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In the search for effective treatments for COVID-19, the initial emphasis has been on re-purposed treatments. To maximize the chances of finding successful treatments, novel treatments that have been developed for this disease in particular, are needed. In this article, we describe and evaluate the statistical design of the AGILE platform, an adaptive randomized seamless Phase I/II trial platform that seeks to quickly establish a safe range of doses and investigates treatments for potential efficacy. The bespoke Bayesian design (i) utilizes randomization during dose-finding, (ii) shares control arm information across the platform, and (iii) uses a time-to-event endpoint with a formal testing structure and error control for evaluation of potential efficacy. Both single-agent and combination treatments are considered. We find that the design can identify potential treatments that are safe and efficacious reliably with small to moderate sample sizes. [ABSTRACT FROM AUTHOR]

In cancer research, basket trials aim to assess the efficacy of a drug using baskets, wherein patients are organized into subgroups according to their tumor type. In this context, using information borrowing strategy may increase the probability of detecting drug efficacy in active baskets, by shrinking together the estimates of the parameters characterizing the drug efficacy in baskets with similar drug activity. Here, we propose to use fusion-penalized logistic regression models to borrow information in the setting of a phase 2 single-arm basket trial with binary outcome. We describe our proposed strategy and assess its performance via a simulation study. We assessed the impact of heterogeneity in drug efficacy, prevalence of each tumor types and implementation of interim analyses on the operating characteristics of our proposed design. We compared our approach with two existing designs, relying on the specification of prior information in a Bayesian framework to borrow information across similar baskets. Notably, our approach performed well when the effect of the drug varied greatly across the baskets. Our approach offers several advantages, including limited implementation efforts and fast computation, which is essential when planning a new trial as such planning requires intensive simulation studies. [ABSTRACT FROM AUTHOR]

This article presents an objective Bayesian approach to estimating the binomial parameter in group sequential experiments with a binary endpoint. The idea of deriving design-dependent priors was first introduced using Jeffreys criterion. Another class of priors was developed based on the reference prior theory. A theoretical framework was established showing that explicit reference to the experimental design in the prior is fully Bayesian justified. Using a design-dependent prior which generalizes the reference prior, I propose a comprehensive and unified approach to the point and the interval estimations in group sequential experiments, and I evidence the good frequentist properties of the posterior estimators through comparative studies with the existing methods. The effect of the prior correction on the posterior estimates is studied in three classical designs of clinical trials. Finally, I discuss the idea of using this approach as a default choice for estimation upon sequential experiment termination. [ABSTRACT FROM AUTHOR]

There are multiple possible cluster randomised trial designs that vary in when the clusters cross between control and intervention states, when observations are made within clusters, and how many observations are made at each time point. Identifying the most efficient study design is complex though, owing to the correlation between observations within clusters and over time. In this article, we present a review of statistical and computational methods for identifying optimal cluster randomised trial designs. We also adapt methods from the experimental design literature for experimental designs with correlated observations to the cluster trial context. We identify three broad classes of methods: using exact formulae for the treatment effect estimator variance for specific models to derive algorithms or weights for cluster sequences; generalised methods for estimating weights for experimental units; and, combinatorial optimisation algorithms to select an optimal subset of experimental units. We also discuss methods for rounding experimental weights, extensions to non-Gaussian models, and robust optimality. We present results from multiple cluster trial examples that compare the different methods, including determination of the optimal allocation of clusters across a set of cluster sequences and selecting the optimal number of single observations to make in each cluster-period for both Gaussian and non-Gaussian models, and including exchangeable and exponential decay covariance structures. [ABSTRACT FROM AUTHOR]

Three-arm 'gold-standard' non-inferiority trials are recommended for indications where only unstable reference treatments are available and the use of a placebo group can be justified ethically. For such trials, several study designs have been suggested that use the placebo group for testing 'assay sensitivity', that is, the ability of the trial to replicate efficacy. Should the reference fail in the given trial, then non-inferiority could also be shown with an ineffective experimental treatment and hence becomes useless. In this article, we extend the so-called Koch-Röhmel design where a proof of efficacy for the experimental treatment is required in order to qualify for the non-inferiority test. While the efficacy of the experimental treatment is an indication of assay sensitivity, it does not guarantee that the reference is sufficiently efficient to let the non-inferiority claim be meaningful. It has, therefore, been suggested to adaptively test the non-inferiority only if the reference demonstrates superiority to placebo and otherwise to test δ -superiority of the experimental treatment over placebo, where δ is chosen in such a way that it provides proof of non-inferiority with regard to the reference's historical effect. In this article, we extend the previous work by complementing its adaptive test with compatible simultaneous confidence intervals. Confidence intervals are commonly used and suggested by regulatory guidelines for non-inferiority trials. We show how to adopt different approaches to simultaneous confidence intervals from the literature to the setting of three-arm non-inferiority trials and compare these methods in a simulation study. Finally, we apply these methods to a real clinical trial example. [ABSTRACT FROM AUTHOR]

A model for cross-over designs with repeated measures within each period was developed. It was obtained using an extension of generalized estimating equations that includes a parametric component to model treatment effects and a non-parametric component to model time and carry-over effects; the estimation approach for the non-parametric component is based on splines. A simulation study was carried out to explore the model properties. Thus, when there is a carry-over effect or a functional temporal effect, the proposed model presents better results than the standard models. Among the theoretical properties, the solution is found to be analogous to weighted least squares. Therefore, model diagnostics can be made by adapting the results from a multiple regression. The proposed methodology was implemented in the data sets of the cross-over experiments that motivated the approach of this work: systolic blood pressure and insulin in rabbits. [ABSTRACT FROM AUTHOR]

When a clinical trial stops early for benefit, the maximum likelihood estimate (MLE) of the treatment effect may be subject to overestimation bias. Several authors have proposed adjusting for this bias using the conditional MLE, which is obtained by conditioning on early stopping. However, this approach has a fundamental problem in that the adjusted estimate may not be in the direction of benefit, even though the study has stopped early due to benefit. In this paper, we address this problem by embedding both the MLE and the conditional MLE within a broader class of penalised likelihood estimates, and choosing a member of the class that is a favourable compromise between the two. This penalised MLE, and its associated confidence interval, always lie in the direction of benefit when the study stops early for benefit. We study its properties using both simulations and analyses of the ENZAMET trial in metastatic prostate cancer. Conditional on stopping early for benefit, the method is found to have good unbiasedness and coverage properties, along with very favourable efficiency at earlier interim analyses. We recommend the penalised MLE as a supplementary analysis to a conventional primary analysis when a clinical trial stops early for benefit. [ABSTRACT FROM AUTHOR]

In the development of new cancer treatment, an essential step is to determine the maximum tolerated dose in a phase I clinical trial. In general, phase I trial designs can be classified as either model-based or algorithm-based approaches. Model-based phase I designs are typically more efficient by using all observed data, while there is a potential risk of model misspecification that may lead to unreliable dose assignment and incorrect maximum tolerated dose identification. In contrast, most of the algorithm-based designs are less efficient in using cumulative information, because they tend to focus on the observed data in the neighborhood of the current dose level for dose movement. To use the data more efficiently yet without any model assumption, we propose a novel approximate Bayesian computation approach to phase I trial design. Not only is the approximate Bayesian computation design free of any dose–toxicity curve assumption, but it can also aggregate all the available information accrued in the trial for dose assignment. Extensive simulation studies demonstrate its robustness and efficiency compared with other phase I trial designs. We apply the approximate Bayesian computation design to the MEK inhibitor selumetinib trial to demonstrate its satisfactory performance. The proposed design can be a useful addition to the family of phase I clinical trial designs due to its simplicity, efficiency and robustness. [ABSTRACT FROM AUTHOR]

More often than not, clinical trials and even nonclinical medical experiments have to be run with observational units sampled from populations to be assumed heterogeneous with respect to covariates associated with the outcome. Relevant covariates which are known prior to randomization are usually categorical in type, and the corresponding subpopulations are called strata. In contrast to randomization which in most cases is performed in a way ensuring approximately constant sample size ratios across the strata, sample size planning is rarely done taking stratification into account. This holds true although the statistical literature provides a reasonably rich repertoire of testing procedures for stratified comparisons between two treatments in a parallel group design. For all of them, at least approximate methods of power calculation are available from which algorithms or even closed-form formulae for required sample sizes can be derived. The objective of this tutorial is to give a systematic review of the most frequently applicable of these methods and to compare them in terms of their efficiency under standard settings. Based on the results, recommendations for the sample size planning of stratified two-arm trials are given. [ABSTRACT FROM AUTHOR]

This paper investigates statistical reproducibility of the t-test. We formulate reproducibility as a predictive inference problem and apply the nonparametric predictive inference method. Within our research framework, statistical reproducibility provides inference on the probability that the same test outcome would be reached, if the test were repeated under identical conditions. We present an nonparametric predictive inference algorithm to calculate the reproducibility of the t-test and then use simulations to explore the reproducibility both under the null and alternative hypotheses. We then apply nonparametric predictive inference reproducibility to a real-life scenario of a preclinical experiment, which involves multiple pairwise comparisons of test groups, where different groups are given a different concentration of a drug. The aim of the experiment is to decide the concentration of the drug which is most effective. In both simulations and the application scenario, we study the relationship between reproducibility and two test statistics, the Cohen's d and the p-value. We also compare the reproducibility of the t-test with the reproducibility of the Wilcoxon Mann-Whitney test. Finally, we examine reproducibility for the final decision of choosing a particular dose in the multiple pairwise comparisons scenario. This paper presents advances on the topic of test reproducibility with relevance for tests used in pharmaceutical research. [ABSTRACT FROM AUTHOR]

In a recent paper, Jarrett, Farewell and Herzberg discussed a strategy for developing the analysis of a previously published two-phase experiment that investigated the effect of training on pain rating by occupational and physical therapy students. Here, their example is used to illustrate how a multi-step factor-allocation paradigm can be employed (i) to design an experiment, (ii) to understand the confounding in the design and (iii) to formulate linear mixed models, called prior allocation models, for the design. These models are intended as starting models for the analysis of the data, when it becomes available. An understanding of the confounding intrinsic to a design is achieved through an anatomy of the design presented in an analysis-of-variance-style table that can be obtained using functions from the R package dae. The analysis of the pain-rating experiment is re-examined and it is recommended that conclusions be based on a model with heterogeneous residual variances, in addition to the previously proposed block-treatment interactions. The paradigm is also used in producing an alternative design, taking into account the results of the re-analysis. [ABSTRACT FROM AUTHOR]

The partial potential impact fraction describes the proportion of disease cases that can be prevented if the distribution of modifiable continuous exposures is shifted in a population, while other risk factors are not modified. It is a useful quantity for evaluating the burden of disease in epidemiologic and public health studies. When exposures are measured with error, the partial potential impact fraction estimates may be biased, which necessitates methods to correct for the exposure measurement error. Motivated by the health professionals follow-up study, we develop a Bayesian approach to adjust for exposure measurement error when estimating the partial potential impact fraction under the main study/internal validation study design. We adopt the reclassification approach that leverages the strength of the main study/internal validation study design and clarifies transportability assumptions for valid inference. We assess the finite-sample performance of both the point and credible interval estimators via extensive simulations and apply the proposed approach in the health professionals follow-up study to estimate the partial potential impact fraction for colorectal cancer incidence under interventions exploring shifting the distributions of red meat, alcohol, and/or folate intake. [ABSTRACT FROM AUTHOR]

Regression analysis of multivariate interval-censored failure time data has been discussed by many authors1-6. For most of the existing methods, however, one limitation is that they only apply to the situation where the censoring is non-informative or the failure time of interest is independent of the censoring mechanism. It is apparent that this may not be true sometimes and as pointed out by some authors, the analysis that does not take the dependent censoring into account could lead to biased or misleading results7,8. In this study, we consider regression analysis of multivariate interval-censored data arising from the additive hazards model and propose an estimating equation-based approach that allows for the informative censoring. The method can be easily implemented and the asymptotic properties of the proposed estimator of regression parameters are established. Also we perform a simulation study for the evaluation of the proposed method and it suggests that the method works well for practical situations. Finally, the proposed approach is applied to a set of real data. [ABSTRACT FROM AUTHOR]

We consider partially observed binary matched-pair data. We assume that the incomplete subjects are missing at random. Within this missing framework, we propose an EM-algorithm based approach to construct an interval estimator of the proportion difference incorporating all the subjects. In conjunction with our proposed method, we also present two improvements to the interval estimator through some correction factors. The performances of the three competing methods are then evaluated through extensive simulation. Recommendation for the method is given based on the ability to preserve type-I error for various sample sizes. Finally, the methods are illustrated in two real-world data sets. An R-function is developed to implement the three proposed methods. [ABSTRACT FROM AUTHOR]

Late-onset toxicities often occur in phase I trials investigating novel immunotherapy and molecular targeted therapies. For trials with cohort based designs (such as modified toxicity probability interval, Bayesian optimal interval, and i3+3), patients are often turned away since the current cohort are still being followed without definite dose-limiting toxicities, which results in prolonged trial duration and waste of patient resources. In this paper, we incorporate a probability-of-decision framework into the i3+3 design and allow real-time dosing inference when the next patient becomes available. Both follow-up time for the pending patients and time to dose-limiting toxicities for the observed patients are used in calculating the posterior probability of each possible dosing decision. An intensive simulation study is conducted to evaluate the operating characteristics of the newly proposed probability-of-decision-i3+3 design under various dosing scenarios and patient accrual settings. Results show that the probability-of-decision-i3+3 design achieves comparable safety and reliability performances but much shorter trial duration compared to the complete designs. [ABSTRACT FROM AUTHOR]

Multiple different screening tests for candidate leads in drug development may often yield conflicting or ambiguous results, sometimes making the selection of leads a nontrivial maximum-likelihood ranking problem. Here, we employ methods from the field of multiple criteria decision making (MCDM) to the problem of screening candidate antibody therapeutics. We employ the SMAA-TOPSIS method to rank a large cohort of antibodies using up to eight weighted screening criteria, in order to find lead candidate therapeutics for Alzheimer's disease, and determine their robustness to both uncertainty in screening measurements, as well as uncertainty in the user-defined weights of importance attributed to each screening criterion. To choose lead candidates and measure the confidence in their ranking, we propose two new quantities, the Retention Probability and the Topness, as robust measures for ranking. This method may enable more systematic screening of candidate therapeutics when it becomes difficult intuitively to process multi-variate screening data that distinguishes candidates, so that additional candidates may be exposed as potential leads, increasing the likelihood of success in downstream clinical trials. The method properly identifies true positives and true negatives from synthetic data, its predictions correlate well with known clinically approved antibodies vs. those still in trials, and it allows for ranking analyses using antibody developability profiles in the literature. We provide a webserver where users can apply the method to their own data: http://bjork.phas.ubc.ca. [ABSTRACT FROM AUTHOR]

Bayesian adaptive randomization is a heuristic approach that aims to randomize more patients to the putatively superior arms based on the trend of the accrued data in a trial. Many statistical aspects of this approach have been explored and compared with other approaches; yet only a limited number of works has focused on improving its performance and providing guidance on its application to real trials. An undesirable property of this approach is that the procedure would randomize patients to an inferior arm in some circumstances, which has raised concerns in its application. Here, we propose an adaptive clip method to rectify the problem by incorporating a data-driven function to be used in conjunction with Bayesian adaptive randomization procedure. This function aims to minimize the chance of assigning patients to inferior arms during the early time of the trial. Moreover, we propose a utility approach to facilitate the selection of a randomization procedure. A cost that reflects the penalty of assigning patients to the inferior arm(s) in the trial is incorporated into our utility function along with all patients benefited from the trial, both within and beyond the trial. We illustrate the selection strategy for a wide range of scenarios. [ABSTRACT FROM AUTHOR]

The inactivity time, or lost lifespan specifically for mortality data, concerns time from occurrence of an event of interest to the current time point and has recently emerged as a new summary measure for cumulative information inherent in time-to-event data. This summary measure provides several benefits over the traditional methods, including more straightforward interpretation yet less sensitivity to heavy censoring. However, there exists no systematic modeling approach to inferring the quantile inactivity time in the literature. In this paper, we propose a semi-parametric regression method for the quantiles of the inactivity time distribution under right censoring. The consistency and asymptotic normality of the regression parameters are established. To avoid estimation of the probability density function of the inactivity time distribution under censoring, we propose a computationally efficient method for estimating the variance-covariance matrix of the regression coefficient estimates. Simulation results are presented to validate the finite sample properties of the proposed estimators and test statistics. The proposed method is illustrated with a real dataset from a clinical trial on breast cancer. [ABSTRACT FROM AUTHOR]

Log-rank tests have been widely used to compare two survival curves in biomedical research. We describe a unified approach to power and sample size calculation for the unweighted and weighted log-rank tests in superiority, noninferiority and equivalence trials. It is suitable for both time-driven and event-driven trials. A numerical algorithm is suggested. It allows flexible specification of the patient accrual distribution, baseline hazards, and proportional or nonproportional hazards patterns, and enables efficient sample size calculation when there are a range of choices for the patient accrual pattern and trial duration. A confidence interval method is proposed for the trial duration of an event-driven trial. We point out potential issues with several popular sample size formulae. Under proportional hazards, the power of a survival trial is commonly believed to be determined by the number of observed events. The belief is roughly valid for noninferiority and equivalence trials with similar survival and censoring distributions between two groups, and for superiority trials with balanced group sizes. In unbalanced superiority trials, the power depends also on other factors such as data maturity. Surprisingly, the log-rank test usually yields slightly higher power than the Wald test from the Cox model under proportional hazards in simulations. We consider various nonproportional hazards patterns induced by delayed effects, cure fractions, and/or treatment switching. Explicit power formulae are derived for the combination test that takes the maximum of two or more weighted log-rank tests to handle uncertain nonproportional hazards patterns. Numerical examples are presented for illustration. [ABSTRACT FROM AUTHOR]

Adaptive seamless Phase 2-3 design has been considered as one possible way to expedite development time for a drug program by allowing the expansion from an ongoing Phase 2 trial into a Phase 3 trial. Multiple endpoints are often tested when a regulatory approval is pursued. Here we propose an adaptive seamless Phase 2-3 design with multiple endpoints which can expand an ongoing Phase 2 trial into a Phase 3 trial based on an intermediate endpoint for adaptive decision and test the endpoints with a powerful multiple test procedure. It is proved that the proposed design can preserve the familywise Type I error under a mild assumption that is expected to hold in practical considerations. We illustrate our proposed design with an example trial design for oncology. Simulations are conducted to confirm the control of the familywise Type I error and the adaptive seamless Phase 2-3 design is illustrated with an example. [ABSTRACT FROM AUTHOR]

Immunotherapy, gene therapy or adoptive cell therapies, such as the chimeric antigen receptor+ T-cell therapies, have demonstrated promising therapeutic effects in oncology patients. We consider statistical designs for dose-finding adoptive cell therapy trials, in which the monotonic dose-response relationship assumed in traditional oncology trials may not hold. Building upon a previous design called "TEPI", we propose a new dose finding method - Probability Intervals of Toxicity and Efficacy (PRINTE), which utilizes toxicity and efficacy jointly in making dosing decisions, does not require a pre-elicited decision table and at the same time can handle Ockham's razor properly in the statistical inference. We show that optimizing the joint posterior expected utility of toxicity and efficacy under a 0-1 loss is equivalent to maximizing the marginal model posterior probability in the two-dimensional probability space. An extensive simulation study under various scenarios are conducted and results show that PRINTE outperforms existing designs in the literature since it assigns more patients to optimal doses and less to toxic ones, and selects optimal doses with higher percentages. The simple and transparent features together with good operating characteristics make PRINTE an improved design for dose-finding trials in oncology trials. [ABSTRACT FROM AUTHOR]

Breakthroughs in cancer biology have defined new research programs emphasizing the development of therapies that target specific pathways in tumor cells. Innovations in clinical trial design have followed with master protocols defined by inclusive eligibility criteria and evaluations of multiple therapies and/or histologies. Consequently, characterization of subpopulation heterogeneity has become central to the formulation and selection of a study design. However, this transition to master protocols has led to challenges in identifying the optimal trial design and proper calibration of hyperparameters. We often evaluate a range of null and alternative scenarios; however, there has been little guidance on how to synthesize the potentially disparate recommendations for what may be optimal. This may lead to the selection of suboptimal designs and statistical methods that do not fully accommodate the subpopulation heterogeneity. This article proposes novel optimization criteria for calibrating and evaluating candidate statistical designs of master protocols in the presence of the potential for treatment effect heterogeneity among enrolled patient subpopulations. The framework is applied to demonstrate the statistical properties of conventional study designs when treatments offer heterogeneous benefit as well as identify optimal designs devised to monitor the potential for heterogeneity among patients with differing clinical indications using Bayesian modeling. [ABSTRACT FROM AUTHOR]

Increasingly, medical research is dependent on data collected for non-research purposes, such as electronic health records data. Health records data and other large databases can be prone to measurement error in key exposures, and unadjusted analyses of error-prone data can bias study results. Validating a subset of records is a cost-effective way of gaining information on the error structure, which in turn can be used to adjust analyses for this error and improve inference. We extend the mean score method for the two-phase analysis of discrete-time survival models, which uses the unvalidated covariates as auxiliary variables that act as surrogates for the unobserved true exposures. This method relies on a two-phase sampling design and an estimation approach that preserves the consistency of complete case regression parameter estimates in the validated subset, with increased precision leveraged from the auxiliary data. Furthermore, we develop optimal sampling strategies which minimize the variance of the mean score estimator for a target exposure under a fixed cost constraint. We consider the setting where an internal pilot is necessary for the optimal design so that the phase two sample is split into a pilot and an adaptive optimal sample. Through simulations and data example, we evaluate efficiency gains of the mean score estimator using the derived optimal validation design compared to balanced and simple random sampling for the phase two sample. We also empirically explore efficiency gains that the proposed discrete optimal design can provide for the Cox proportional hazards model in the setting of a continuous-time survival outcome. [ABSTRACT FROM AUTHOR]

Simulation offers a simple and flexible way to estimate the power of a clinical trial when analytic formulae are not available. The computational burden of using simulation has, however, restricted its application to only the simplest of sample size determination problems, often minimising a single parameter (the overall sample size) subject to power being above a target level. We describe a general framework for solving simulation-based sample size determination problems with several design parameters over which to optimise and several conflicting criteria to be minimised. The method is based on an established global optimisation algorithm widely used in the design and analysis of computer experiments, using a non-parametric regression model as an approximation of the true underlying power function. The method is flexible, can be used for almost any problem for which power can be estimated using simulation, and can be implemented using existing statistical software packages. We illustrate its application to a sample size determination problem involving complex clustering structures, two primary endpoints and small sample considerations. [ABSTRACT FROM AUTHOR]

Propensity score methods are commonly used in statistical analyses of observational data to reduce the impact of confounding bias in estimations of average treatment effect. While the propensity score is defined as the conditional probability of a subject being in the treatment group given that subject's covariates, the most precise estimation of average treatment effect results from specifying the propensity score as a function of true confounders and predictors only. This property has been demonstrated via simulation in multiple prior research articles. However, we have seen no theoretical explanation as to why this should be so. This paper provides that theoretical proof. Furthermore, this paper presents a method for performing the necessary variable selection by means of elastic net regression, and then estimating the propensity scores so as to obtain optimal estimates of average treatment effect. The proposed method is compared against two other recently introduced methods, outcome-adaptive lasso and covariate balancing propensity score. Extensive simulation analyses are employed to determine the circumstances under which each method appears most effective. We applied the proposed methods to examine the effect of pre-cardiac surgery coagulation indicator on mortality based on a linked dataset from a retrospective review of 1390 patient medical records at Jewish Hospital (Louisville, KY) with the Society of Thoracic Surgeons database. [ABSTRACT FROM AUTHOR]

This article investigates the homogeneity testing problem of binomial proportions for stratified partially validated data obtained by double-sampling method with two fallible classifiers. Several test procedures, including the weighted-least-squares test with/without log-transformation, logit-transformation and double log-transformation, and likelihood ratio test and score test, are developed to test the homogeneity under two models, distinguished by conditional independence assumption of two classifiers. Simulation results show that score test performs better than other tests in the sense that the empirical size is generally controlled around the nominal level, and hence be recommended to practical applications. Other tests also perform well when both binomial proportions and sample sizes are not small. Approximate sample sizes based on score test, likelihood ratio test and the weighted-least-squares test with double log-transformation are generally accurate in terms of the empirical power and type I error rate with the estimated sample sizes, and hence be recommended. An example from the malaria study is illustrated by the proposed methodologies. [ABSTRACT FROM AUTHOR]

In semi-competing risks, the occurrence of some non-terminal event is subject to a terminal event, usually death. While existing methods for semi-competing risks data analysis assume complete information on all relevant covariates, data on at least one covariate are often not readily available in practice. In this setting, for standard univariate time-to-event analyses, researchers may choose from several strategies for sub-sampling patients on whom to collect complete data, including the nested case-control study design. Here, we consider a semi-competing risks analysis through the reuse of data from an existing nested case-control study for which risk sets were formed based on either the non-terminal or the terminal event. Additionally, we introduce the supplemented nested case-control design in which detailed data are collected on additional events of the other type. We propose estimation with respect to a frailty illness-death model through maximum weighted likelihood, specifying the baseline hazard functions either parametrically or semi-parametrically via B-splines. Two standard error estimators are proposed: (i) a computationally simple sandwich estimator and (ii) an estimator based on a perturbation resampling procedure. We derive the asymptotic properties of the proposed methods and evaluate their small-sample properties via simulation. The designs/methods are illustrated with an investigation of risk factors for acute graft-versus-host disease among N = 8838 patients undergoing hematopoietic stem cell transplantation, for which death is a significant competing risk. [ABSTRACT FROM AUTHOR]

Due to the inevitable inter-study correlation between test sensitivity (Se) and test specificity (Sp), mostly because of threshold variability, hierarchical or bivariate random-effects models are widely used to perform a meta-analysis of diagnostic test accuracy studies. Conventionally, these models assume that the random-effects follow the bivariate normal distribution. However, the inference made using the well-established bivariate random-effects models, when outlying and influential studies are present, may lead to misleading conclusions, since outlying or influential studies can extremely influence parameter estimates due to their disproportional weight. Therefore, we developed a new robust bivariate random-effects model that accommodates outlying and influential observations and gives robust statistical inference by down-weighting the effect of outlying and influential studies. The marginal model and the Monte Carlo expectation-maximization algorithm for our proposed model have been derived. A simulation study has been carried out to validate the proposed method and compare it against the standard methods. Regardless of the parameters varied in our simulations, the proposed model produced robust point estimates of Se and Sp compared to the standard models. Moreover, our proposed model resulted in precise estimates as it yielded the narrowest confidence intervals. The proposed model also generated a similar point and interval estimates of Se and Sp as the standard models when there are no outlying and influential studies. Two published meta-analyses have also been used to illustrate the methods. [ABSTRACT FROM AUTHOR]

Clinical trials often evaluate multiple outcome variables to form a comprehensive picture of the effects of a new treatment. The resulting multidimensional insight contributes to clinically relevant and efficient decision-making about treatment superiority. Common statistical procedures to make these superiority decisions with multiple outcomes have two important shortcomings, however: (1) Outcome variables are often modeled individually, and consequently fail to consider the relation between outcomes; and (2) superiority is often defined as a relevant difference on a single, on any, or on all outcome(s); and lacks a compensatory mechanism that allows large positive effects on one or multiple outcome(s) to outweigh small negative effects on other outcomes. To address these shortcomings, this paper proposes (1) a Bayesian model for the analysis of correlated binary outcomes based on the multivariate Bernoulli distribution; and (2) a flexible decision criterion with a compensatory mechanism that captures the relative importance of the outcomes. A simulation study demonstrates that efficient and unbiased decisions can be made while Type I error rates are properly controlled. The performance of the framework is illustrated for (1) fixed, group sequential, and adaptive designs; and (2) non-informative and informative prior distributions. [ABSTRACT FROM AUTHOR]

Missing information is a major drawback in analyzing data collected in many routine health care settings. Multiple imputation assuming a missing at random mechanism is a popular method to handle missing data. The missing at random assumption cannot be confirmed from the observed data alone, hence the need for sensitivity analysis to assess robustness of inference. However, sensitivity analysis is rarely conducted and reported in practice. We analyzed routine paediatric data collected during a cluster randomized trial conducted in Kenyan hospitals. We imputed missing patient and clinician-level variables assuming the missing at random mechanism. We also imputed missing clinician-level variables assuming a missing not at random mechanism. We incorporated opinions from 15 clinical experts in the form of prior distributions and shift parameters in the delta adjustment method. An interaction between trial intervention arm and follow-up time, hospital, clinician and patient-level factors were included in a proportional odds random-effects analysis model. We performed these analyses using R functions derived from the jomo package. Parameter estimates from multiple imputation under the missing at random mechanism were similar to multiple imputation estimates assuming the missing not at random mechanism. Our inferences were insensitive to departures from the missing at random assumption using either the prior distributions or shift parameters sensitivity analysis approach. [ABSTRACT FROM AUTHOR]

Diagnostic test accuracy studies observe the result of a gold standard procedure that defines the presence or absence of a disease and the result of a diagnostic test. They typically report the number of true positives, false positives, true negatives and false negatives. However, diagnostic test outcomes can also be either non-evaluable positives or non-evaluable negatives. We propose a novel model for the meta-analysis of diagnostic studies in the presence of non-evaluable outcomes, which assumes independent multinomial distributions for the true and non-evaluable positives, and, the true and non-evaluable negatives, conditional on the latent sensitivity, specificity, probability of non-evaluable positives and probability of non-evaluable negatives in each study. For the random effects distribution of the latent proportions, we employ a drawable vine copula that can successively model the dependence in the joint tails. Our methodology is demonstrated with an extensive simulation study and applied to data from diagnostic accuracy studies of coronary computed tomography angiography for the detection of coronary artery disease. The comparison of our method with the existing approaches yields findings in the real data application that change the current conclusions. [ABSTRACT FROM AUTHOR]

Several modeling approaches have been developed to quantify differences in multiple sclerosis lesion evolution on magnetic resonance imaging to identify the effect of treatment on disease progression. These studies have limited clinical applicability due to onerous scan frequency and lengthy study duration. Efficient methods are needed to reduce the required sample size, study duration, and sampling frequency in longitudinal magnetic resonance imaging studies. We develop a data-driven approach to identify parameters of study design for evaluation of longitudinal magnetic resonance imaging biomarkers of multiple sclerosis lesion evolution. Our design strategies are considerably shorter than those described in previous studies, thus having the potential to lower costs of clinical trials. From a dataset of 36 multiple sclerosis patients with at least six monthly magnetic resonance imagings, we extracted new lesions and performed principal component analysis to estimate a biomarker that recapitulated lesion recovery. We tested the effect of multiple sclerosis disease modifying therapy on the lesion evolution index in three experimental designs and calculated sample sizes needed to appropriately power studies. Our proposed methods can be used to calculate required sample size and scan frequency in observational studies of multiple sclerosis disease progression as well as in designing clinical trials to find effects of treatment on multiple sclerosis lesion evolution. [ABSTRACT FROM AUTHOR]

Master protocol designs are often proposed to improve the efficiency of drug development with multiple subgroups. In the basket trial design, different subgroups can have similar biological pathogenesis pathways. Hence, a target therapy can result in similar responses. A good information sharing strategy between different subgroups can potentially improve the efficiency of evaluating treatment efficacy. In traditional hierarchical models, based on the exchangeability assumption, all subgroups are placed into the same sharing pool for cross subgroup information sharing. However, due to the heterogeneity between subgroups, there can be large differences in drug efficacy. Under such cases, strong borrowing across all subgroups is not suitable and no borrowing can be inefficient, because the treatment effect is analyzed in each subgroup separately. We propose a Bayesian cluster hierarchical model (BCHM) to improve the operating characteristics of estimating the treatment effect in multiple subgroups in basket trials. Bayesian nonparametric method is applied to dynamically calculate the number of clusters by conducting a multiple cluster classification based on subgroup outcomes. A hierarchical model is used to compute the posterior probability of the treatment effect, with the borrowing strength determined by the Bayesian nonparametric clustering and the similarities between subgroups. We apply the BCHM to clinical trials with binary endpoints. For treatment effect estimation, the BCHM yields lower mean squared error values, when compared to the independent analyses. In scenarios with a heterogeneous treatment effect, the BCHM provides lower mean squared error values compared to traditional hierarchical models. In addition, we can construct a loss function to optimize the design parameters. BCHM provides a balanced approach and smart borrowing, which yields better results in assessing the treatment effect in different scenarios compared to other conventional methods. [ABSTRACT FROM AUTHOR]

Coefficients of variations are unit-free measures that can, for example, be used to compare the variability of different samples. To this end, we study inference methods for them as well as their reciprocal given by standardised means in general heterogeneous one-way ANOVA designs. As no specific model assumptions are made, a permutation method is proposed to guarantee good finite sample performance. Building on recent limit theorems for randomisation techniques, we prove that the permutation procedure is asymptotically correct in general and finitely exact when data is exchangeable. These results are fostered in extensive simulation studies and two illustrative data analyses. [ABSTRACT FROM AUTHOR]

Quantile regressions are increasingly used to provide population norms for quantitative variables. Indeed, they do not require any Gaussian assumption for the response and allow to characterize its entire distribution through different quantiles. Quantile regressions are especially useful to provide norms of cognitive scores in the elderly that may help general practitioners to identify subjects with unexpectedly low cognitive level in routine examinations. These norms may be estimated from cohorts of elderly using quantile regression for longitudinal data, but this requires to properly account for selection by death, dropout and intermittent missing data. In this work, we extend the weighted estimating equation approach to estimate conditional quantiles in the population currently alive from mortal cohorts with dropout and intermittent missing data. Suitable weight estimation procedures are provided for both monotone and intermittent missing data and under two missing-at-random assumptions, when the observation probability given that the subject is alive depends on the survival time (p-MAR assumption) or not (u-MAR assumption). Inference is performed through subject-level bootstrap. The method is validated in a simulation study and applied to the French cohort Paquid to estimate quantiles of a cognitive test in the elderly population currently alive. On one hand, the simulations show that the u-MAR analysis is quite robust when the true missingness mechanism is p-MAR. This is a useful result because computation of suitable weights for intermittent missing data under the p-MAR assumption is untractable. On the other hand, the simulations highlight, along with the real data analysis, the usefulness of suitable weights for intermittent missing data. This method is implemented in the R package weightQuant. [ABSTRACT FROM AUTHOR]

Within paediatric populations, there may be distinct age groups characterised by different exposure-response relationships. Several regulatory guidance documents have suggested general age groupings. However, it is not clear whether these categorisations will be suitable for all new medicines and in all disease areas. We consider two model-based approaches to quantify how exposure-response model parameters vary over a continuum of ages: Bayesian penalised B-splines and model-based recursive partitioning. We propose an approach for deriving an optimal dosing rule given an estimate of how exposure-response model parameters vary with age. Methods are initially developed for a linear exposure-response model. We perform a simulation study to systematically evaluate how well the various approaches estimate linear exposure-response model parameters and the accuracy of recommended dosing rules. Simulation scenarios are motivated by an application to epilepsy drug development. Results suggest that both bootstrapped model-based recursive partitioning and Bayesian penalised B-splines can estimate underlying changes in linear exposure-response model parameters as well as (and in many scenarios, better than) a comparator linear model adjusting for a categorical age covariate with levels following International Conference on Harmonisation E11 groupings. Furthermore, the Bayesian penalised B-splines approach consistently estimates the intercept and slope more accurately than the bootstrapped model-based recursive partitioning. Finally, approaches are extended to estimate Emax exposure-response models and are illustrated with an example motivated by an in vitro study of cyclosporine. [ABSTRACT FROM AUTHOR]

Clustered and multivariate survival times, such as times to recurrent events, commonly arise in biomedical and health research, and marginal survival models are often used to model such data. When a large number of predictors are available, variable selection is always an important issue when modeling such data with a survival model. We consider a Cox's proportional hazards model for a marginal survival model. Under the sparsity assumption, we propose a penalized generalized estimating equation approach to select important variables and to estimate regression coefficients simultaneously in the marginal model. The proposed method explicitly models the correlation structure within clusters or correlated variables by using a prespecified working correlation matrix. The asymptotic properties of the estimators from the penalized generalized estimating equations are established and the number of candidate covariates is allowed to increase in the same order as the number of clusters does. We evaluate the performance of the proposed method through a simulation study and analyze two real datasets for the application. [ABSTRACT FROM AUTHOR]

Controversy over the validity of significance tests in the analysis of contingency tables is motivated by the disagreement between asymptotic and exact p values and its dependence on the magnitude of expected frequencies. Variants of Pearson's X2 statistic and their asymptotic distributions were proposed to overcome the difficulties, but several approaches also exist to conduct exact tests. This paper shows that discrepant asymptotic and exact results may or may not occur whether expected frequencies are large or small: Eventual inaccuracy of asymptotic p values is instead caused by idiosyncrasies of the discrete distribution of X2. More importantly, discrepancies are also artificially created by the hypergeometric sampling model used to perform exact tests. Exact computations under the alternative full-multinomial or product-multinomial models require eliminating nuisance parameters and we propose a novel method that integrates them out. The resultant exact distributions are very accurately approximated by the asymptotic distribution, which eliminates concerns about the accuracy of the latter. We also discuss that the two-stage approach that tests for significance of residuals conditional on a significant X2 test is inadvisable and that an alternative single-stage test preserves Type-I error rates and further eliminates concerns about asymptotic accuracy. [ABSTRACT FROM AUTHOR]

In cluster randomized trials, the intraclass correlation coefficient (ICC) is classically used to measure clustering. When the outcome is binary, the ICC is known to be associated with the prevalence of the outcome. This association challenges its interpretation and can be problematic for sample size calculation. To overcome these situations, Crespi et al. extended a coefficient named R, initially proposed by Rosner for ophthalmologic data, to cluster randomized trials. Crespi et al. asserted that R may be less influenced by the outcome prevalence than is the ICC, although the authors provided only empirical data to support their assertion. They also asserted that "the traditional ICC approach to sample size determination tends to overpower studies under many scenarios, calling for more clusters than truly required", although they did not consider empirical power. The aim of this study was to investigate whether R could indeed be considered independent of the outcome prevalence. We also considered whether sample size calculation should be better based on the R coefficient or the ICC. Considering the particular case of 2 individuals per cluster, we theoretically demonstrated that R is not symmetrical around the 0.5 prevalence value. This in itself demonstrates the dependence of R on prevalence. We also conducted a simulation study to explore the case of both fixed and variable cluster sizes greater than 2. This simulation study demonstrated that R decreases when prevalence increases from 0 to 1. Both the analytical and simulation results demonstrate that R depends on the outcome prevalence. In terms of sample size calculation, we showed that an approach based on the ICC is preferable to an approach based on the R coefficient because with the former, the empirical power is closer to the nominal one. Hence, the R coefficient does not outperform the ICC for binary outcomes because it does not offer any advantage over the ICC. [ABSTRACT FROM AUTHOR]

When establishing an effective treatment with binary data in a two-stage design, one-sided tests for a proportion p are employed. Researchers use the parameter configuration at the boundary of the null hypothesis space to determine a rejection region and an optimal design. However, it is unclear whether the (maximum) Type I error rate is achieved at the boundary especially when the sample size in stage 2 varies. In this paper, we first prove that this is true for a large family of tests in adaptive two-stage designs by showing that any test in the family has a nondecreasing power in p and then derive optimal designs. Second, similar results are established for m-stage designs with m > 2. Supplementary materials for this article are available online. [ABSTRACT FROM AUTHOR]

We propose a general hurdle methodology to model a response from a homogeneous or a non-homogeneous Poisson process with excess zeros, based on two forests. The first forest in the two parts model is used to estimate the probability of having a zero. The second forest is used to estimate the Poisson parameter(s), using only the observations with at least one event. To build the trees in the second forest, we propose specialized splitting criteria derived from the zero truncated homogeneous and non-homogeneous Poisson likelihood. The particular case of a homogeneous process is investigated in details to stress out the advantages of the proposed method over the existing ones. Simulation studies show that the proposed methods perform well in hurdle (zero-altered) and zero-inflated settings, for both homogeneous and non-homogeneous processes. We illustrate the use of the new method with real data on the demand for medical care by the elderly. [ABSTRACT FROM AUTHOR]

We propose four confidence intervals for the ratio of two independent Poisson rates. We apply a parametric bootstrap approach, two modified asymptotic results, and we propose an ad-hoc approximate-estimate method to construct confidence intervals. We justify the correctness of the proposed methods asymptotically in the case of non-rare events (when the Poisson rates are large). We also compare the proposed confidence intervals with some recommended ones in the case of rare events (when the Poisson rates are small) via an extensive simulation study. The results show that the proposed modified asymptotic and the approximate-estimate confidence intervals perform reasonably well in terms of coverage probability and average length. [ABSTRACT FROM AUTHOR]

Estimating the medical costs from disease diagnosis to a terminal event is of immense interest to researchers. However, most of existing literature on such research focused on the estimation of cumulative mean function (CMF) for history process. In this paper, the combined scheme of both inverse probability of censoring weighting (IPCW) technique and longitudinal quantile regression model is used to develop a novel procedure to the estimation of cumulative quantile function (CQF) based on history process with time-dependent covariates and right censored time-to-event variable. The consistency of proposed estimator is derived. The extensive simulation study is conducted to investigate the performance of the estimator given in this paper. A medical cost data from a multicenter automatic defibrillator implantation trial (MADIT) is analyzed to illustrate the application of developed method. [ABSTRACT FROM AUTHOR]

The relationship between the mean and variance is an implicit assumption of parametric modeling. While many distributions in the exponential family have a theoretical mean-variance relationship, it is often the case that the data under investigation are correlated, thus varying from the relation. We present a generalized method of moments estimation technique for modeling certain correlated data by adjusting the mean-variance relationship parameters based on a canonical parameterization. The proposed mean-variance form describes overdispersion using two parameters and implements an adjusted canonical parameter which makes this approach feasible for all distributions in the exponential family. Test statistics and confidence intervals are used to measure the deviations from the mean-variance relation parameters. We use the modified relation as a means of fitting generalized quasi-likelihood models to correlated data. The performance of the proposed modified generalized quasi-likelihood model is demonstrated through a simulation study and the importance of accounting for overdispersion is highlighted through the evaluation of adolescent obesity data collected from a U.S. longitudinal study. [ABSTRACT FROM AUTHOR]

During drug evaluation trials, information from clinical trials previously conducted on another population, indications or schedules may be available. In these cases, it might be desirable to share information by efficiently using the available resources. In this work, we developed an adaptive power prior with a commensurability parameter for using historical or external information. It allows, at each stage, full borrowing when the data are not in conflict, no borrowing when the data are in conflict or "tuned" borrowing when the data are in between. We propose to apply our adaptive power prior method to bridging studies between Caucasians and Asians, and we focus on the sequential adaptive allocation design, although other design settings can be used. We weight the prior information in two steps: the effective sample size approach is used to set the maximum desirable amount of information to be shared from historical data at each step of the trial; then, in a sort of Empirical Bayes approach, a commensurability parameter is chosen using a measure of distribution distance. This approach avoids elicitation and computational issues regarding the usual Empirical Bayes approach. We propose several versions of our method, and we conducted an extensive simulation study evaluating the robustness and sensitivity to prior choices. [ABSTRACT FROM AUTHOR]

We describe a procedure for imputing missing values of time-dependent covariates in a discrete time Cox model using the chained equations method. The procedure multiply imputes the missing values for each time-period in a time-sequential manner, using covariates from the current and previous time-periods as well as the survival outcome. The form of the outcome variable used in the imputation model depends on the functional form of the time-dependent covariate(s) and differs from the case of Cox regression with only baseline covariates. This time-sequential approach provides an approximation to a fully conditional approach. We illustrate the procedure with data on diabetics, evaluating the association of their glucose control with the risk of selected cancers. Using simulations we show that the suggested estimator performed well (in terms of bias and coverage) for completely missing at random, missing at random and moderate non-missing-at-random patterns. However, for very strong non-missing-at-random patterns, the estimator was seriously biased and the coverage was too low. The procedure can be implemented using multiple imputation with the Fully conditional Specification (FCS) method (MI procedure in SAS with FCS statement or similar packages in other software, e.g. MICE in R). For use with event times on a continuous scale, the events would need to be grouped into time-intervals. [ABSTRACT FROM AUTHOR]

Confidence interval (CI) methods for the ratio of two proportions in the presence of correlated bilateral binary data are constructed for comparative clinical trials with stratified design. Simulations are conducted to evaluate the performance of the presented CIs with respect to mean coverage probability (MCP), mean interval width (MIW), and the ratio of mesial non-coverage probability to the distal non-coverage probability (RMNCP). Based on the empirical results, we suggest the use of the proposed CI method based on the complete score statistics (CS) for general applications. An example from a rheumatology study is used to demonstrate the proposed methodologies. [ABSTRACT FROM AUTHOR]

In longitudinal clinical trials with daily patient-reported outcomes, the analysis endpoints are often defined as the averaged daily diary outcomes in a treatment cycle (such as a month or a week). Conventional methods often deal with missing data at the cycle level by imputing the average, and the cycle average is treated as missing if the number of days with available outcomes in the treatment cycle is less than a certain number. This was the method used for a case study of a phase 3 clinical trial evaluating a treatment for insomnia with daily patient-reported outcomes. Such methods may introduce bias. Motivated by this, we propose methods to impute missing daily outcomes in this paper. Specifically, we define a two-level missing pattern for clinical trials with daily patient-reported outcomes, and propose two-level methods to impute missing data at daily base. Other than the standard methods by multiple imputations, we derive analytic formulas for the proposed two-level methods to reduce computational intensity and improve the estimates of variances. The proposed two-level methods provide more powerful approaches to estimate the treatment difference compared to the conventional cycle-level methods, which are evaluated by theoretical development and simulation studies. In addition, the methods are applied to the motivating phase 3 trial evaluating a treatment for insomnia with daily patient-reported outcomes. [ABSTRACT FROM AUTHOR]

Sequential monitoring of efficacy and safety is an important part of clinical trials. A Group Sequential design allows researchers to perform interim monitoring after groups of patients have completed the study. Statistical literature is well developed for continuous and binary outcomes and relies on asymptotic normality of the test statistic. However, in the case of time-to-event data, existing methods of sample size calculation are done either assuming proportional hazards or assuming exponentially distributed lifetimes. In scenarios where these assumptions are not true, as evidenced from historical data, these traditional methods are restrictive and cannot always be used. As interim monitoring is driven by ethical, financial, and administrative considerations, it is imperative that sample size calculations be done in an efficient manner keeping in mind the specific needs of a clinical trial with a time-to-event outcome. To address these issues, a novel group sequential design is proposed using the concept of Proportional Time. This method utilizes the generalized gamma ratio distribution to calculate the efficacy and safety boundaries and can be used for all distributions that are members of the generalized gamma family using an error spending approach. The design incorporates features specific to survival data such as loss to follow-up, administrative censoring, varying accrual times and patterns, binding or non-binding futility rules with or without skips, and flexible alpha and beta spending mechanisms. Three practical examples are discussed, followed by discussion of the important aspects of the proposed design. [ABSTRACT FROM AUTHOR]

Clinicians and researchers alike are increasingly interested in how best to personalize interventions. A dynamic treatment regimen is a sequence of prespecified decision rules which can be used to guide the delivery of a sequence of treatments or interventions that is tailored to the changing needs of the individual. The sequential multiple-assignment randomized trial is a research tool which allows for the construction of effective dynamic treatment regimens. We derive easy-to-use formulae for computing the total sample size for three common two-stage sequential multiple-assignment randomized trial designs in which the primary aim is to compare mean end-of-study outcomes for two embedded dynamic treatment regimens which recommend different first-stage treatments. The formulae are derived in the context of a regression model which leverages information from a longitudinal outcome collected over the entire study. We show that the sample size formula for a sequential multiple-assignment randomized trial can be written as the product of the sample size formula for a standard two-arm randomized trial, a deflation factor that accounts for the increased statistical efficiency resulting from a longitudinal analysis, and an inflation factor that accounts for the design of a sequential multiple-assignment randomized trial. The sequential multiple-assignment randomized trial design inflation factor is typically a function of the anticipated probability of response to first-stage treatment. We review modeling and estimation for dynamic treatment regimen effect analyses using a longitudinal outcome from a sequential multiple-assignment randomized trial, as well as the estimation of standard errors. We also present estimators for the covariance matrix for a variety of common working correlation structures. Methods are motivated using the ENGAGE study, a sequential multiple-assignment randomized trial aimed at developing a dynamic treatment regimen for increasing motivation to attend treatments among alcohol- and cocaine-dependent patients. [ABSTRACT FROM AUTHOR]