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Adaptive designs for clinical trials permit alterations to a study in response to accumulating data in order to make trials more flexible, ethical, and efficient. These benefits are achieved while preserving the integrity and validity of the trial, through the pre-specification and proper adjustment for the possible alterations during the course of the trial. Despite much research in the statistical literature highlighting the potential advantages of adaptive designs over traditional fixed designs, the uptake of such methods in clinical research has been slow. One major reason for this is that different adaptations to trial designs, as well as their advantages and limitations, remain unfamiliar to large parts of the clinical community. The aim of this paper is to clarify where adaptive designs can be used to address specific questions of scientific interest; we introduce the main features of adaptive designs and commonly used terminology, highlighting their utility and pitfalls, and illustrate their use through case studies of adaptive trials ranging from early-phase dose escalation to confirmatory phase III studies.

Adaptive enrichment designs involve preplanned rules for modifying enrolment criteria based on accruing data in a randomized trial. We focus on designs where the overall population is partitioned into two predefined subpopulations, e.g. based on a biomarker or risk score measured at baseline. The goal is to learn which populations benefit from an experimental treatment. Two critical components of adaptive enrichment designs are the decision rule for modifying enrolment, and the multiple-testing procedure.We provide a general method for simultaneously optimizing these components for two-stage, adaptive enrichment designs.We minimize the expected sample size under constraints on power and the familywise type I error rate. It is computationally infeasible to solve this optimization problem directly because of its non-convexity. The key to our approach is a novel, discrete representation of this optimization problem as a sparse linear program, which is large but computationally feasible to solve by using modern optimization techniques.We provide an R package that implements our method and is compatible with linear program solvers in several software languages. Our approach produces new, approximately optimal trial designs.

In precision medicine, a patient is treated with targeted therapies that are predicted to be effective based on the patient's baseline characteristics such as biomarker profiles. Oftentimes, patient subgroups are unknown and must be learned through inference using observed data. We present SCUBA, a Subgroup ClUster-based Bayesian Adaptive design aiming to fulfill two simultaneous goals in a clinical trial, 1) to treatments enrich the allocation of each subgroup of patients to their precision and desirable treatments and 2) to report multiple subgroup-treatment pairs (STPs). Using random partitions and semiparametric Bayesian models, SCUBA provides coherent and probabilistic assessment of potential patient subgroups and their associated targeted therapies. Each STP can then be used for future confirmatory studies for regulatory approval. Through extensive simulation studies, we present an application of SCUBA to an innovative clinical trial in gastroesphogeal cancer.

Background Adaptive clinical trials have been increasingly commonly employed to select a potential target population for one trial without conducting trials separately. Such enrichment designs typically consist of two or three stages, where the first stage serves as a screening process for selecting a specific subpopulation. Methods We propose a Bayesian design for randomized clinical trials with a binary outcome that focuses on restricting the inclusion to a subset of patients who are likely to benefit the most from the treatment during trial accrual. Several Bayesian measures of efficacy and treatment-by-subset interactions were used to dictate the enrichment, either based on Gail and Simon’s or Millen’s criteria. A simulation study was used to assess the performance of our design. The method is exemplified in a real randomized clinical trial conducted in patients with respiratory failure that failed to show any benefit of high flow oxygen supply compared with standard oxygen. Results The use of the enrichment rules allowed the detection of the existence of a treatment-by-subset interaction more rapidly compared with Gail and Simon’s criteria, with decreasing proportions of enrollment in the whole sample, and the proportions of enrichment lower, in the presence of interaction based on Millen’s criteria. In the real dataset, this may have allowed the detection of the potential interest of high flow oxygen in patients with a SOFA neurological score ≥ 1. Conclusion Enrichment designs that handle the uncertainty in treatment efficacy by focusing on the target population offer a promising balance for trial efficiency and ease of interpretation.

Background Adaptive enrichment designs for clinical trials have great potential for the development of targeted therapies. They enable researchers to stop the recruitment process for a certain population in mid-course based on an interim analysis. However, adaptive enrichment designs increase the total trial period owing to the stoppage in patient recruitment to make interim decisions. This is a major drawback; it results in delays in the submission of clinical trial reports and the appearance of drugs on the market. Here, we explore three types of patient recruitment strategy for the development of targeted therapies based on the adaptive enrichment design. Methods We consider recruitment methods which provide an option to continue recruiting patients from the overall population or only from the biomarker-positive population even during the interim decision period. A simulation study was performed to investigate the operating characteristics by comparing an adaptive enrichment design using the recruitment methods with a non-enriched design. Results The number of patients was similar for both recruitment methods. Nevertheless, the adaptive enrichment design was beneficial in settings in which the recruitment period is expected to be longer than the follow-up period. In these cases, the adaptive enrichment design with continued recruitment from the overall population or only from the biomarker-positive population even during the interim decision period conferred a major advantage, since the total trial period did not differ substantially from that of trials employing the non-enriched design. By contrast, the non-enriched design should be used in settings in which the follow-up period is expected to be longer than the recruitment period, since the total trial period was notably shorter than that of the adaptive enrichment design. Furthermore, the utmost care is needed when the distribution of patient recruitment is concave, i.e., when patient recruitment is slow during the early period, since the total trial period is extended. Conclusions Adaptive enrichment designs that entail continued recruitment methods are beneficial owing to the shorter total trial period than expected in settings in which the recruitment period is expected to be longer than the follow-up period and the biomarker-positive population is promising.

Run-in periods are occasionally used in randomized clinical trials to exclude patients after inclusion, but before randomization. In theory, run-in periods increase the probability of detecting a potential treatment effect, at the cost of possibly affecting external and internal validity. Adequate reporting of exclusions during the run-in period is a prerequisite for judging the risk of compromised validity. Our study aims were to assess the proportion of randomized clinical trials with run-in periods, to characterize such trials and the types of run-in periods and to assess their reporting. This was an observational study of 470 PubMed-indexed randomized controlled trial publications from 2014. We compared trials with and without run-in periods, described the types of run-in periods and evaluated the completeness of their reporting by noting whether publications stated the number of excluded patients, reasons for exclusion and baseline characteristics of the excluded patients. Twenty-five trials reported a run-in period (5%). These were larger than other trials (median number of randomized patients 217 vs 90, =0.01) and more commonly industry trials (11% vs 3%, <0.01). The run-in procedures varied in design and purpose. In 23 out of 25 trials (88%), the run-in period was incompletely reported, mostly due to missing baseline characteristics. Approximately 1 in 20 trials used run-in periods, though much more frequently in industry trials. Reporting of the run-in period was often incomplete, precluding a meaningful assessment of the impact of the run-in period on the validity of trial results. We suggest that current trials with run-in periods are interpreted with caution and that updates of reporting guidelines for randomized trials address the issue.

Background Combination therapies directed at multiple targets have potentially improved treatment effects for cancer patients. Compared to monotherapy, targeted combination therapy leads to an increasing number of subgroups and complicated biomarker-based efficacy profiles, making it more difficult for efficacy evaluation in clinical trials. Therefore, it is necessary to develop innovative clinical trial designs to explore the efficacy of targeted combination therapy in different subgroups and identify patients who are more likely to benefit from the investigational combination therapy. Methods We propose a statistical tool called ‘IBIS’ to Identify BIomarker-based Subgroups and apply it to the enrichment design framework. The IBIS contains three main elements: subgroup division, efficacy evaluation and subgroup identification. We first enumerate all possible subgroup divisions based on biomarker levels. Then, Jensen–Shannon divergence is used to distinguish high-efficacy and low-efficacy subgroups, and Bayesian hierarchical model (BHM) is employed to borrow information within these two subsets for efficacy evaluation. Regarding subgroup identification, a hypothesis testing framework based on Bayes factors is constructed. This framework also plays a key role in go/no-go decisions and enriching specific population. Simulation studies are conducted to evaluate the proposed method. Results The accuracy and precision of IBIS could reach a desired level in terms of estimation performance. In regard to subgroup identification and population enrichment, the proposed IBIS has superior and robust characteristics compared with traditional methods. An example of how to obtain design parameters for an adaptive enrichment design under the IBIS framework is also provided. Conclusions IBIS has the potential to be a useful tool for biomarker-based subgroup identification and population enrichment in clinical trials of targeted combination therapy.

Background: Run-in periods are occasionally used in randomized clinical trials to exclude patients after inclusion, but before randomization. In theory, run-in periods increase the probability of detecting a potential treatment effect, at the cost of possibly affecting external and internal validity. Adequate reporting of exclusions during the run-in period is a prerequisite forjudging the risk of compromised validity. Our study aims were to assess the proportion of randomized clinical trials with run-in periods, to characterize such trials and the types of run-in periods and to assess their reporting. Materials and methods: This was an observational study of 470 PubMed-indexed randomized controlled trial publications from 2014. We compared trials with and without run-in periods, described the types of run-in periods and evaluated the completeness of their reporting by noting whether publications stated the number of excluded patients, reasons for exclusion and baseline characteristics of the excluded patients. Results: Twenty-five trials reported a run-in period (5%). These were larger than other trials (median number of randomized patients 217 vs 90, .P=0.01) and more commonly industry trials (11% vs 3%, P<0.01). The run-in procedures varied in design and purpose. In 23 out of 25 trials (88%), the run-inperiod was incompletely reported, mostly due to missing baseline characteristics. Conclusion: Approximately 1 in 20 trials used run-in periods, though much more frequently in industry trials. Reporting of the run-in period was often incomplete, precluding a meaningful assessment of the impact of the run-in period on the validity of trial results. We suggest that current trials with run-in periods are interpreted with caution and that updates of reporting guidelines for randomized trials address the issue. Keywords: run-in periods, lead-in periods, enrichment design, single-blind placebo, washout periods, research methodology

It is a challenge to evaluate experimental treatments where it is suspected that the treatment effect may only be strong for certain subpopulations, such as those having a high initial severity of disease, or those having a particular gene variant. Standard randomized controlled trials can have low power in such situations. They also are not optimized to distinguish which subpopulations benefit from a treatment. With the goal of overcoming these limitations, we consider randomized trial designs in which the criteria for patient enrollment may be changed, in a preplanned manner, based on interim analyses. Since such designs allow data-dependent changes to the population enrolled, care must be taken to ensure strong control of the familywise Type I error rate. Our main contribution is a general method for constructing randomized trial designs that allow changes to the population enrolled based on interim data using a prespecified decision rule, for which the asymptotic, familywise Type I error rate is strongly controlled at a specified level α. As a demonstration of our method, we prove new, sharp results for a simple, two-stage enrichment design. We then compare this design to fixed designs, focusing on each design's ability to determine the overall and subpopulation-specific treatment effects.

Background Limitations in the primary studies constitute one important factor to be considered in the grading of recommendations assessment, development, and evaluation (GRADE) system of rating quality of evidence. However, in the network meta-analysis (NMA), such evaluation poses a special challenge because each network estimate receives different amounts of contributions from various studies via direct as well as indirect routes and because some biases have directions whose repercussion in the network can be complicated. Findings In this report we use the NMA of maintenance pharmacotherapy of bipolar disorder (17 interventions, 33 studies) and demonstrate how to quantitatively evaluate the impact of study limitations using netweight , a STATA command for NMA. For each network estimate, the percentage of contributions from direct comparisons at high, moderate or low risk of bias were quantified, respectively. This method has proven flexible enough to accommodate complex biases with direction, such as the one due to the enrichment design seen in some trials of bipolar maintenance pharmacotherapy. Conclusions Using netweight , therefore, we can evaluate in a transparent and quantitative manner how study limitations of individual studies in the NMA impact on the quality of evidence of each network estimate, even when such limitations have clear directions.