A bivariate Bayesian dose‐finding procedure applied to a seamless phase I/II trial in rheumatoid arthritis

We describe a dose escalation procedure for a combined phase I/II clinical trial. The procedure is based on a Bayesian model for the joint distribution of the occurrence of a dose limiting event and of some indicator of efficacy (both considered binary variables), making no assumptions other than monotonicity. Thus, the chances of each outcome are assumed to be non‐decreasing in dose level. We applied the procedure to the design of a placebo‐controlled, sequential trial in rheumatoid arthritis, in each stage of which patients were randomized between placebo and all dose levels that currently appeared safe and non‐futile. On the basis of data from a pilot study, we constructed five different scenarios for the dose–response relationships under which we simulated the trial and assessed the performance of the procedure. The new design appears to have satisfactory operating characteristics and can be adapted to the requirements of a range of trial situations. Copyright © 2012 John Wiley & Sons, Ltd.     

Bayesian optimal phase II designs with dual-criterion decision making

The conventional phase II trial design paradigm is to make the go/no-go decision based on the hypothesis testing framework. Statistical significance itself alone, however, may not be sufficient to establish that the drug is clinically effective enough to warrant confirmatory phase III trials. We propose the Bayesian optimal phase II trial design with dual-criterion decision making (BOP2-DC), which incorporates both statistical significance and clinical relevance into decision making. Based on the posterior probability that the treatment effect reaches the lower reference value (statistical significance) and the clinically meaningful value (clinical significance), BOP2-DC allows for go/consider/no-go decisions, rather than a binary go/no-go decision. BOP2-DC is highly flexible and accommodates various types of endpoints, including binary, continuous, time-to-event, multiple, and coprimary endpoints, in single-arm and randomized trials. The decision rule of BOP2-DC is optimized to maximize the probability of a go decision when the treatment is effective or minimize the expected sample size when the treatment is futile. Simulation studies show that the BOP2-DC design yields desirable operating characteristics. The software to implement BOP2-DC is freely available at www.trialdesign.org .     

Early stopping in seamless phase I/II clinical trials

In recent years, seamless phase I/II clinical trials have drawn much attention, as they consider both toxicity and efficacy endpoints in finding an optimal dose (OD). Engaging an appropriate number of patients in a trial is a challenging task. This paper attempts a dynamic stopping rule to save resources in phase I/II trials. That is, the stopping rule aims to save patients from unnecessary toxic or subtherapeutic doses. We allow a trial to stop early when widths of the confidence intervals for the dose-response parameters become narrower or when the sample size is equal to a predefined size, whichever comes first. The simulation study of dose-response scenarios in various settings demonstrates that the proposed stopping rule can engage an appropriate number of patients. Therefore, we suggest its use in clinical trials.     

Modelling and simulation to improve decision‐making in clinical development

Modelling and simulation are buzz words in clinical drug development. But is clinical trial simulation (CTS) really a revolutionary technique? There is not much more to CTS than applying standard methods of modelling, statistics and decision theory. However, doing this in a systematic way can mean a significant improvement in pharmaceutical research. This paper describes in simple examples how modelling could be used in clinical development. Four steps are identified: gathering relevant information about a drug and the disease; building a mathematical model; predicting the results of potential future trials; and optimizing clinical trials and the entire clinical programme. We discuss these steps and give a number of examples of model components, demonstrating that relatively unsophisticated models may also prove useful. We stress that modelling and simulation are decision tools and point out the benefits of integrating them with decision analysis. Copyright © 2005 John Wiley & Sons, Ltd.     

The shrinking or disappearing observed treatment effect

It is frequently noted that an initial clinical trial finding was not reproduced in a later trial. This is often met with some surprise. Yet, there is a relatively straightforward reason partially responsible for this observation. In this article, we examine this reason by first reviewing some findings in a recent publication in the Journal of the American Medical Association. To help explain the non‐negligible chance of failing to reproduce a previous positive finding, we compare a series of trials to successive diagnostic tests used for identifying a condition. To help explain the suspicion that the treatment effect, when observed in a subsequent trial, seems to have decreased in magnitude, we draw a conceptual analogy between phases II–III development stages and interim analyses of a trial with a group sequential design. Both analogies remind us that what we observed in an early trial could be a false positive or a random high. We discuss statistical sources for these occurrences and discuss why it is important for statisticians to take these into consideration when designing and interpreting trial results. Copyright © 2014 John Wiley & Sons, Ltd.     

Adaptive designs for pivotal trials: discussion points from the PSI Adaptive Design Expert Group

The Committee for Medicinal Products for Human Use (CHMP) is currently preparing a guideline on 'methodological issues in confirmatory clinical trials with flexible design and analysis plan'. PSI (Statisticians in the Pharmaceutical Industry) sponsored a meeting of pharmaceutical statisticians with an interest in the area to share experiences and identify potential opportunities for adaptive designs in late-phase clinical drug development. This article outlines the issues raised, resulting discussions and consensus views reached. Adaptive designs have potential utility in late-phase clinical development. Sample size re-estimation seems to be valuable and widely accepted, but should be made independent of the observed treatment effect where possible. Where unblinding is necessary, careful consideration needs to be given to preserving the integrity of the trial. An area where adaptive designs can be particularly beneficial is to allow dose selection in pivotal trials via adding/dropping treatment arms; for example, combining phase II and III of the drug development program. The more adaptations made during a late-phase clinical trial, the less likely that the clinical trial would be considered as a confirmatory trial. In all cases it would be advisable to consult with regulatory agencies at the protocol design stage. All involved should remain open to scientifically valid opportunities to improve drug development.     

Group-sequential logrank methods for trial designs using bivariate non-competing event-time outcomes

We discuss the multivariate (2L-variate) correlation structure and the asymptotic distribution for the group-sequential weighted logrank statistics formulated when monitoring two correlated event-time outcomes in clinical trials. The asymptotic distribution and the variance–covariance for the 2L-variate weighted logrank statistic are derived as available in various group-sequential trial designs. These methods are used to determine a group-sequential testing procedure based on calendar times or information fractions. We apply the theoretical results to a group-sequential method for monitoring a clinical trial with early stopping for efficacy when the trial is designed to evaluate the joint effect on two correlated event-time outcomes. We illustrate the method with application to a clinical trial and describe how to calculate the required sample sizes and numbers of events.

     

“Super-covariates”: Using predicted control group outcome as a covariate in randomized clinical trials

The power of randomized controlled clinical trials to demonstrate the efficacy of a drug compared with a control group depends not just on how efficacious the drug is, but also on the variation in patients' outcomes. Adjusting for prognostic covariates during trial analysis can reduce this variation. For this reason, the primary statistical analysis of a clinical trial is often based on regression models that besides terms for treatment and some further terms (e.g., stratification factors used in the randomization scheme of the trial) also includes a baseline (pre-treatment) assessment of the primary outcome. We suggest to include a “super-covariate”—that is, a patient-specific prediction of the control group outcome—as a further covariate (but not as an offset). We train a prognostic model or ensembles of such models on the individual patient (or aggregate) data of other studies in similar patients, but not the new trial under analysis. This has the potential to use historical data to increase the power of clinical trials and avoids the concern of type I error inflation with Bayesian approaches, but in contrast to them has a greater benefit for larger sample sizes. It is important for prognostic models behind “super-covariates” to generalize well across different patient populations in order to similarly reduce unexplained variability whether the trial(s) to develop the model are identical to the new trial or not. In an example in neovascular age-related macular degeneration we saw efficiency gains from the use of a “super-covariate”.     

Assurance in clinical trial design

Conventional clinical trial design involves considerations of power, and sample size is typically chosen to achieve a desired power conditional on a specified treatment effect. In practice, there is considerable uncertainty about what the true underlying treatment effect may be, and so power does not give a good indication of the probability that the trial will demonstrate a positive outcome. Assurance is the unconditional probability that the trial will yield a ‘positive outcome’. A positive outcome usually means a statistically significant result, according to some standard frequentist significance test. The assurance is then the prior expectation of the power, averaged over the prior distribution for the unknown true treatment effect. We argue that assurance is an important measure of the practical utility of a proposed trial, and indeed that it will often be appropriate to choose the size of the sample (and perhaps other aspects of the design) to achieve a desired assurance, rather than to achieve a desired power conditional on an assumed treatment effect. We extend the theory of assurance to two‐sided testing and equivalence trials. We also show that assurance is straightforward to compute in some simple problems of normal, binary and gamma distributed data, and that the method is not restricted to simple conjugate prior distributions for parameters. Several illustrations are given. Copyright © 2005 John Wiley & Sons, Ltd.     

TSNP: A two-stage nonparametric phase I/II clinical trial design for immunotherapy

We develop a transparent and efficient two-stage nonparametric (TSNP) phase I/II clinical trial design to identify the optimal biological dose (OBD) of immunotherapy. We propose a nonparametric approach to derive the closed-form estimates of the joint toxicity–efficacy response probabilities under the monotonic increasing constraint for the toxicity outcomes. These estimates are then used to measure the immunotherapy's toxicity–efficacy profiles at each dose and guide the dose finding. The first stage of the design aims to explore the toxicity profile. The second stage aims to find the OBD, which can achieve the optimal therapeutic effect by considering both the toxicity and efficacy outcomes through a utility function. The closed-form estimates and concise dose-finding algorithm make the TSNP design appealing in practice. The simulation results show that the TSNP design yields superior operating characteristics than the existing Bayesian parametric designs. User-friendly computational software is freely available to facilitate the application of the proposed design to real trials. We provide comprehensive illustrations and examples about implementing the proposed design with associated software.     

A Phase I/II adaptive design for heterogeneous groups with application to a stereotactic body radiation therapy trial

Dose‐finding studies that aim to evaluate the safety of single agents are becoming less common, and advances in clinical research have complicated the paradigm of dose finding in oncology. A class of more complex problems, such as targeted agents, combination therapies and stratification of patients by clinical or genetic characteristics, has created the need to adapt early‐phase trial design to the specific type of drug being investigated and the corresponding endpoints. In this article, we describe the implementation of an adaptive design based on a continual reassessment method for heterogeneous groups, modified to coincide with the objectives of a Phase I/II trial of stereotactic body radiation therapy in patients with painful osseous metastatic disease. Operating characteristics of the Institutional Review Board approved design are demonstrated under various possible true scenarios via simulation studies. Copyright © 2015 John Wiley & Sons, Ltd.     

Response-adaptive trial designs with accelerated Thompson sampling

In a clinical trial, sometimes it is desirable to allocate as many patients as possible to the best treatment, in particular, when a trial for a rare disease may contain a considerable portion of the whole target population. The Gittins index rule is a powerful tool for sequentially allocating patients to the best treatment based on the responses of patients already treated. However, its application in clinical trials is limited due to technical complexity and lack of randomness. Thompson sampling is an appealing approach, since it makes a compromise between optimal treatment allocation and randomness with some desirable optimal properties in the machine learning context. However, in clinical trial settings, multiple simulation studies have shown disappointing results with Thompson samplers. We consider how to improve short-run performance of Thompson sampling and propose a novel acceleration approach. This approach can also be applied to situations when patients can only be allocated by batch and is very easy to implement without using complex algorithms. A simulation study showed that this approach could improve the performance of Thompson sampling in terms of average total response rate. An application to a redesign of a preference trial to maximize patient's satisfaction is also presented.     

Planning a Bayesian early-phase phase I/II study for human vaccines in HER2 carcinomas

Recent innovative statistical approaches for phase I/II clinical trials allow one to jointly model the toxicity and efficacy of a new treatment, taking into account the information gathered during the trial. Prior probabilities are then updated with interim data and thus predictive probabilities become more accurate as the trial progresses. In this study, prior distribution elicited from a physician's opinion on the available dose levels planned for a vaccination dose-finding trial, with human DNA in patients with HER2-positive tumours in terms of toxicity and therapeutic response is presented and discussed. A simulation study was conducted in order to quantify the impact of the choice of prior on study results, i.e. the recommended dose level at the end of the trial.     

Bayesian sequential analysis for multiple-arm clinical trials

Use of full Bayesian decision-theoretic approaches to obtain optimal stopping rules for clinical trial designs typically requires the use of Backward Induction. However, the implementation of Backward Induction, apart from simple trial designs, is generally impossible due to analytical and computational difficulties. In this paper we present a numerical approximation of Backward Induction in a multiple-arm clinical trial design comparing k experimental treatments with a standard treatment where patient response is binary. We propose a novel stopping rule, denoted by τ ^p , as an approximation of the optimal stopping rule, using the optimal stopping rule of a single-arm clinical trial obtained by Backward Induction. We then present an example of a double-arm (k=2) clinical trial where we use a simulation-based algorithm together with τ ^p to estimate the expected utility of continuing and compare our estimates with exact values obtained by an implementation of Backward Induction. For trials with more than two treatment arms, we evaluate τ ^p by studying its operating characteristics in a three-arm trial example. Results from these examples show that our approximate trial design has attractive properties and hence offers a relevant solution to the problem posed by Backward Induction.     

Adaptive two-treatment two-period crossover design for binary treatment responses incorporating carry-over effects

Adaptive designs are sometimes used in a phase III clinical trial with the goal of allocating a larger number of patients to the better treatment. In the present paper we use some adaptive designs in a two-treatment two-period crossover trial in the presence of possible carry-over effects, where the treatment responses are binary. We use some simple designs to choose between the possible treatment combinations AA, AB, BA or BB. The goal is to use the better treatment a larger proportion of times. We calculate the allocation proportions to the possible treatment combinations and their standard deviations. We also investigate related inferential problems, for which related asymptotics are derived. The proposed procedure is compared with a possible competitor. Finally we use real data sets to illustrate the applicability of our proposed design.     

Multi-treatment covariate-adjusted adaptive design under informative censoring

In the present work, we find a set of reliability functionals to fix up an allocation strategy among K(≥2) treatments when the response distributions, conditionally dependent on some continuous prognostic variable, are exponential with unknown linear regression functions as the means of the respective conditional distributions. Targeting such reliability functionals, we propose a covariate-adjusted response-adaptive randomization procedure for the multi-treatment single-period clinical trial under the Koziol–Green model for informative censoring. We compare the proposed procedure with its competitive covariate-eliminated procedure.     

Combining evidence from clinical trials in conditional or accelerated approval

Conditional (European Medicines Agency) or accelerated (U.S. Food and Drug Administration) approval of drugs allows earlier access to promising new treatments that address unmet medical needs. Certain post-marketing requirements must typically be met in order to obtain full approval, such as conducting a new post-market clinical trial. We study the applicability of the recently developed harmonic mean ${\chi }^2$-test to this conditional or accelerated approval framework. The proposed approach can be used both to support the design of the post-market trial and the analysis of the combined evidence provided by both trials. Other methods considered are the two-trials rule, Fisher's criterion and Stouffer's method. In contrast to some of the traditional methods, the harmonic mean ${\chi }^2$-test always requires a post-market clinical trial. If the $p$-value from the pre-market clinical trial is $\ll 0.025$, a smaller sample size for the post-market clinical trial is needed than with the two-trials rule. For illustration, we apply the harmonic mean ${\chi }^2$-test to a drug which received conditional (and later full) market licensing by the EMA. A simulation study is conducted to study the operating characteristics of the harmonic mean ${\chi }^2$-test and two-trials rule in more detail. We finally investigate the applicability of these two methods to compute the power at interim of an ongoing post-market trial. These results are expected to aid in the design and assessment of the required post-market studies in terms of the level of evidence required for full approval.     

Missing data in clinical trials: control‐based mean imputation and sensitivity analysis

In some randomized (drug versus placebo) clinical trials, the estimand of interest is the between‐treatment difference in population means of a clinical endpoint that is free from the confounding effects of “rescue” medication (e.g., HbA1c change from baseline at 24 weeks that would be observed without rescue medication regardless of whether or when the assigned treatment was discontinued). In such settings, a missing data problem arises if some patients prematurely discontinue from the trial or initiate rescue medication while in the trial, the latter necessitating the discarding of post‐rescue data. We caution that the commonly used mixed‐effects model repeated measures analysis with the embedded missing at random assumption can deliver an exaggerated estimate of the aforementioned estimand of interest. This happens, in part, due to implicit imputation of an overly optimistic mean for “dropouts” (i.e., patients with missing endpoint data of interest) in the drug arm. We propose an alternative approach in which the missing mean for the drug arm dropouts is explicitly replaced with either the estimated mean of the entire endpoint distribution under placebo (primary analysis) or a sequence of increasingly more conservative means within a tipping point framework (sensitivity analysis); patient‐level imputation is not required. A supplemental “dropout = failure” analysis is considered in which a common poor outcome is imputed for all dropouts followed by a between‐treatment comparison using quantile regression. All analyses address the same estimand and can adjust for baseline covariates. Three examples and simulation results are used to support our recommendations.     

Estimation of the cumulative incidence function under multiple dependent and independent censoring mechanisms

Competing risks occur in a time-to-event analysis in which a patient can experience one of several types of events. Traditional methods for handling competing risks data presuppose one censoring process, which is assumed to be independent. In a controlled clinical trial, censoring can occur for several reasons: some independent, others dependent. We propose an estimator of the cumulative incidence function in the presence of both independent and dependent censoring mechanisms. We rely on semi-parametric theory to derive an augmented inverse probability of censoring weighted (AIPCW) estimator. We demonstrate the efficiency gained when using the AIPCW estimator compared to a non-augmented estimator via simulations. We then apply our method to evaluate the safety and efficacy of three anti-HIV regimens in a randomized trial conducted by the AIDS Clinical Trial Group, ACTG A5095.     

Permutation Methods for Comparing the Accuracy of Nested Prediction Models in Survival Analysis

When making patient-specific prediction, it is important to compare prediction models to evaluate the gain in prediction accuracy for including additional covariates. We propose two statistical testing methods, the complete data permutation (CDP) and the permutation cross-validation (PCV) for comparing prediction models. We simulate clinical trial settings extensively and show that both methods are robust and achieve almost correct test sizes; the methods have comparable power in moderate to large sample situations, while the CDP is more efficient in computation. The methods are also applied to ovarian cancer clinical trial data.