Bayesian semiparametric meta-analytic-predictive prior for historical control borrowing in clinical trials

Covariate adjusted meta-analytic predictive (CA-MAP) prior for historical borrowing using patient-level data

Utilization of historical data is increasingly common for gaining efficiency in the drug development and decision-making processes. The underlying issue of between-trial heterogeneity in clinical trials is a barrier in making these methods standard practice in the pharmaceutical industry. Common methods for historical borrowing discount the borrowed information based on the similarity between outcomes in the historical and current data. However, individual clinical trials and their outcomes are intrinsically heterogenous due to differences in study design, patient characteristics, and changes in standard of care. Additionally, differences in covariate distributions can produce inconsistencies in clinical outcome data between historical and current data when there may be a consistent covariate effect. In such scenario, borrowing historical data is still advantageous even though the population level outcome summaries are different. In this paper, we propose a covariate adjusted meta-analytic-predictive (CA-MAP) prior for historical control borrowing. A MAP prior is assigned to each covariate effect, allowing the amount of borrowing to be determined by the consistency of the covariate effects across the current and historical data. This approach integrates between-trial heterogeneity with covariate level heterogeneity to tune the amount of information borrowed. Our method is unique as it directly models the covariate effects instead of using the covariates to select a similar population to borrow from. In summary, our proposed patient-level extension of the MAP prior allows for the amount of historical control borrowing to depend on the similarity of covariate effects rather than similarity in clinical outcomes.

DOD-Combo: Bayesian dose finding design in combination trials with meta-analytic-predictive prior

Combination therapy, a treatment modality that involves multiple treatment agents, has become imperative for improving treatment effectiveness and addressing resistance in the field of oncology. However, determining the most effective dose for these combinations, particularly when dealing with intricate drug interactions and diverse toxicity patterns, presents a substantial challenge. This paper introduces a novel Bayesian dose-finding design for combination therapies with information borrowing, named the DOD-Combo design. Leveraging historical single-agent trials and the meta-analytic-predictive (MAP) power prior, our approach utilizes a copula-type model to connect individual drug priors with joint toxicity probabilities in combination treatments. The MAP power prior allows the integration of information from multiple historical trials, constructing informative priors for each agent. Extensive simulations confirm our method's superior performance compared to combination designs with no information borrowing. By adaptively incorporating historical data, our approach reduces sample sizes and enhances efficiency in selecting the maximum tolerated dose (MTD), effectively addressing the intricate challenges presented by combination trials.

Evaluating hybrid controls methodology in early-phase oncology trials: A simulation study based on the MORPHEUS-UC trial

Phase Ib/II oncology trials, despite their small sample sizes, aim to provide information for optimal internal company decision-making concerning novel drug development. Hybrid controls (a combination of the current control arm and controls from one or more sources of historical trial data [HTD]) can be used to increase statistical precision. Here we assess combining two sources of Roche HTD to construct a hybrid control in targeted therapy for decision-making via an extensive simulation study. Our simulations are based on the real data of one of the experimental arms and the control arm of the MORPHEUS-UC Phase Ib/II study and two Roche HTD for atezolizumab monotherapy. We consider potential complications such as model misspecification, unmeasured confounding, different sample sizes of current treatment groups, and heterogeneity among the three trials. We evaluate two frequentist methods (with both Cox and Weibull accelerated failure time [AFT] models) and three different commensurate priors in Bayesian dynamic borrowing (with a Weibull AFT model), and modifications within each of those, when estimating the effect of treatment on survival outcomes and measures of effect such as marginal hazard ratios. We assess the performance of these methods in different settings and the potential of generalizations to supplement decisions in early-phase oncology trials. The results show that the proposed joint frequentist methods and noninformative priors within Bayesian dynamic borrowing with no adjustment on covariates are preferred, especially when treatment effects across the three trials are heterogeneous. For generalization of hybrid control methods in such settings, we recommend more simulation studies.

BEATS: Bayesian hybrid design with flexible sample size adaptation for time-to-event endpoints

As the roles of historical trials and real-world evidence in drug development have substantially increased, several approaches have been proposed to leverage external data and improve the design of clinical trials. While most of these approaches focus on methodology development for borrowing information during the analysis stage, there is a risk of inadequate or absent enrollment of concurrent control due to misspecification of heterogeneity from external data, which can result in unreliable estimates of treatment effect. In this study, we introduce a Bayesian hybrid design with flexible sample size adaptation (BEATS) that allows for adaptive borrowing of external data based on the level of heterogeneity to augment the control arm during both the design and interim analysis stages. Moreover, BEATS extends the Bayesian semiparametric meta-analytic predictive prior (BaSe-MAP) to incorporate time-to-event endpoints, enabling optimal borrowing performance. Initially, BEATS calibrates the expected sample size and initial randomization ratio based on heterogeneity among the external data. During the interim analysis, flexible sample size adaptation is performed to address conflicts between the concurrent and historical control, while also conducting futility analysis. At the final analysis, estimation is provided by incorporating the calibrated amount of external data. Therefore, our proposed design allows for an approximation of an ideal randomized controlled trial with an equal randomization ratio while controlling the size of the concurrent control to benefit patients and accelerate drug development. BEATS also offers optimal power and robust estimation through flexible sample size adaptation when conflicts arise between the concurrent control and external data.

Use of external control arms in immune-mediated inflammatory diseases: a systematic review

OBJECTIVES

External control arms (ECAs) provide useful comparisons in clinical trials when randomised control arms are limited or not feasible. We conducted a systematic review to summarise applications of ECAs in trials of immune-mediated inflammatory diseases (IMIDs).

DESIGN

Systematic review with an appraisal of ECA source quality rated across five domains (data collection, study populations, outcome definitions, reliability and comprehensiveness of the dataset, and other potential limitations) as high, low or unclear quality.

DATA SOURCES

Embase, Medline and Cochrane Central Register of Controlled Trial were searched through to 12 September 2023.

ELIGIBILITY CRITERIA

Eligible studies were single-arm or randomised controlled trials (RCTs) of inflammatory bowel disease, pouchitis, rheumatoid arthritis, juvenile idiopathic arthritis, ankylosing spondylitis, psoriatic arthritis, psoriasis and atopic dermatitis in which an ECA was used as the comparator.

DATA EXTRACTION AND SYNTHESIS

Two authors independently screened the search results in duplicate. The characteristics of included studies, external data source(s), outcomes and statistical methods were recorded, and the quality of the ECA data source was assessed by two independent authors.

RESULTS

Forty-three studies met the inclusion criteria (inflammatory bowel disease: 16, pouchitis: 1, rheumatoid arthritis: 12, juvenile idiopathic arthritis: 1, ankylosing spondylitis: 5, psoriasis: 3, multiple indications: 4). The majority of these trials were single-arm (33/43) and enrolled adult patients (34/43). All included studies used a historical control rather than a contemporaneous ECA. In RCTs, ECAs were most often derived from the placebo arm of another RCT (6/10). In single-arm trials, historical case series were the most common ECA source (19/33). Most studies (31/43) did not employ a statistical approach to generate the ECA from historical data.

CONCLUSIONS

Standardised ECA methodology and reporting conventions are lacking for IMIDs trials. The establishment of ECA reporting guidelines may enhance the rigour and transparency of future research.

Adaptively leveraging external data with robust meta-analytical-predictive prior using empirical Bayes

The robust meta-analytical-predictive (rMAP) prior is a popular method to robustly leverage external data. However, a mixture coefficient would need to be pre-specified based on the anticipated level of prior-data conflict. This can be very challenging at the study design stage. We propose a novel empirical Bayes robust MAP (EB-rMAP) prior to address this practical need and adaptively leverage external/historical data. Built on Box's prior predictive p-value, the EB-rMAP prior framework balances between model parsimony and flexibility through a tuning parameter. The proposed framework can be applied to binomial, normal, and time-to-event endpoints. Implementation of the EB-rMAP prior is also computationally efficient. Simulation results demonstrate that the EB-rMAP prior is robust in the presence of prior-data conflict while preserving statistical power. The proposed EB-rMAP prior is then applied to a clinical dataset that comprises 10 oncology clinical trials, including the prospective study.

On the use of non-concurrent controls in platform trials: a scoping review

BACKGROUND

Platform trials gained popularity during the last few years as they increase flexibility compared to multi-arm trials by allowing new experimental arms entering when the trial already started. Using a shared control group in platform trials increases the trial efficiency compared to separate trials. Because of the later entry of some of the experimental treatment arms, the shared control group includes concurrent and non-concurrent control data. For a given experimental arm, non-concurrent controls refer to patients allocated to the control arm before the arm enters the trial, while concurrent controls refer to control patients that are randomised concurrently to the experimental arm. Using non-concurrent controls can result in bias in the estimate in case of time trends if the appropriate methodology is not used and the assumptions are not met.

METHODS

We conducted two reviews on the use of non-concurrent controls in platform trials: one on statistical methodology and one on regulatory guidance. We broadened our searches to the use of external and historical control data. We conducted our review on the statistical methodology in 43 articles identified through a systematic search in PubMed and performed a review on regulatory guidance on the use of non-concurrent controls in 37 guidelines published on the EMA and FDA websites.

RESULTS

Only 7/43 of the methodological articles and 4/37 guidelines focused on platform trials. With respect to the statistical methodology, in 28/43 articles, a Bayesian approach was used to incorporate external/non-concurrent controls while 7/43 used a frequentist approach and 8/43 considered both. The majority of the articles considered a method that downweights the non-concurrent control in favour of concurrent control data (34/43), using for instance meta-analytic or propensity score approaches, and 11/43 considered a modelling-based approach, using regression models to incorporate non-concurrent control data. In regulatory guidelines, the use of non-concurrent control data was considered critical but was deemed acceptable for rare diseases in 12/37 guidelines or was accepted in specific indications (12/37). Non-comparability (30/37) and bias (16/37) were raised most often as the general concerns with non-concurrent controls. Indication specific guidelines were found to be most instructive.

CONCLUSIONS

Statistical methods for incorporating non-concurrent controls are available in the literature, either by means of methods originally proposed for the incorporation of external controls or non-concurrent controls in platform trials. Methods mainly differ with respect to how the concurrent and non-concurrent data are combined and temporary changes handled. Regulatory guidance for non-concurrent controls in platform trials are currently still limited.

A novel power prior approach for borrowing historical control data in clinical trials

There has been an increased interest in borrowing information from historical control data to improve the statistical power for hypothesis testing, therefore reducing the required sample sizes in clinical trials. To account for the heterogeneity between the historical and current trials, power priors are often considered to discount the information borrowed from the historical data. However, it can be challenging to choose a fixed power prior parameter in the application. The modified power prior approach, which defines a random power parameter with initial prior to control the amount of historical information borrowed, may not directly account for heterogeneity between the trials. In this paper, we propose a novel approach to pick a power prior based on some direct measures of distributional differences between historical control data and current control data under normal assumptions. Simulations are conducted to investigate the performance of the proposed approach compared with current approaches (e.g. commensurate prior, meta-analytic-predictive, and modified power prior). The results show that the proposed power prior improves the study power while controlling the type I error within a tolerable limit when the distribution of the historical control data is similar to that of the current control data. The method is developed for both superiority and non-inferiority trials and is illustrated with an example from vaccine clinical trials.

An Improved Matching Practice for Augmenting a Randomized Clinical Trial with External Control

The use of information from real world to assess the effectiveness of medical products is becoming increasingly popular and more acceptable by regulatory agencies. According to a strategic real-world evidence framework published by U.S. Food and Drug Administration, a hybrid randomized controlled trial that augments internal control arm with real-world data is a pragmatic approach worth more attention. In this paper, we aim to improve on existing matching designs for such a hybrid randomized controlled trial. In particular, we propose to match the entire concurrent randomized clinical trial (RCT) such that (1) the matched external control subjects used to augment the internal control arm are as comparable as possible to the RCT population, (2) every active treatment arm in an RCT with multiple treatments is compared with the same control group, and (3) matching can be conducted and the matched set locked before treatment unblinding to better maintain the data integrity and increase the credibility of the analysis. Besides a weighted estimator, we also introduce a bootstrap method to obtain its variance estimation. The finite sample performance of the proposed method is evaluated by simulations based on data from a real clinical trial.

Bayesian Additive Regression Trees (BART) with covariate adjusted borrowing in subgroup analyses

It is crucial in clinical trials to investigate treatment effect consistency across subgroups defined by patient baseline characteristics. However, there may be treatment effect variability across subgroups due to small subgroup sample size. Various Bayesian models have been proposed to incorporate this variability when borrowing information across subgroups. These models rely on the underlying assumption that patients with similar characteristics will have similar outcomes to the same treatment. Patient populations within each subgroup must subjectively be deemed similar enough Pocock (1976) to borrow response information across subgroups. We propose utilizing the machine learning method of Bayesian Additive Regression Trees (BART) to provide a method for subgroup borrowing that does not rely on an underlying assumption of homogeneity between subgroups. BART is a data-driven approach that utilizes patient-level observations. The amount of borrowing between subgroups automatically adjusts as BART learns the covariate-response relationships. Modeling patient-level data rather than treating the subgroup as a single unit minimizes assumptions regarding homogeneity across subgroups. We illustrate the use of BART in this context by comparing performance from existing subgroup borrowing methods in a simulation study and a case study in non-small cell lung cancer. The application of BART in the context of subgroup analyses alleviates the need to subjectively choose how much information to borrow based on subgroup similarity. Having the amount of borrowing be analytically determined and controlled for based on the similarity of individual patient-level characteristics allows for more objective decision making in the drug development process with many other applications including basket trials.

Statistical methods of indirect comparison with real-world data for survival endpoint under non-proportional hazards

In clinical studies that utilize real-world data, time-to-event outcomes are often germane to scientific questions of interest. Two main obstacles are the presence of non-proportional hazards and confounding bias. Existing methods that could adjust for NPH or confounding bias, but no previous work delineated the complexity of simultaneous adjustments for both. In this paper, a propensity score stratified MaxCombo and weighted Cox model is proposed. This model can adjust for confounding bias and NPH and can be pre-specified when NPH pattern is unknown in advance. The method has robust performance as demonstrated in simulation studies and in a case study.

Optimal sample size determination for single-arm trials in pediatric and rare populations with Bayesian borrowing

In many therapeutic areas with unmet medical needs, such as pediatric oncology and rare diseases, one of the deterrent factors for clinical trial interpretability is the limited sample size with less-than-ideal operating characteristics. Single arm is usually the only viable design due to feasibility and ethical concerns. For the trial results to be more interpretable and conclusive, the evaluation of operating characteristics, such as type I error rate and power, and the appropriate utilization of prior information for study design, shall be prespecified and fully investigated during the trial planning phase. So far, very few existing literature addressed optimal sample size determination issues for the planning of pediatric and rare population trials, with majority of research focusing on analysis perspective with focus on Bayesian borrowing. In practice, when a single-arm trial is designed for rare population, it is not uncommon that the only information available is from an earlier trial and/or a few clinical publications based on observational studies, often constituting mixed or uncertain conclusions. In light of this, an optimal Bayesian sample size determination method for single-arm trial with binary or continuous endpoint is proposed, where conflicting prior beliefs can be readily incorporated. Prior effective sample size can be calculated to assess the robustness as well as the prior information borrowed. Moreover, due to the lack of closed-form posterior distributions in general, an alternative approach for calculating Bayesian power is described. Simulation studies are provided to demonstrate the utility of the proposed methods. In addition, a case study in pediatric patients with leukemia is included to illustrate the proposed method with the existing approaches.

Machine Learning and Artificial Intelligence in Pharmaceutical Research and Development: a Review

Over the past decade, artificial intelligence (AI) and machine learning (ML) have become the breakthrough technology most anticipated to have a transformative effect on pharmaceutical research and development (R&D). This is partially driven by revolutionary advances in computational technology and the parallel dissipation of previous constraints to the collection/processing of large volumes of data. Meanwhile, the cost of bringing new drugs to market and to patients has become prohibitively expensive. Recognizing these headwinds, AI/ML techniques are appealing to the pharmaceutical industry due to their automated nature, predictive capabilities, and the consequent expected increase in efficiency. ML approaches have been used in drug discovery over the past 15–20 years with increasing sophistication. The most recent aspect of drug development where positive disruption from AI/ML is starting to occur, is in clinical trial design, conduct, and analysis. The COVID-19 pandemic may further accelerate utilization of AI/ML in clinical trials due to an increased reliance on digital technology in clinical trial conduct. As we move towards a world where there is a growing integration of AI/ML into R&D, it is critical to get past the related buzz-words and noise. It is equally important to recognize that the scientific method is not obsolete when making inferences about data. Doing so will help in separating hope from hype and lead to informed decision-making on the optimal use of AI/ML in drug development. This manuscript aims to demystify key concepts, present use-cases and finally offer insights and a balanced view on the optimal use of AI/ML methods in R&D.

Propensity-score-based meta-analytic predictive prior for incorporating real-world and historical data

As the availability of real-world data sources (eg, EHRs, claims data, registries) and historical data has rapidly surged in recent years, there is an increasing interest and need from investigators and health authorities to leverage all available information to reduce patient burden and accelerate both drug development and regulatory decision making. Bayesian meta-analytic approaches are a popular historical borrowing method that has been developed to leverage such data using robust hierarchical models. The model structure accounts for various degrees of between-trial heterogeneity, resulting in adaptively discounting the external information in the case of data conflict. In this article, we propose to integrate the propensity score method and Bayesian meta-analytic-predictive (MAP) prior to leverage external real-world and historical data. The propensity score methodology is applied to select a subset of patients from external data that are similar to those in the current study with regards to key baseline covariates and to stratify the selected patients together with those in the current study into more homogeneous strata. The MAP prior approach is used to obtain stratum-specific MAP prior and derive the overall propensity score integrated meta-analytic predictive (PS-MAP) prior. Additionally, we allow for tuning the prior effective sample size for the proposed PS-MAP prior, which quantifies the amount of information borrowed from external data. We evaluate the performance of the proposed PS-MAP prior by comparing it to the existing propensity score-integrated power prior approach in a simulation study and illustrate its implementation with an example of a single-arm phase II trial.