In vivo alkaline comet assay: Statistical considerations on historical negative and positive control data.

The alkaline comet assay is frequently used as in vivo follow-up test within different regulatory environments to characterize the DNA-damaging potential of different test items. The corresponding OECD Test guideline 489 highlights the importance of statistical analyses and historical control data (HCD) but does not provide detailed procedures. Therefore, the working group "Statistics" of the German-speaking Society for Environmental Mutation Research (GUM) collected HCD from five laboratories and >200 comet assay studies and performed several statistical analyses. Key results included that (I) observed large inter-laboratory effects argue against the use of absolute quality thresholds, (II) > 50% zero values on a slide are considered problematic, due to their influence on slide or animal summary statistics, (III) the type of summarizing measure for single-cell data (e.g., median, arithmetic and geometric mean) may lead to extreme differences in resulting animal tail intensities and study outcome in the HCD. These summarizing values increase the reliability of analysis results by better meeting statistical model assumptions, but at the cost of information loss. Furthermore, the relation between negative and positive control groups in the data set was always satisfactorily (or sufficiently) based on ratio, difference and quantile analyses.

Statistical analysis of in vivo alkaline comet assay data - Comparison of median and geometric mean as centrality measures.

The comet assay is one of the standard tests for evaluating the genotoxic potential of a test item able to detect DNA strand breaks in cells or isolated nuclei from various tissues. The in vivo alkaline comet assay is part of the standard test battery, given in option 2 of the ICH guidance S2 (R1) and a follow-up test in the EFSA framework on genotoxicity testing. The current OECD guideline for the testing of chemicals No. 489 directly affects the statistical analysis of comet data as it suggests using the median per slide and the mean of all medians per animal. However, alternative approaches can be used if scientifically justified. In this work, we demonstrated that the selection of different centrality measures to describe an average value per slide may lead to fundamentally different statistical test results and contradicting interpretations. Our focus was on geometric means and medians per slide for the primary endpoint "tail intensity". We compared both strategies using original and simulated data in different experimental settings incl. a varying number of animals, slides and cells per slide. In general, it turned out that the chosen centrality measure has an immense impact on the final statistical test result.

Evaluation of high-sensitivity C-reactive protein and uric acid in vericiguat-treated patients with heart failure with reduced ejection fraction.

AIMS: The effects of vericiguat vs. placebo on high-sensitivity C-reactive protein (hsCRP) and serum uric acid (SUA) were assessed in patients with heart failure with reduced ejection fraction (HFrEF) in the Phase 2 SOCRATES-REDUCED study (NCT01951625). METHODS AND RESULTS: Changes from baseline hsCRP and SUA values at 12 weeks with placebo and vericiguat (1.25 mg, 2.5 mg, 5.0 mg and 10.0 mg, respectively) were assessed. The probability of achieving an hsCRP value of ≤3.0 mg/L or SUA value of <7.0 mg/dL at week 12 was tested. Median baseline hsCRP and SUA levels were 3.68 mg/L [interquartile range (IQR) 1.41-8.41; n = 335] and 7.80 mg/dL (IQR 6.40-9.33; n = 348), respectively. Baseline-adjusted mean percentage changes in hsCRP were 0.2%, -19.5%, -24.3%, -25.7% and -31.9% in the placebo and vericiguat 1.25 mg, 2.5 mg, 5.0 mg and 10.0 mg groups, respectively; significance vs. placebo was observed in the vericiguat 10.0 mg group (P = 0.035). Baseline-adjusted mean percentage changes in SUA were 5.0%, -1.3%, -1.1%, -3.5% and -5.3% in the placebo, and vericiguat 1.25 mg, 2.5 mg, 5.0 mg and 10.0 mg groups, respectively; significance vs. placebo was observed in the 5.0 mg and 10.0 mg groups (P = 0.0202 and P = 0.004, respectively). Estimated probability for an end-of-treatment hsCRP value of ≤3.0 mg/L and SUA value of <7.0 mg/dL was higher with vericiguat compared with placebo. The effect was dose-dependent, with the greatest effect observed in the 10.0 mg group. CONCLUSIONS: Vericiguat treatment for 12 weeks was associated with reductions in hsCRP and SUA, and a higher likelihood of achieving an hsCRP value of ≤3.0 mg/L and SUA value of <7.0 mg/dL.

The rat bone marrow micronucleus test: Statistical considerations on historical negative control data.

Recent updates of the OECD Guidelines for the Testing of Chemicals (Section 4: Health Effects) on genotoxicity testing emphasize the use of appropriate statistical methods for data analysis and proficiency proof. Updates also concern the mammalian erythrocyte micronucleus test (OECD 474), as the currently most often performed regulatory in vivo test. As the updated guideline gives high importance to adequate statistical assessment of historical negative control data to estimate validity of experiments and judge results, the present study evaluated statistical methodologies for handling of historical negative control data sets, and comes forward with respective proposals and reference data. Therefore, the working group "Statistics" within the German-speaking "Gesellschaft für Umwelt-Mutationsforschung e.V." (GUM) compiled a data set of 891 negative control rats from valid OECD 474-studies of four laboratories. Based on these data, Analysis-of-Variance (ANOVA) identified "laboratory" and "strain", but not "gender" as relevant stratification parameters, and argued for approximately normally distributed micronucleus frequencies in polychromatic erythrocytes per animal. This assumption provided the basis for further specifying one-sided parametric tolerance intervals for determination of corresponding upper historical negative control limits. Finally, the stability of such limits was investigated as a function of the number of experiments performed, using a simulation-based statistical strategy.

A statistical approach for analyzing data from the in vivo Pig-a gene mutation assay.

The in vivo Pig-a gene mutation assay serves to evaluate the genotoxic potential of chemicals. In the rat blood-based assay, the lack of CD59 on the surface of erythrocytes is quantified via fluorophore-labeled antibodies in conjunction with flow cytometric analysis to determine the frequency of Pig-a mutant phenotype cells. The assay has achieved regulatory relevance as it is suggested as an in vivo follow-up test for Ames mutagens in the recent ICH M7 [25] step 4 document. However, very little work exists regarding suitable statistical approaches for analyzing Pig-a data. In the current report, we present a statistical strategy based on a two factor model involving 'treatment' and 'time' incl. their interaction and a baseline covariate for log proportions to compare treatment and vehicle data per time point as well as in time. In doing so, multiple contrast tests allow us to discover time-related changes within and between treatment groups in addition to multiple treatment comparisons to a control group per single time point. We compare our proposed strategy with the results of classical Dunnett and Wilcoxon-Mann-Whitney tests using two data sets describing the mode of action of Chlorambucil and Glycidyl methacrylate both analyzed in a 28-day treatment schedule.

ECG telemetry in conscious guinea pigs.

INTRODUCTION: During preclinical drug development, monitoring of the electrocardiogram (ECG) is an important part of cardiac safety assessment. To detect potential pro-arrhythmic liabilities of a drug candidate and for internal decision-making during early stage drug development an in vivo model in small animals with translatability to human cardiac function is required. METHODS: Over the last years, modifications/improvements regarding animal housing, ECG electrode placement, and data evaluation have been introduced into an established model for ECG recordings using telemetry in conscious, freely moving guinea pigs. Pharmacological validation using selected reference compounds affecting different mechanisms relevant for cardiac electrophysiology (quinidine, flecainide, atenolol, dl-sotalol, dofetilide, nifedipine, moxifloxacin) was conducted and findings were compared with results obtained in telemetered Beagle dogs. RESULTS AND CONCLUSION: Under standardized conditions, reliable ECG data with low variability allowing largely automated evaluation were obtained from the telemetered guinea pig model. The model is sensitive to compounds blocking cardiac sodium channels, hERG K(+) channels and calcium channels, and appears to be even more sensitive to ß-blockers as observed in dogs at rest. QT interval correction according to Bazett and Sarma appears to be appropriate methods in conscious guinea pigs. Overall, the telemetered guinea pig is a suitable model for the conduct of early stage preclinical ECG assessment.

Endpoints of drug discovery for menopausal vasomotor symptoms: interpretation of data from a proxy of disease.

OBJECTIVE: Estrogen supplementation is considered a reliable therapeutic approach to symptoms of vasomotor dysregulation (hot flashes) associated with the menopausal transition and sex hormone deprivation. Implication of changes in central neurotransmission in the pathogenesis of hot flashes has prompted the off-label use of serotonergic and γ-aminobutyric acid-ergic drugs as a therapeutic alternative, claiming similarity of outcomes to those of estrogen treatment. METHODS: Using telemetric recordings in a rat model of estrogen deficit-induced vasomotor dysregulation, we compared the long- and short-term effects of estrogen supplementation and treatment with neuropharmaceuticals (venlafaxine, desvenlafaxine, fluoxetine, agomelatine, gabapentin) on endpoints of thermoregulation. RESULTS: Among the tested drugs, only fluoxetine was capable to emulate the restorative action of estradiol on the diurnal oscillations in skin temperature and control of heat dissipation. Unlike estradiol, several of the tested compounds produced marked transient decreases in skin temperature within the first 2 hours of application while being unable to restore physiological diurnal patterns of thermoregulation. CONCLUSIONS: Our findings suggest that in this animal model of impaired thermoregulation, neuropharmaceuticals may simulate therapeutic effects by eliciting immediate but transient hypothermia, which is not associated with the recovery of physiological control of heat dissipation. Therefore, short-term monitoring of drug actions in this disease model may considerably bias readouts of drug discovery for menopausal vasomotor symptoms.

A dynamic model of circadian rhythms in rodent tail skin temperature for comparison of drug effects.

Menopause-associated thermoregulatory dysfunction can lead to symptoms such as hot flushes severely impairing quality of life of affected women. Treatment effects are often assessed by the ovariectomized rat model providing time series of tail skin temperature measurements in which circadian rhythms are a fundamental ingredient. In this work, a new statistical strategy is presented for analyzing such stochastic-dynamic data with the aim of detecting successful drugs in hot flush treatment. The circadian component is represented by a nonlinear dynamical system which is defined by the van der Pol equation and provides well-interpretable model parameters. Results regarding the statistical evaluation of these parameters are presented.

HDAC2 and TXNL1 distinguish aneuploid from diploid colorectal cancers.

DNA aneuploidy has been identified as a prognostic factor for epithelial malignancies. Further understanding of the translation of DNA aneuploidy into protein expression will help to define novel biomarkers to improve therapies and prognosis. DNA ploidy was assessed by image cytometry. Comparison of gel-electrophoresis-based protein expression patterns of three diploid and four aneuploid colorectal cancer cell lines detected 64 ploidy-associated proteins. Proteins were identified by mass spectrometry and subjected to Ingenuity Pathway Analysis resulting in two overlapping high-ranked networks maintaining Cellular Assembly and Organization, Cell Cycle, and Cellular Growth and Proliferation. CAPZA1, TXNL1, and HDAC2 were significantly validated by Western blotting in cell lines and the latter two showed expression differences also in clinical samples using a tissue microarray of normal mucosa (n=19), diploid (n=31), and aneuploid (n=47) carcinomas. The results suggest that distinct protein expression patterns, affecting TXNL1 and HDAC2, distinguish aneuploid with poor prognosis from diploid colorectal cancers.

Autoantibodies against epidermal transglutaminase are a sensitive diagnostic marker in patients with dermatitis herpetiformis on a normal or gluten-free diet.

BACKGROUND: Dermatitis herpetiformis (DH) is a cutaneous manifestation of gluten-sensitive enteropathy (celiac disease). Patients with DH demonstrate circulating IgA antibodies against epidermal transglutaminase (eTG) and tissue transglutaminase (tTG). It has been suggested that eTG is the autoantigen of DH. OBJECTIVE: The purpose of this study was to characterize the autoimmune response to eTG and tTG in patients with DH on a normal or gluten-free diet (GFD). METHODS: Sera from 52 patients with DH were studied for the presence of IgA antibodies to eTG and tTG by enzyme-linked immunosorbant assay. In 38 patients, serum was obtained before initiation of a GFD, whereas 14 patients had been on a GFD for at least 2 years. RESULTS: Autoantibodies against eTG were detected in 36 of 38 patients (95%) and those against tTG in 30 of 38 patients (79%) with DH on a normal diet. Of 14 patients on a long-term GFD, 7 patients were free of DH lesions and did not require dapsone treatment. None of these patients showed circulating antibodies against eTG or tTG. The remaining 7 patients on a GFD were not able to stop taking dapsone. All these patients demonstrated anti-eTG antibodies, whereas only 3 of them showed additional reactivity against tTG. LIMITATION: Autoantibody levels against eTG and tTG before and after introduction of a GFD were not examined in the same patients. CONCLUSION: Our data suggest that antibodies to eTG are the most sensitive serologic marker in treated and untreated patients with DH and confirm the central role of eTG in the pathogenesis of this disease.

What do we mean by 'replication' and 'validation' in genome-wide association studies?

It has been acknowledged that results from genome-wide association studies need to be reproduced in further independent samples. This includes both aspects of replication and validation. Although often used interchangeably, both of these terms have a specific unique meaning and are not synonyms. Based on a number of applications from the literature producing a certain amount of confusion, our aim therefore is to clarify the definition of 'replication' and 'validation' and propose standards of their usage.

[The influence of bone quality and the fixation procedure on the primary stability of cementless implanted tibial plateaus]. / Der Einfluss der Knochenmineraldichte und des Verankerungsverfahrens auf die Primärstabilitat von zementfrei implantierten Tibiakomponenten.

BACKGROUND: An overview of prospective studies on cementless and cemented primary knee joint endoprosthetics carried out between 1988 and 2004 reveals that the aseptic tibial loosening rate of cemented prostheses implanted with fixed meniscal bearings amounts to 2-6% within a period of 4-14 years, while cementless implanted prostheses show loosening rates of up to 28% within a period of 4-10 years. If these results arise from a lack of proper initial osseointegration as a result of insufficient primary stability, and how this is influenced by the tibial bone quality and the tibial fixation procedure has not yet been investigated. MATERIALS AND METHODS: Tibial plateaus were press-fit implanted, both screwed and unscrewed, into each of six pairs of tibial heads from corpses. Stability testing was conducted applying eccentric axial load, shear and torsion. RESULTS: The average amounts of relative movement at the medial and lateral plateau are clearly different in the screwed version and the unscrewed version when loaded axially, but the difference was significant (p = 0.016) only at the medial plateau. Relative movements under shear and torsion showed no significant differences. The bone density of the tibial metaphyses had no significant effect on the primary stability of the cementless implanted tibial plateau. CONCLUSION: When using cementless knee endoprostheses, the fixation of the tibial plateau with screws--in addition to a flawless press-fit and form-fit customization of the tibial head--appears indispensable for guaranteeing proper osseointegration under physiological axial loads.

The intraindividual agreement of the bone density of the human proximal tibia.

The interindividual variability in the biomechanical properties of cadaver bones has remained an unsolved problem in biomechanical investigation procedures. For this reason, it is postulated to use matched bone pairs from the same individual for comparative biomechanical tests. The rationale behind this procedure is based on the assumption that biomechanically similar behaviour is to be expected in an intraindividual rather than an interindividual comparison. Systematic studies confirming this thesis were performed on the human femur. However, investigations regarding the intraindividual properties of the proximal tibial metaphysis with respect to the underlying bone densities, have not yet been performed. In order to verify the hypothesis that matched proximal tibial metaphyses from the same donor imply corresponding bone density values, densitometric measurements (pQCT) were performed in 14 matched cadaver tibias (average age 61 years, 9 men, 5 women) which were fresh-frozen at -40 degrees C after removal. After statistical analysis of the bone density values, five tibial pairs were identified as differing on the basis of missing correlations and the existence of systematic differences within the pairwise data. In other words, only about 2/3 of the data in the random sample available was classified as comparable. As the bone density measured by pQCT technique significantly correlates with the biomechanical properties of the bone, it can be concluded from the test result available that matched human tibiae show no concurring bone density values in 1/3 of cases. Thus the pairing of corpse tibiae does not necessarily imply suitability for comparative biomechanical experiments.

Genetic association studies for gene expressions: permutation-based mutual information in a comparison with standard ANOVA and as a novel approach for feature selection.

Mutual information (MI) is a robust nonparametric statistical approach for identifying associations between genotypes and gene expression levels. Using the data of Problem 1 provided for the Genetic Analysis Workshop 15, we first compared a quantitative MI (Tsalenko et al. 2006 J Bioinform Comput Biol 4:259-4) with the standard analysis of variance (ANOVA) and the nonparametric Kruskal-Wallis (KW) test. We then proposed a novel feature selection approach using MI in a classification scenario to address the small n - large p problem and compared it with a feature selection that relies on an asymptotic chi2 distribution. In both applications, we used a permutation-based approach for evaluating the significance of MI. Substantial discrepancies in significance were observed between MI, ANOVA, and KW that can be explained by different empirical distributions of the data. In contrast to ANOVA and KW, MI detects shifts in location when the data are non-normally distributed, skewed, or contaminated with outliers. ANOVA but not MI is often significant if one genotype with a small frequency had a remarkable difference in the average gene expression level relative to the other two genotypes. MI depends on genotype frequencies and cannot detect these differences. In the classification scenario, we show that our novel approach for feature selection identifies a smaller list of markers with higher accuracy compared to the standard method. In conclusion, permutation-based MI approaches provide reliable and flexible statistical frameworks which seem to be well suited for data that are non-normal, skewed, or have an otherwise peculiar distribution. They merit further methodological investigation.