative (PPD). Three nontuberculous mycobacterial antigens (PPD-G, PPD-Y, and PPD-B) were also applied with the first tuberculin test. By widely used criteria, 14 volunteers (6.6 per cent) converted their tuberculin tests from negative to positive on the second testing. Whereas 13 of 103 subjects (12.6 per cent) with nontuberculous antigen sensitivity converted their tuberculin test to positive, only one of 110 subjects (0.9 per cent) with no known prior mycobacterial sensitivity converted to positive (P less than 0.005; x2 = 10.05). When retested with 5 TU of tuberculin PPD 6.5 months after the second test, nine of 13 converters reverted to negative. We conclude that tuberculin conversion may occur when the skin test is repeated at 1 month, and that boosting of cross-reacting mycobacterial sensitivity might have caused a portion of the conversions in this population of young, healthy midwestern volunteers. Sensitivity to Mycobacterium tuberculosis might also be boosted by tuberculin testing. Because the prevalence of sensitization by tuberculous and nontuberculous mycobacteria can be expected to vary in different populations, the significance of tuberculin conversion will also vary with the population being tested.

Adolescent↗

Staining intensities in the fluorescent treponemal antibody-absorption (FTA-Abs) test: association with the diagnosis of syphilis.

In 1984 the reporting system for the fluorescent treponemal antibody-absorption (FTA-Abs) test was changed by the Centers for Disease Control (CDC; Atlanta, GA) to eliminate the borderline report. Factors influencing the reliability of the FTA-Abs test results, i.e., sensitivity, specificity, prevalence of syphilis, prescreening of sera with nontreponemal tests, and reproducibility, were considered before the change in the reporting system was recommended and are reported here. The borderline report, when associated with syphilis, was most frequently also associated with the diagnosis of early primary, dark-field-positive, nontreponemal test-nonreactive syphilis. Whereas elimination of the borderline report decreased the sensitivity of the FTA-Abs test as a confirmatory test from 100% to 99.5%, the specificity increased from 82.5% to 88.7%. The 1+ staining intensity had an association of approximately 5% with the diagnosis of syphilis. The changes in the reporting system were designed to assist the clinician in interpreting the results of the FTA-Abs test in those cases that present diagnostic dilemmas.

Fluorescent Antibody Technique↗

Statistical validity for testing associations between genetic markers and quantitative traits in family data.

In genetic analysis it is often of interest to analyze associations between traits of unknown genetic etiology and genetic markers from pedigree data. Statistical methods that assume independence of pedigree members cannot be used because they disregard the statistical dependencies of members in a pedigree. For quantitative traits, a regression model proposed by George and Elston [Genet Epidemiol 4:193-201, 1987] uses an asymptotic likelihood ratio test and incorporates a correlation structure that allows for statistical dependence among the pedigree members. The statistical validity of this test is assessed for finite samples by measuring the discrepancy between the empirical and theoretical chi-square distributions. The variance of the mean of the dependent variable is determined to be related to this discrepancy and can be used to determine whether a pedigree structure is large enough for making valid statistical inferences on the basis of the asymptotic test. A multi-generational pedigree of 200 or so individuals should in many cases be sufficient for valid results when using the asymptotic likelihood ratio test for the association between markers and continuous traits.

Family↗

PedGenie: an analysis approach for genetic association testing in extended pedigrees and genealogies of arbitrary size.

BACKGROUND: We present a general approach to perform association analyses in pedigrees of arbitrary size and structure, which also allows for a mixture of pedigree members and independent individuals to be analyzed together, to test genetic markers and qualitative or quantitative traits. Our software, PedGenie, uses Monte Carlo significance testing to provide a valid test for related individuals that can be applied to any test statistic, including transmission disequilibrium statistics. Single locus at a time, composite genotype tests, and haplotype analyses may all be performed. We illustrate the validity and functionality of PedGenie using simulated and real data sets. For the real data set, we evaluated the role of two tagging-single nucleotide polymorphisms (tSNPs) in the DNA repair gene, NBS1, and their association with female breast cancer in 462 cases and 572 controls selected to be BRCA1/2 mutation negative from 139 high-risk Utah breast cancer families. RESULTS: The results from PedGenie were shown to be valid both for accurate p-value calculations and consideration of pedigree structure in the simulated data set. A nominally significant association with breast cancer was observed with the NBS1 tSNP rs709816 for carriage of the rare allele (OR = 1.61, 95% CI = 1.10-2.35, p = 0.019). CONCLUSION: PedGenie is a flexible and valid statistical tool that is intuitively simple to understand, makes efficient use of all the data available from pedigrees without requiring trimming, and is flexible to the types of tests to which it can be applied. Further, our analyses of real data indicate NBS1 may play a role in the genetic etiology of heritable breast cancer.

Biomarkers, Tumor↗

Combined linkage and association tests in mx.

Statistical methods aimed at the detection of genes for quantitative traits suffer from two problems: (i) when a linkage approach is employed, relatively large sample sizes are usually required; and (ii) when an association approach is employed, effects of population stratification may blur genuine locus-trait associations. The variance components method proposed by Fulker et al. (1999) addressed both these problems; it is statistically powerful because it involves a combined analysis of linkage and association and can include information from multiplex families, which reduces the overall amount of necessary individual genotypes. In addition, it includes an explicit test for the presence of spurious association. After a brief illustration of the various ways in which population stratification may affect locus-trait associations, the implementation in Mx (Neale, 1997) of the method as proposed by Fulker et al. (1999) is discussed and illustrated. In addition, an extension to this method is proposed that allows the use of (variable) sibship sizes greater than two, the estimation of additive and dominance association effects, and the use of multiple alleles. These extensions can be implemented when parental genotypes are available or unavailable.

Alleles↗

Positive allergy prick tests associated with bronchial histamine responsiveness in an unselected population.

Bronchial responsiveness to histamine and skin prick test reactions to airborne allergens were measured in a random population sample of 891 adults and 1293 schoolchildren. Total serum IgE concentrations were measured in a subset of 389 adults. The prevalence of bronchial histamine responsiveness (BHR) in the adults increased from 5.8% in those who did not respond to allergen prick tests to 22.2% in those who responded to all five allergen groups (p less than 0.00001). Similarly, the prevalence of BHR in the children increased progressively from 3.5% to 35.3% as the number of positive allergen responses increased from zero through five (p less than 0.0001). In adults for whom IgE data were also available, those with BHR had a significantly higher total serum IgE concentration (p less than 0.002).

Adult↗

Systematic common and rare variant association testing in 392,030 whole genomes in All of Us.

Large-scale genome-wide association studies (GWAS) and rare variant association studies (RVAS) from population biobanks provide valuable resources for gene discovery in complex human traits. We present an analysis of the All of Us Research Program v8 release, which includes whole genome sequencing data and harmonized phenotypic information of 392,030 participants after quality control, enabling a unified investigation of rare and common variants across a spectrum of human traits and diseases. We build an extensive phenome- and genome-wide ("All by All") computational framework to perform GWAS and RVAS on 3,602 phenotypes and identify 49,863 approximately independent, high-quality single-variant and gene-level associations. Meta-analyses of All of Us and UK Biobank, with sample sizes as large as 786,871 participants, further enhance statistical power and find 193 pLoF gene-phenotype associations that are not significant in either cohort alone, including 22 associations not highlighted by previous studies. We also present a public interactive browser that integrates association results for common and rare variants to facilitate interpretation and rapid querying of summary statistics, along with supporting documentation, and a Featured Workspace in the All of Us Researcher Workbench. Our framework will apply to iterative data releases as All of Us grows, empowering researchers worldwide to uncover insights into the functional effects of genetic components on complex traits and diseases.

Journal Article↗

Application of a rank-based genetic association test to age-at-onset data from the Collaborative Study on the Genetics of Alcoholism study.

Association studies of quantitative traits have often relied on methods in which a normal distribution of the trait is assumed. However, quantitative phenotypes from complex human diseases are often censored, highly skewed, or contaminated with outlying values. We recently developed a rank-based association method that takes into account censoring and makes no distributional assumptions about the trait. In this study, we applied our new method to age-at-onset data on ALDX1 and ALDX2. Both traits are highly skewed (skewness > 1.9) and often censored. We performed a whole genome association study of age at onset of the ALDX1 trait using Illumina single-nucleotide polymorphisms. Only slightly more than 5% of markers were significant. However, we identified two regions on chromosomes 14 and 15, which each have at least four significant markers clustering together. These two regions may harbor genes that regulate age at onset of ALDX1 and ALDX2. Future fine mapping of these two regions with densely spaced markers is warranted.

Adult↗

Parasympathetic-mediated atrial fibrillation during tilt test associated with increased baroreflex sensitivity.

The autonomic mechanism that triggered atrial fibrillation in a patient during tilt test was investigated. Neurocardiogenic syncope is often characterized by diminished baroreflex sensitivity during the hypotension period. Increased barorereflex sensitivity preceding the onset of atrial fibrillation in tilt testing may indicate the involvement of a vagally mediated mechanism, as shown in the present case.

Aged↗