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PubMed2004

Genetic predictive factors in restenosis.

Restenosis is still the main drawback of percutaneous transluminal coronary angioplasty (PTCA). It is thought to be a multifactorial process where recoil of the vessel, neointimal proliferation and thrombus formation are thought to play a role. Until now it has proven difficult to predict restenosis on clinical and procedural grounds, however, genetic epidemiology might provide more insights. In this review several genetic variables, i.e. polymorphisms that were determined in relation to restenosis are described. The single nucleotide polymorphisms (SNPs) described in the literature so far involve; the renin-angiotensin system, platelet aggregation, the inflammatory response, matrix metalloproteinases, smooth muscle cell proliferation, lipids and oxidative stress and nitric oxide. Nowadays DNA-microarrays have been developed which make it possible to test 50 or 60 polymorphisms at once. However, the risk of error due to multiple testing should be kept in mind. The results of the studies described should be interpreted with care. Many of the published studies are of relatively small sample size, which sometimes show more positive outcomes than the larger studies, this is possibly due to publication bias towards more positive results. The small sample size studies also exhibit wide confidence intervals. On the other hand, one must take into account that the process of restenosis is a multifactorial one and it is likely that multiple genes are involved. Thus, relatively small odds ratios relating to single gene contribution to restenosis can be of paramount importance when encompassed in the overall picture. Although still much research has to be done, stratification according to genetic make-up may enable tailoring of the interventional treatment to the individual patient.

Angioplasty, Balloon, Coronary↗

PubMed1994

[Study on the use of multiple choice type test of speech audiometry in Shanghai area].

Using the speech audiometry material worked out by Sheng Ye et al, we performed multiple choice tests on 20 medical students with normal hearing in an attempt to prove the practicability of this material in Shanghai dialect area. The results showed that the equilibrium of the standard Chinese pronunciation word-lists used in Shanghai is not as good as in Beijing. Equilibrium calibration is necessary for Shanghai subjects. Meanwhile, the educational level and psychological state of the subjects and environment of the test may affect the results of the test. Thus a detailed explanation of this method and a pretest with exercise word-list are very important. The results indicate that multiple choice type test of speech audiometry is applicable to the comparison of the hearing level of the same subject and is useful in hearing-aid fitting.

Adult↗

PubMed2004

Effect of multiple sampling on diagnostic sensitivity.

Overall diagnostic sensitivity is the probability that a diagnostic procedure will detect an agent if the tested animal is indeed infected. The overall or effective sensitivity is a function of both the probability that the assay will detect the agent if it is present in the sample tested and the probability that the agent will be present in the sample tested if the animal is infected with the agent. Thus, even with a highly sensitive assay, the probability of detecting an infected animal may be low or nil if the sampling procedure failed to capture the agent in samples tested by the assay. In this article, it is demonstrated how increased frequency of testing, such as testing multiple subsamples, can have a profound effect on increasing the overall sensitivity of a diagnostic procedure.

Animals↗

PubMed2005

Tumor necrosis factor promoter haplotype associated with schizophrenia reveals a linked locus on 1q44.

Using restriction fragment length polymorphism and pyrosequencing methods, we genotyped two TNFA gene promoter SNPs (-G308A, -G238A) and analyzed the haplotype structure in 24 Canadian families of primarily Celtic origin. Our results demonstrate that after correction for multiple testing based on simulations of 10 000 replicates of unlinked/unassociated data, there is evidence for association (P=0.026) of a specific haplotype (-308A, -238G) with schizophrenia and schizophrenia spectrum disorders with a family-based trimmed haplotype linkage disequilibrium test (Trimhap). Stratifying the 22 families with genome scan data by TNFA promoter haplotypes followed by reanalysis of linkage to schizophrenia throughout the genome, we identified few loci that exhibit a considerable increase in LOD/HLOD scores. A locus on chromosome 1q44 (D1S1609) demonstrated a significant increase (P=0.025) in LOD score from 0.15 to 3.01 with a broad definition of the schizophrenia phenotype and a dominant mode of inheritance. This result replicates a previously reported positive result of linkage of schizophrenia spectrum disorders to this area of the genome. We also illustrated that simulation studies are pivotal in evaluating the significance of results obtained with newer statistical methods, when multiple, but not independent, tests are performed, and when sample stratification is utilized to reduce the impact of heterogeneity or assess the interaction between loci.

Chromosomes, Human, Pair 1↗

PubMed1991

Analysis of the crossover design in the presence of residual effects.

When a residual effect is suspected in a two-period crossover trial, an analysis of the first-period data is often chosen instead of the potentially biased crossover analysis. This paper indicates how the usual crossover test has to be interpreted correctly and that its bias has two different consequences, namely a conservative or a liberal test decision if a positive (carryover) or a negative (withdrawal) residual effect exists. A multiple testing procedure is presented allowing for simultaneous crossover and first-period analysis controlling the experimental error rate. This procedure together with the correct interpretation of the crossover test enables many useful applications of crossover designs.

Bias↗

PubMed2003

Quantitative, multiplexed detection of bacterial pathogens: DNA and protein applications of the Luminex LabMAP system.

Escherichia coli, Salmonella, Listeria monocytogenes and Campylobacter jejuni are bacterial pathogens commonly implicated in foodborne illnesses. Generally used detection methods (i.e., culture, biochemical testing, ELISA and nucleic acid amplification) can be laborious, time-consuming and require multiple tests to detect all of the pathogens. Our objective was to develop rapid assays to simultaneously detect these four organisms through the presence of antigen or DNA using the Luminex LabMAP system. For nucleic acid detection, organism-specific capture probes corresponding to the 23S ribosomal RNA gene (rrl) were coupled covalently to LabMAP microspheres. Target molecules included synthetic complementary oligonucleotides and genomic DNA isolated from ATCC type strains or other well-characterized strains of each organism. Universal PCR primers were designed to amplify variable regions of bacterial 23S ribosomal DNA, yielding biotinylated amplicons of 86 to 109 bp in length. Varying quantities of targets were hybridized to the combined microsphere sets, labeled with streptavidin-R-phycoerythrin and analyzed on the Luminex(100) system. Results of nucleic acid detection assays, obtained in 30 to 40 min following amplification, correctly and specifically identified each bacterial species with a detection sensitivity of 10(3) to 10(5) genome copies. Capture-sandwich immunoassays were developed with organism-specific antibodies coupled to different microsphere sets. Microspheres were incubated with organism-specific standards and reactivity was assessed with biotinylated detection antibodies and streptavidin-R-phycoerythrin. In the immunoassays, microsphere-associated fluorescence was organism concentration dependent with detectable response at < or = 1000 organisms/ml and with no apparent cross-reactivity. We have demonstrated that the Luminex LabMAP system is a rapid, flexible platform capable of simultaneous, sensitive and specific detection of pathogens. The practical significance of this multiplexing approach would be to provide more timely, economical and comprehensive information than is available with conventional isolation and identification methodologies.

Antigens, Bacterial↗

PubMed2006

Inferential, robust non-negative matrix factorization analysis of microarray data.

MOTIVATION: Modern methods such as microarrays, proteomics and metabolomics often produce datasets where there are many more predictor variables than observations. Research in these areas is often exploratory; even so, there is interest in statistical methods that accurately point to effects that are likely to replicate. Correlations among predictors are used to improve the statistical analysis. We exploit two ideas: non-negative matrix factorization methods that create ordered sets of predictors; and statistical testing within ordered sets which is done sequentially, removing the need for correction for multiple testing within the set. RESULTS: Simulations and theory point to increased statistical power. Computational algorithms are described in detail. The analysis and biological interpretation of a real dataset are given. In addition to the increased power, the benefit of our method is that the organized gene lists are likely to lead better understanding of the biology. AVAILABILITY: An SAS JMP executable script is available from http://www.niss.org/irMF

Algorithms↗

PubMed1983

Neuropsychological testing of Huntington's patients. Clues to progression.

A battery of neuropsychological and academic tests was administered to 16 patients with Huntington's chorea, several of whom received multiple testings. Generalized mental impairment was evident for most of the present sample of patients, but performance IQ was more affected than verbal IQ. Comparisons of impairments on the different tasks relative to expectations for normal adults suggest that measures requiring psychomotor problem solving, sequencing, and memory were most impaired. Sensory, fine motor, and visual motor tasks, however, also revealed relatively severe deficits. Elementary language and academic skills showed least impairment. Follow-up data were congruent with these trends. Results are consistent with other findings in the suggestion they offer for commonalities in the progression of mental impairment associated with this disease. The scarcity of severe impairment in elementary language and academic functions also supports the view that focal deficits are uncharacteristic of Huntington's dementia.

Adult↗

PubMed2005

Evaluating the risk of cervical precancer with a combination of cytologic, virologic, and visual methods.

Several test modalities (cytologic, molecular, and visual) may be used for cervical cancer screening, triage, and follow-up. Although no currently available single test for cervical neoplasia can detect disease with both high sensitivity and specificity, combinations of available tests allow for improved risk prediction. We therefore evaluated the combination of liquid-based cytology (LBC), human papillomavirus (HPV) DNA testing, and visual inspection (cervicography), taken at a single point in time, to predict risk of subsequent cervical intraepithelial neoplasia 3 (CIN3) or cancer developing within 2 years in a triage population of 5,060 women referred for equivocal or mildly abnormal cytology. The concurrent administration of all three test modalities showed that combinations of these test modalities permitted clear and distinct risk stratification. Among HPV-positive women with high-grade LBC and high-grade cervicography results, 79.1 % [95% confidence interval (95% CI), 64.0- 90.0] were diagnosed with histologic CIN3 or cancer within 2 years, supporting a "see-and-treat" clinical application. Conversely, only 1.4% (95% CI, 0.7-2.5) of women with a negative HPV, normal cervigram, and second normal cytology result developed CIN3 or cancer. Because this low absolute risk was largely attributable to the negative HPV test, our results suggest a lack of benefit for a secondary or tertiary test result given an HPV-negative test result. Within HPV-positive women, however, we observed a steadily increasing absolute risk for cervical precancer/cancer with increasing numbers and severity of abnormal test results. We conclude that the clear discrimination of cervical cancer risk provided by multiple test modalities is consistent with our understanding of cervical etiology related to HPV natural history.

Adult↗

PubMed2005

Tango's maximized excess events test with different weights.

BACKGROUND: Tango's maximized excess events test (MEET) has been shown to have very good statistical power in detecting global disease clustering. A nice feature of this test is that it considers a range of spatial scale parameters, adjusting for the multiple testing. This means that it has good power to detect a wide range of clustering processes. The test depends on the functional form of a weight function, and it is unknown how sensitive the test is to the choice of this weight function and what function provides optimal power for different clustering processes. In this study, we evaluate the performance of the test for a wide range of weight functions. RESULTS: The power varies greatly with different choice of weight. Tango's original choice for the weight function works very well. There are also other weight functions that provide good power. CONCLUSION: We recommend the use of Tango's MEET to test global disease clustering, either with the original weight or one of the alternate weights that have good power.

Journal Article↗

PubMed1986

Ascorbate interference in the estimation of urinary glucose by test strips.

Currently used test strip methods for the detection of glucose in urine are influenced by ascorbate and may thus give false negative results, e.g. in screening for diabetes. Six different test strips for urine glucose were evaluated for interference by ascorbate in vitro. Interference by ascorbate varied markedly, being highest at low glucose concentrations. Interference coefficients for the individual tests were calculated to serve as an approximate index of interference by ascorbate. A new test (BM 33.071, Boehringer Mannheim GmbH, currently used in Combur-9-Test/Chemstrip-9 and other multiple test strips of Boehringer Mannheim) was clearly much less influenced as no urine containing 5.5 mmol/l glucose was read as negative even at very high ascorbate concentration. Readability of test strips differed due to patchy colour reactions. Precision was good within-test strip and within-urine but markedly less between urines.

Ascorbic Acid↗

PubMed1995

The guinea pig maximization test--with a multiple dose design.

The guinea pig maximization test (GPMT) is usually performed with one moderately irritant induction dose of the allergen and gives a qualitative assessment-hazard identification-of the allergenicity of the chemical. We refined the GPMT by applying a multiple dose design and used 30 guinea pigs in a test divided into a control group and 5 test groups of 5 animals. Each group was treated with different induction concentrations of the allergens: formaldehyde, cinnamic aldehyde, propyl paraben, lidocaine, mercaptobenzothiazole or chlormethylisothiazolinone/methylisothiazolinone. The test results were analysed using a logistic multidose response model. The precision of the results depends only on the total number of animals, the dose design and the response pattern. The maximal sensitization rate for a chemical was determined, and the intracutaneous induction concentration that sensitized 50% of the animals (EC50) (or another percentage) was estimated. Further studies are needed to prove the validity of this idea. However, improvements in protocols for the GPMT are needed to reduce interlaboratory variability in results and to reduce the number of animals used for allergenicity tests.

Acrolein↗

PubMedDate not supplied

Comparison of multiple-antigen simultaneous test and CAP systems for diagnosis of nasal allergy.

The multiple-antigen simultaneous test (MAST) is a simple system that uses no radioactive agents and allows simultaneous examination of multiple antigens. CAP is a quick new, in vitro system that is more sensitive than the radio-allergosorbent test (RAST). To evaluate their clinical efficacies, we examined the correlation between the MAST and CAP systems. Serum samples were collected from 33 patients with nasal allergies, 13 males and 20 females, mean age 31.1 years. The MAST and CAP were used for 7 inhaled allergens: house dust, Dermatophagoides farinae, Japanese cedar, timothy, sweet vernal grass, ragweed and mugwort. The correlation coefficients found for MAST and CAP were significant for all the allergens tested. In addition, high values for sensitivity, specificity and efficiency were obtained for all the allergens. The MAST system provided the same information as the CAP system. Although CAP tended to have better sensitivity, some of its positive results may clinically be false-positive. We believe that the MAST and CAP are both useful for the detection of allergens but that the diagnosis of allergy must be based on results of detailed examinations such as use of the skin test, the nasal provocation test and clinical symptoms.

Adolescent↗

PubMed2026

A Guide for Exploring Pleiotropic Associations in Genome-Wide Association Studies Using Summary Statistics.

Genome-wide association studies (GWAS) have shown that pleiotropy, whereby a single genetic variant or gene influences multiple traits, is common in complex human diseases. Detecting cross-phenotype associations from GWAS summary statistics remains challenging because of small effect sizes, extensive multiple testing, heterogeneous effects, and possible differences in effect direction across traits. Methods that jointly analyze multiple traits can improve the ability to detect pleiotropic signals while retaining the practical advantages of summary statistic-based analyses. Although a range of statistical approaches has been developed for this purpose, practical guidance on their application, assumptions, and interpretation remains limited. This tutorial reviews several widely used methods for pleiotropy detection from GWAS summary statistics, including ASSET, PLACO, GPA, CPBayes, and GCPBayes, and demonstrates their application using breast and thyroid cancer datasets. We also highlight the importance of accounting for effect heterogeneity, correlation, and biological group structure at the gene and pathway levels in the detection and interpretation of pleiotropic association signals.

Genome-Wide Association Study↗

PubMed1984

Repeated confidence intervals for group sequential clinical trials.

We describe methods for the construction of valid confidence intervals for parameters of interest at repeated times during the course of a clinical trial with two treatments. This approach gives the investigator a way to monitor the trial and allows greater flexibility than methods that have rigid statistical stopping rules. Two situations are considered. In the first, responses are available immediately and normally distributed, the parameter of interest being the difference in means. In the second, observations are survival times and a proportional hazards model is assumed. Here the parameter of interest is the hazard ratio. Group sequential tests can be based on repeated confidence interval methods and these are compared to other multiple testing procedures that have been proposed.

Clinical Trials as Topic↗

PubMed2003

Development of a sensitive assay for detection of replication-competent recombinant lentivirus in large-scale HIV-based vector preparations.

Lentiviral vectors have demonstrated great potential as gene therapy vectors mediating efficient ex vivo and in vivo gene delivery and long-term transgene expression in both dividing and nondividing cells. However, for clinical studies it must be demonstrated that lentiviral vector preparations are safe and not contaminated by replication-competent recombinants related to the parental pathogenic virus. Here we describe a sensitive assay for the detection of replication-competent lentiviruses (RCL) in large-scale preparations of HIV-based lentiviral vectors. This RCL assay for lentiviral vectors is based on the principles used for retroviral vectors, using a highly permissive cell line, C8166-45, for RCL amplification and an appropriate positive control virus to establish the assay sensitivity. The assay is capable of detecting 1 RCL infectious unit in a background of 2.5 x 10(8) transducing units of vector in a single test culture. Statistically representative samples from large-scale lentiviral vector productions were assayed using multiple test cultures for each lot. Overall, a total of 1.4 x 10(10) transducing units of vector from 10 independent 14-liter production lots were screened and no RCL was detected. We propose to implement this assay as a release testing for clinical-grade lentiviral vector preparations intended for gene therapy clinical trials.

Animals↗

PubMed1995

University of Southern California Repeatable Episodic Memory Test.

The University of Southern California Repeatable Episodic Memory Test (USC-REMT) was developed to provide a brief assay of memory in clinical drug trials where the same subject is tested multiple times over days or weeks. Therefore, it had to be minimally affected by repeated testing. The test also provides a measure of subjective organization, a cognitive strategy that might be sensitive to frontal lobe dysfunction and HIV-related memory deficits. The USC-REMT has seven different lists, each composed of 15 semantically unrelated, high-frequency nouns. The words are presented in a different order on three study-test trials. After each study trial the subject recalls the words in any order. The test takes about 10 min to administer and score. The recall protocol can be scored for (a) global mnemonic efficiency, (b) primary and secondary memory, (c) subjective organization, (d) recall consistency and (e) recall as a function of serial position. We report initial data showing that the test is sensitive to memory decrements. Thirty-six HIV-1 seropositive men, at various stages of illness, recalled significantly fewer words and exhibited less subjective organization than 14 matched controls. The test had no significant practice effects over the first three administrations when separated by several days. The seven alternate lists are essentially equivalent. The USC-REMT appears to complement currently published verbal memory tasks.

Adult↗

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↗