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1.
J Dermatol ; 40(5): 363-9, 2013 May.
Article in English | MEDLINE | ID: mdl-23414058

ABSTRACT

We investigated the optimum application for evaluating skin irritation response by using samples of irritants commonly used as additives in cosmetics and other common household products. We studied 47 volunteers (16 men and 31 women). We selected three types of surfactant, one moisturizer, one anti-infective agent and one oil solution. Using Finn chambers on Scanpor tape, we performed the patch test. A total of 0.015 mL of each sample was applied to the Finn chamber. For liquids, circular filter paper was soaked in 0.015 mL of the sample. Samples were placed on the upper back of participants, and closed for 4, 24 or 48 h. A patch application time of 24 h is sufficient to detect primary skin irritation from irritants in cosmetics and other common household products. In addition, we found that skin irritation reactions were strongest at 24 h after patch removal and that the reaction tended to be weaker at 48 h after patch removal. Patch testing to evaluate irritants should be performed by means of a 24-h patch test with a follow-up reading at 24 h after patch removal. An application time of 24 h places less of a burden on patients than a 48-h patch test.


Subject(s)
Patch Tests/methods , Skin Irritancy Tests/methods , Adult , Female , Healthy Volunteers , Humans , Male , Middle Aged , Reference Standards , Time Factors , Young Adult
2.
Altern Lab Anim ; 40(1): 33-50, 2012 Mar.
Article in English | MEDLINE | ID: mdl-22558976

ABSTRACT

A validation study on an in vitro skin irritation assay was performed with the reconstructed human epidermis (RhE) LabCyte EPI-MODEL24, developed by Japan Tissue Engineering Co. Ltd (Gamagori, Japan). The protocol that was followed in the current study was an optimised version of the EpiSkin protocol (LabCyte assay). According to the United Nations Globally Harmonised System (UN GHS) of classification for assessing the skin irritation potential of a chemical, 12 irritants and 13 non-irritants were validated by a minimum of six laboratories from the Japanese Society for Alternatives to Animal Experiments (JSAAE) skin irritation assay validation study management team (VMT). The 25 chemicals were listed in the European Centre for the Validation of Alternative Methods (ECVAM) performance standards. The reconstructed tissues were exposed to the chemicals for 15 minutes and incubated for 42 hours in fresh culture medium. Subsequently, the level of interleukin-1 alpha (IL-1 α) present in the conditioned medium was measured, and tissue viability was assessed by using the MTT assay. The results of the MTT assay obtained with the LabCyte EPI-MODEL24 (LabCyte MTT assay) demonstrated high within-laboratory and between-laboratory reproducibility, as well as high accuracy for use as a stand-alone assay to distinguish skin irritants from non-irritants. In addition, the IL-1α release measurements in the LabCyte assay were clearly unnecessary for the success of this model in the classification of chemicals for skin irritation potential.


Subject(s)
Animal Testing Alternatives , Skin Irritancy Tests , Tissue Culture Techniques , Epidermis , Humans , Quality Control , Reproducibility of Results
3.
J Biopharm Stat ; 22(2): 260-75, 2012.
Article in English | MEDLINE | ID: mdl-22251173

ABSTRACT

When identifying the differentially expressed genes (DEGs) in microarray data, we often observe heteroscedasticity between groups and dependence among genes. Incorporating these factors is necessary for sample size calculation in microarray experiments. A penalized t-statistic is widely used to improve the identifiability of DEGs. We develop a formula to calculate sample size with dependence adjustment for the penalized t-statistic. Sample size is determined on the basis of overall power under certain conditions to maintain a certain false discovery rate. The usefulness of the proposed method is demonstrated by numerical studies using both simulated data and real data.


Subject(s)
Gene Expression Profiling/statistics & numerical data , Oligonucleotide Array Sequence Analysis/statistics & numerical data , Sample Size , Algorithms , Computer Simulation , Data Interpretation, Statistical , False Positive Reactions , Models, Genetic , Models, Statistical , Normal Distribution
4.
J Appl Toxicol ; 31(1): 63-74, 2011 Jan.
Article in English | MEDLINE | ID: mdl-20677212

ABSTRACT

The murine local lymph node assay (LLNA) is a well-established alternative to the guinea pig maximization test (GPMT) or Buehler test (BT) for the assessment of the skin sensitizing ability of a drug, cosmetic material, pesticide or industrial chemical. Instead of radioisotope using in this method, Takeyoshi M. et al. (2001) has developed a modified LLNA based on the 5-bromo-2'-deoxyuridine (BrdU) incorporation (LLNA:BrdU-ELISA). The LLNA:BrdU-ELISA is practically identical to the LLNA methodology excluding the use of BrdU, for which a single intraperitoneal injection of BrdU is made on day 4, and colorimetric detection of cell turnover. We conducted the validation study to evaluate the reliability and relevance of LLNA:BrdU-ELISA. The experiment involved 7 laboratories, wherein 10 chemicals were examined under blinded conditions. In this study, 3 chemicals were examined in all laboratories and the remaining 7 were examined in 3 laboratories. The data were expressed as the BrdU incorporation using an ELISA method for each group, and the stimulation index (SI) for each chemical-treated group was determined as the increase in the BrdU incorporation relative to the concurrent vehicle control group. An SI of 2 was set as the cut-off value for exhibiting skin sensitization activity. The results obtained in the experiments conducted for all 10 chemicals were sufficiently consistent with small variations in their SI values. The sensitivity, specificity, and accuracy of LLNA:BrdU-ELISA against those of GPMT/BT were 7/7 (100%), 3/3 (100%), and 10/10 (100%), respectively.


Subject(s)
Bromodeoxyuridine/metabolism , Local Lymph Node Assay , Organic Chemicals/analysis , Animals , Dermatitis, Allergic Contact/diagnosis , Dermatitis, Allergic Contact/etiology , Enzyme-Linked Immunosorbent Assay , Female , Laboratories , Mice , Mice, Inbred CBA , Organic Chemicals/toxicity , Quality Control , Random Allocation , Reproducibility of Results , Sensitivity and Specificity
5.
Altern Lab Anim ; 38(1): 11-27, 2010 Mar.
Article in English | MEDLINE | ID: mdl-20377301

ABSTRACT

The Non-genotoxic Carcinogen Study Group in the Environmental Mutagen Society of Japan organised the second step of the inter-laboratory collaborative study on one-stage and two-stage cell transformation assays employing BALB/c 3T3 cells, with the objective of confirming whether the respective laboratories could independently produce results relevant to initiation or promotion. The method was modified to use a medium consisting of DMEM/F12 supplemented with 2% fetal bovine serum and a mixture of insulin, transferrin, ethanolamine and sodium selenite, at the stationary phase of cell growth. Seventeen laboratories collaborated in this study, and each chemical was tested by three to five laboratories. Comparison between the one-stage and two-stage assays revealed that the latter method would be beneficial in the screening of chemicals. In the test for initiating activity with the two-stage assay (post-treated with 0.1microg/ml 12-O-tetradecanoylphorbol-13-acetate), the relevant test laboratories all obtained positive results for benzo[a]pyrene and methylmethane sulphonate, and negative results for phenanthrene. Of those laboratories assigned phenacetin for the initiation phase, two returned positive results and two returned negative results, where the latter laboratories tested up to one dose lower than the maximum dose used by the former laboratories. In the exploration of promoting activity with the twostage assay (pretreated with 0.2microg/ml 3-methylcholanthrene), the relevant test laboratories obtained positive results for mezerein, sodium orthovanadate and TGF-beta1, and negative results for anthralin, phenacetin and phorbol. Two results returned for phorbol 12,13-didecanoate were positive, but one result was negative - again, the maximum dose to achieve the latter result was lower than that which produced the former results. These results suggest that this modified assay method is relevant, reproducible and transferable, provided that dosing issues, such as the determination of the maximum dose, are adequately considered. The application of this two-stage assay for screening the initiating and promoting potential of chemicals is recommended for consideration by other research groups and regulatory authorities.


Subject(s)
Carcinogenicity Tests/methods , Cell Transformation, Neoplastic , Animals , BALB 3T3 Cells , Cooperative Behavior , Japan , Mice
6.
Stat Appl Genet Mol Biol ; 8: Article 46, 2009.
Article in English | MEDLINE | ID: mdl-19954418

ABSTRACT

A genome-wide association study (GWAS) is a standard strategy for detecting disease susceptibility genes, despite unsettled controversies on many aspects, including optimal study design and statistical analysis. As for study design, a two-stage design has been applied to maximize cost-effectiveness. However, there has been little consensus on appropriate statistical analysis for two-stage design. Thereby perplexing the researchers as to which statistical measures should be applied at the first stage, and how to determine the significance level of the differences at the second stage. Here, using simulation studies, we compared statistical operating characteristics of the screening in a two-stage GWAS by taking into consideration the proper balance of false-positive and false-negative error. As a result, the lower bound of confidence interval for odds ratios is recommended as the first stage measure, and then the second stage criteria should primarily depend on the purpose of the genome screen or its role in the overall gene-hunting scheme. Based on the simulation study, we suggest rules of thumb about which statistics to use in a given situation. An application of all operating characteristics of the screening method to an actual GWAS for gastric cancer illustrates the practical relevance of our discussion.


Subject(s)
Genetic Predisposition to Disease , Genome-Wide Association Study , Models, Statistical , Computer Simulation , Genome, Human , Humans , Stomach Neoplasms/genetics
7.
Methods Inf Med ; 48(2): 104-12, 2009.
Article in English | MEDLINE | ID: mdl-19283306

ABSTRACT

OBJECTIVES: In a literature-based meta-analysis for time-to-event data, the hazard ratio in each trial is often estimated from the summary statistics described in the article. Several methods have been proposed: the direct method (Peto method); the indirect method using a p-value by the log-rank test and the number of total events; and the survival curve method using the Kaplan-Meier estimate. However, there has been no published report on a detailed investigation of these methods. We evaluated the performance of these methods by simulation. METHODS: In a set of simulation experiments, performance of five methods was evaluated by the bias of estimated log hazard ratio and coverage probability of the confidence interval. The methods evaluated were: 1) Cox regression analysis, 2) direct method, 3) indirect method, 4) survival curve method, and 5) modified survival curve method with an alternative weighting scheme. RESULTS: The direct method was confirmed to have a high degree of accuracy. Although the indirect method was also highly accurate, it tended to underestimate effect size when there was a strong effect. The survival curve method tended to underestimate effect size when event numbers were small and effect size was large. The modified survival curve method could alleviate this tendency toward underestimation of effect size found with the original survival curve method. CONCLUSIONS: When the Kaplan-Meier curve is used to estimate hazard ratios in trials with small sample size in the literature-based meta-analysis, we should check critically whether those trials' hazard ratios and overall hazard ratio are underestimated or not.


Subject(s)
Evidence-Based Practice , Meta-Analysis as Topic , Neoplasms/mortality , Computer Simulation , Confidence Intervals , Humans , Kaplan-Meier Estimate , Linear Models , Models, Statistical , Proportional Hazards Models , Survival Analysis , Time Factors
8.
J Biopharm Stat ; 19(4): 721-31, 2009 Jul.
Article in English | MEDLINE | ID: mdl-20183436

ABSTRACT

Phase II clinical trials are conducted to test whether a drug has a minimum desired effect and to assess whether further development of the drug is warranted. They are often designed as one-arm trials with response rate as the primary endpoint, and a two-stage design is often used to ensure early termination of the trial for futility. To control the type I error rate and guarantee the specified power of the study, planned sample sizes for both stages must be rigidly followed, but a literature review suggests that actual sample size often differs from that planned. We propose to extend simple two-stage designs to allow more flexible sampling plans in both stages. Our designs are preferable to similar extensions proposed to control type I and II error probabilities. Additionally, our assumptions regarding distribution of the actual sample size at the end of stage 1 are more lenient. A list of optimal designs for typical error rates and the selected null and alternative response rates is presented.


Subject(s)
Clinical Trials, Phase II as Topic/statistics & numerical data , Models, Statistical , Sample Size , Computer Simulation , Data Interpretation, Statistical , Humans , Treatment Outcome
9.
J Pharmacol Toxicol Methods ; 58(1): 11-26, 2008.
Article in English | MEDLINE | ID: mdl-18593646

ABSTRACT

INTRODUCTION: The murine local lymph node assay (LLNA) is a well-established alternative to the guinea pig maximization test (GPMT) or Buehler test (BT) for the assessment of the skin sensitizing ability of drugs and chemicals. Daicel Chemical Industries Ltd. has developed a modified LLNA based on the adenosine triphosphate (ATP) content (LLNA-DA). We conducted 2 interlaboratory validation studies to evaluate the reliability and relevance of LLNA-DA. METHODS: The experiment involved 17 laboratories, wherein 14 chemicals were examined under blinded conditions. In the first study, 3 chemicals were examined in 10 laboratories and the remaining 9 were examined in 3 laboratories. In the second study, 1 chemical was examined in 7 laboratories and the remaining 4 chemicals were examined in 4 laboratories. The data were expressed as the ATP content for each chemical-treated group, and the stimulation index (SI) for each chemical-treated group was determined as the increase in the ATP content relative to the concurrent vehicle control group. An SI of 3 was set as the cut-off value for exhibiting skin sensitization activity. RESULTS: The results of the first study obtained in the experiments conducted for the 3 chemicals that were examined in all the 10 laboratories and for 5 of the remaining 9 chemicals were sufficiently consistent with small variations in their SI values. The sensitivity, specificity, and accuracy of LLNA-DA against those of GPMT/BT were 7/8 (87.5%), 3/3 (100%), and 10/11 (90.9%), respectively. In the second study, all the 5 chemicals studied demonstrated acceptably small interlaboratory variations. DISCUSSION: In the first study, a large variation was observed for 2 chemicals; in the second study, this variation was small. It was attributed to the application of dimethylsulfoxide as the solvent for the metallic salts. In conclusion, these 2 studies provide good evidence for the reliability of the LLNA-DA.


Subject(s)
Dermatitis, Allergic Contact/etiology , Irritants/toxicity , Local Lymph Node Assay , Adenosine Triphosphate/metabolism , Animals , Dermatitis, Allergic Contact/diagnosis , Female , Mice , Mice, Inbred CBA , Reproducibility of Results , Solvents/chemistry , Toxicity Tests/methods
11.
Cancer Inform ; 3: 140-8, 2008 Jan 22.
Article in English | MEDLINE | ID: mdl-19455258

ABSTRACT

The recent development of DNA microarray technology allows us to measure simultaneously the expression levels of thousands of genes and to identify truly correlated genes with anticancer drug response (differentially expressed genes) from many candidate genes. Significance Analysis of Microarray (SAM) is often used to estimate the false discovery rate (FDR), which is an index for optimizing the identifiability of differentially expressed genes, while the accuracy of the estimated FDR by SAM is not necessarily confirmed. We propose a new method for estimating the FDR assuming a mixed normal distribution on the test statistic and examine the performance of the proposed method and SAM using simulated data. The simulation results indicate that the accuracy of the estimated FDR by the proposed method and SAM, varied depending on the experimental conditions. We applied both methods to actual data comprised of expression levels of 12,625 genes of 10 responders and 14 non-responders to docetaxel for breast cancer. The proposed method identified 280 differentially expressed genes correlated with docetaxel response using a cut-off value for achieving FDR <0.01 to prevent false-positive genes, although 92 genes were previously thought to be correlated with docetaxel response ones.

12.
Altern Lab Anim ; 36(6): 653-65, 2008 Dec.
Article in English | MEDLINE | ID: mdl-19154092

ABSTRACT

The two-stage Balb/c 3T3 model of cell transformation can mimic the two-stage carcinogenicity bioassay, and has been recognised as a screening method for detecting potential tumour initiators and promoters. A technical modification to the original protocol (which involved the use of M10F medium, consisting of MEM plus 10% fetal bovine serum [FBS]) has been previously proposed, in order to increase its efficacy, namely: the introduction of enriched, serum-reduced medium (DF2F medium, comprising DMEM/F12 plus 2% FBS and other supplements). The aim of this study was to further modify the protocol, so as to attain higher practicability for the assay. The protocol was further optimised by: a) reducing the number of plates required, through the use of larger plates; b) reducing the cost of the assay by retaining the reduced serum concentration and by using 2microg/ml insulin, rather than the more-complex insulin-transferrin-ethanolamine-sodium selenite (ITES) supplement (i.e. DF2F2I medium); and c) extending the culture period from 24-25 days to 31-32 days, resulting in clearer foci (the number of medium changes did not increase, as less-frequent medium changes were performed during the extended culture period). Growth curve construction revealed that variations in the saturation densities of the parental Balb/c 3T3 cell line and its three transformed clones were highest when M10F medium was replaced with DF2F2I medium just before cells reached confluence. We applied this newly-optimised protocol to the assessment of: a) the tumour initiating activity of 3-methylcholanthrene (MCA), N-methyl-N'-nitro-N-nitrosoguanidine, mitomycin C, methylmethane sulphonate, CdCl(2) and phenacetin, combining a post-treatment of 100ng/ml 12-O-tetradecanoylphorbol-13-acetate at the promotion stage; and b) the tumour promoting activity of insulin, lithocholic acid, CdCl(2) and phenobarbital, with pre-treatment of 0.2microg/ml MCA at the initiation stage. In the present study, only phenobarbital was negative when tested by using the modified protocol.


Subject(s)
BALB 3T3 Cells/drug effects , Carcinogenicity Tests/methods , Carcinogens/toxicity , Cell Transformation, Neoplastic/chemically induced , Culture Media , Animal Testing Alternatives , Animals , Carcinogenicity Tests/economics , Carcinogens/classification , Cattle , Cell Proliferation/drug effects , Cocarcinogenesis , Dose-Response Relationship, Drug , Drug Combinations , Methylcholanthrene/classification , Methylcholanthrene/toxicity , Mice , Mice, Inbred BALB C , Serum , Time Factors
13.
Bioinform Biol Insights ; 2: 145-56, 2008 Feb 29.
Article in English | MEDLINE | ID: mdl-19812772

ABSTRACT

Choosing an appropriate statistic and precisely evaluating the false discovery rate (FDR) are both essential for devising an effective method for identifying differentially expressed genes in microarray data. The t-type score proposed by Pan et al. (2003) succeeded in suppressing false positives by controlling the underestimation of variance but left the overestimation uncontrolled. For controlling the overestimation, we devised a new test statistic (variance stabilized t-type score) by placing shrunken sample variances of the James-Stein type in the denominator of the t-type score. Since the relative superiority of the mean and median FDRs was unclear in the widely adopted Significance Analysis of Microarrays (SAM), we conducted simulation studies to examine the performance of the variance stabilized t-type score and the characteristics of the two FDRs. The variance stabilized t-type score was generally better than or at least as good as the t-type score, irrespective of the sample size and proportion of differentially expressed genes. In terms of accuracy, the median FDR was superior to the mean FDR when the proportion of differentially expressed genes was large. The variance stabilized t-type score with the median FDR was applied to actual colorectal cancer data and yielded a reasonable result.

14.
Drug Saf ; 30(8): 715-26, 2007.
Article in English | MEDLINE | ID: mdl-17696584

ABSTRACT

BACKGROUND AND OBJECTIVE: Several statistical methods exist for detecting signals of potential adverse drug reactions in spontaneous reporting databases. However, these signal-detection methods were developed using regulatory databases, which contain a far larger number of adverse event reports than the databases maintained by individual pharmaceutical manufacturers. Furthermore, the composition and quality of the spontaneous reporting databases differ between regulatory agencies and pharmaceutical companies. Thus, the signal-detection criteria proposed for regulatory use are considered to be inappropriate for pharmaceutical industry use without modification. The objective of this study was to revise the criteria for signal detection to make them suitable for use by pharmaceutical manufacturers. METHODS: A model comprising 40 drugs and 1000 adverse events was constructed based on a spontaneous reporting database provided by a pharmaceutical company and used in a simulation to investigate appropriate criteria for signal detection. In total, 1000 pseudo datasets were generated with this model, and three statistical methods (proportional reporting ratio [PRR], Bayesian Confidence Propagation Neural Network [BCPNN] and multi-item gamma Poisson shrinker [MGPS]) for signal detection were applied to each dataset. The sensitivity and specificity of each method were evaluated using these pseudo datasets. The optimum critical value for signal detection (i.e. the value that achieved the highest sensitivity with 95% specificity) was identified for each method. The optimum values were also examined with the adverse events classified into two categories according to frequency. The three original detection methods and their revised versions were applied to a real pharmaceutical company database to detect 173 known adverse reactions of four drugs. RESULTS: The 1000 pseudo datasets consisted of an average of 81 862 reports and 11,407 drug-event pairs, including 1192 adverse drug reactions. The sensitivities of PRR, BCPNN and MGPS methods were 49%, 45% and 26%, respectively, whereas their specificities were 95%, 99.6% and 99.99%, respectively; these sensitivities were unacceptably low for pharmaceutical manufacturers, whereas the specificities were acceptable. The highest sensitivity for each method, obtained by changing critical values and maintaining specificity at 95%, was 44%, 62% and 62%, respectively. When adverse events were classified into two categories, sensitivities as high as 75% for regular events and 39% for rare events were achieved with the revised BCPNN method. The critical values of the information component minus two standard deviations (IC - 2SD) index of the revised BCPNN method were greater than -0.7 for regular events and greater than -0.6 for rare events. The revised BCPNN method yielded 51% sensitivity and 89% specificity for the real dataset. CONCLUSION: A lower critical value may be needed when signal-detection methodology is applied to the spontaneous reporting databases of pharmaceutical manufacturers. For example, it is recommended that pharmaceutical manufacturers use the BCPNN method with IC - 2SD criteria of greater than -0.7 for regular events and greater than -0.6 for rare events.


Subject(s)
Adverse Drug Reaction Reporting Systems/statistics & numerical data , Models, Statistical , Algorithms , Computer Simulation , Drug Industry , Drug-Related Side Effects and Adverse Reactions , Humans
15.
Stat Med ; 26(3): 498-511, 2007 Feb 10.
Article in English | MEDLINE | ID: mdl-16596575

ABSTRACT

This paper proposes a statistical method for determining the therapeutic dose of a test drug in a confirmatory clinical trial based on a phase II clinical trial using 3 or 4 doses of the drug. This method assumes the primary variable has a normal distribution with a common variance, that a test-drug effect is seen when the population means show a response pattern indicating a monotonic increase with dose, and that there is a prior distribution for the population means. Under the proposed method, multiple contrast statistics are determined, such as contrast statistics for linear increase and plateau, and a response pattern is selected based on the maximum contrast statistic. The posterior probability that the selected response pattern is the true one is evaluated, and if this exceeds the cut-off value a therapeutic dose is selected based on the estimated response pattern. To select the appropriate cut-off value, a simulation study was conducted using a loss function for which the loss due to overestimation is greater than the loss due to underestimation. It was found that, as a rule, the appropriate cut-off value to reduce the expected loss for various response patterns is 0.75 for a 3-group trial and 0.70 for a 4-group trial. Using these cut-off values, the proposed method was applied to a previous clinical trial of a leukotriene receptor antagonist in patients with bronchial asthma. The method enabled the selection of what are considered appropriate response patterns and a therapeutic dose. Thus, the proposed method appears reasonable.


Subject(s)
Clinical Trials, Phase II as Topic/methods , Data Interpretation, Statistical , Dose-Response Relationship, Drug , Models, Statistical , Asthma/drug therapy , Humans , Leukotriene Antagonists/administration & dosage , Peak Expiratory Flow Rate/drug effects
16.
Pediatr Allergy Immunol ; 17(8): 583-90, 2006 Dec.
Article in English | MEDLINE | ID: mdl-17121586

ABSTRACT

Although many single nucleotide polymorphism (SNP) studies have reported an association of atopy, allergic diseases and total serum immunoglobulin E (IgE) levels, almost all of these studies sought risk factors for the onset of these allergic diseases. Furthermore, many studies have analyzed a single gene and hardly any have analyzed environmental factors. In these analyses, the results could be masked and the effects of other genes and environmental factors may be decreased. Here, we described the correlation between four genes [interleukin (IL)-4 (C-590T), IL-4 receptor (A1652G), FCER1B (G6842A) and STAT6 (G2964A)] in connection with IgE production; the role of IL-10 (C-627A) as a regulatory cytokine of allergy; and the severity of food allergy (FA) and atopic eczema (AE) in 220 Japanese allergic children. In addition to these SNPs, environmental factors, i.e., patient's attitude, indoor environment, and so on, were also investigated in this study. Our study was retrospective, and the correlation was analyzed by our defined clinical scores divided into three terms: worst symptoms, recent symptoms and general amelioration at the most recent examination during the disease course. Our results indicated that IL-10 AA, the genotype with lower IL-10 production, is associated with higher IgE levels in the serum (p < 0.0001, estimate; 0.912). Marginal liver abnormalities were observed in the subject group with both FA and AE (p < 0.1191, estimate; 0.1490). Our defined clinical scores enabled evaluation of various aspects of disease severity. Based on the scores, while no single SNP selected in this study determined severity, the combination of the SNP with laboratory data and environmental factors appeared to determine severity.


Subject(s)
Cytokines/genetics , Dermatitis, Atopic/genetics , Food Hypersensitivity/genetics , Polymorphism, Single Nucleotide , Severity of Illness Index , Adolescent , Air Pollution, Indoor , Attitude , Child , Child, Preschool , Dermatitis, Atopic/epidemiology , Dermatitis, Atopic/etiology , Food Hypersensitivity/epidemiology , Food Hypersensitivity/etiology , Humans , Immunoglobulin E/biosynthesis , Interleukin-10/physiology , Interleukin-4/genetics , Liver Diseases/etiology , Receptors, IgE/genetics , Receptors, Interleukin-4/genetics , Retrospective Studies , Risk Factors , STAT6 Transcription Factor/genetics
17.
J Hum Genet ; 51(9): 772-780, 2006.
Article in English | MEDLINE | ID: mdl-16917678

ABSTRACT

In single nucleotide polymorphism (SNP) data analysis, the allelic odds ratio and its confidence interval (CI) are usually used to evaluate the association between disease and alleles at each SNP. The usual formula for calculating the CI of the allelic odds ratio based on the Hardy-Weinberg equilibrium (HWE) may, however, lead to errors beyond the control assured by the nominal confidence level if HWE is not true. We therefore present a generalized formula for CI that does not assume HWE. CIs calculated by this generalized formula are likely to be wider than those by the usual method if the Hardy-Weinberg disequilibrium (HWD) is toward a relative deficiency of the heterozygotes (fixation index greater than 0), whereas they are likely to be narrower if HWD is toward a relative excess of the heterozygotes (fixation index less than 0). A simulation experiment to examine the influence of the generalization was performed for the case where 2% of SNPs had a fixation index greater than 0. The result revealed that the generalized method slightly decreased the mean number of falsely detected SNPs.


Subject(s)
Models, Genetic , Polymorphism, Single Nucleotide , Alleles , Confidence Intervals , Humans , Linkage Disequilibrium , Mathematics , Odds Ratio
18.
Contemp Clin Trials ; 27(5): 420-31, 2006 Oct.
Article in English | MEDLINE | ID: mdl-16807130

ABSTRACT

This paper proposes a method for balancing prognostic variables between treatment and control groups in design of clinical trials. It assumes that some of prognostic variables are continuous and others are categorical and that they are independently distributed. The proposed method uses the Kullback-Leibler divergence (KLD) as the index of difference in distribution between two groups. It sequentially allocates each subject to a group using a biased coin method so as to reduce the estimate of KLD. That is, when first i subjects have been allocated to two groups and the (i+1)th subject is enrolled, the KLD is estimated if the (i+1)th subject was to be allocated to either of the groups, and the subject is then allocated with a certain probability, e.g. 0.80, so as to make the KLD small. Simulation studies based on the hypothetical prognostic variables and on the actual data of hyperlipidemia patients were carried out in order to compare the proposed method with the Pocock-Simon method, which transforms the continuous prognostic variables into categorical variables by dividing the whole scale into several categories. The p values of homogeneity test of means and variances were used to evaluate the achieved balance. The observed p values in the proposed method were better than those in the Pocock-Simon method. In addition to the balance, the precision of parameter estimates assuming analysis of covariance model was examined. The results showed the precision of estimators tended to be more stable in the proposed method than the Pocock-Simon method.


Subject(s)
Clinical Trials as Topic , Controlled Clinical Trials as Topic/methods , Models, Statistical , Prognosis , Statistical Distributions , Computer Simulation , Confidence Intervals , Diabetes Mellitus/therapy , Humans , Mathematics , Patient Selection , Research Design
19.
Cancer Sci ; 97(6): 453-8, 2006 Jun.
Article in English | MEDLINE | ID: mdl-16734722

ABSTRACT

As exposure to heterocyclic amines might increase the risk of liver cancer, we investigated the carcinogenic potential of MeIQx under conditions of liver damage caused by TAA. Male, 6-week-old F344 rats (n = 280) were divided into 14 groups; groups 1-7 received TAA (0.03% in drinking water) and groups 8-14 received water for the first 12 weeks. Thereafter, the animals received MeIQx at doses from 0, 0.001, 0.01, 0.1, 1, 10 to 100 p.p.m. (groups 1-7 and 8-14, respectively) in pellet basal diet for 16 weeks. All survivors were killed at week 28 for assessment of numbers and areas of GST-P positive foci, considered to be pre-neoplastic lesions of the liver. Values were increased significantly in all the groups receiving TAA-->MeIQx compared to MeIQx alone (P < 0.01). Numbers of GST-P positive foci were significantly increased in groups 7 and 14 (treated with 100 p.p.m. MeIQx) as compared to 0 p.p.m.-MeIQx (groups 1 and 8) (P < 0.01), along with areas in group 14 compared to group 8 (P < 0.01). However, with the maximum likelihood method, the data for numbers of GST-P positive foci (groups 1-7 and groups 8-14) fitted the hockey stick regression model, representing no differences from groups 1-5 and from groups 8-13, despite a linear dose-dependent increase of MeIQx-DNA adducts from 0.1 to 100 p.p.m. We conclude that there is a no effect level for MeIQx hepatocarcinogenicity, even on a background of TAA-induced liver damage.


Subject(s)
Carcinogens/pharmacology , DNA Adducts/drug effects , Liver Neoplasms, Experimental/chemically induced , Quinoxalines/pharmacology , 5-Methylcytosine/metabolism , Animals , Chemical and Drug Induced Liver Injury , Chromatography, High Pressure Liquid , Dose-Response Relationship, Drug , Glutathione Transferase/metabolism , Immunohistochemistry , Liver Diseases/pathology , Male , Rats , Thioacetamide/toxicity
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