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Bayesian clinical trial design using historical data that inform the treatment effect.

ABSTRACT: We consider the problem of Bayesian sample size determination for a clinical trial in the presence of historical data that inform the treatment effect. Our broadly applicable, simulation-based methodology provides a framework for calibrating the informativeness of a prior while simultaneously identifying the minimum sample size required for a new trial such that the overall design has appropriate power to detect a non-null treatment effect and reasonable type I error control. We develop a comprehensive strategy for eliciting null and alternative sampling prior distributions which are used to define Bayesian generalizations of the traditional notions of type I error control and power. Bayesian type I error control requires that a weighted-average type I error rate not exceed a prespecified threshold. We develop a procedure for generating an appropriately sized Bayesian hypothesis test using a simple partial-borrowing power prior which summarizes the fraction of information borrowed from the historical trial. We present results from simulation studies that demonstrate that a hypothesis test procedure based on this simple power prior is as efficient as those based on more complicated meta-analytic priors, such as normalized power priors or robust mixture priors, when all are held to precise type I error control requirements. We demonstrate our methodology using a real data set to design a follow-up clinical trial with time-to-event endpoint for an investigational treatment in high-risk melanoma.

SUBMITTER: Psioda MA

PROVIDER: S-EPMC6587921 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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Bayesian clinical trial design using historical data that inform the treatment effect.

Psioda Matthew A MA Ibrahim Joseph G JG

Biostatistics (Oxford, England) 20190701 3

We consider the problem of Bayesian sample size determination for a clinical trial in the presence of historical data that inform the treatment effect. Our broadly applicable, simulation-based methodology provides a framework for calibrating the informativeness of a prior while simultaneously identifying the minimum sample size required for a new trial such that the overall design has appropriate power to detect a non-null treatment effect and reasonable type I error control. We develop a compre ...[more]

PMID: 29547966

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Project description:BackgroundCentronuclear myopathies are severe rare congenital diseases. The clinical variability and genetic heterogeneity of these myopathies result in major challenges in clinical trial design. Alternative strategies to large placebo-controlled trials that have been used in other rare diseases (e.g., the use of surrogate markers or of historical controls) have limitations that Bayesian statistics may address. Here we present a Bayesian model that uses each patient's own natural history study data to predict progression in the absence of treatment. This prospective multicentre natural history evaluated 4-year follow-up data from 59 patients carrying mutations in the MTM1 or DNM2 genes.MethodsOur approach focused on evaluation of forced expiratory volume in 1 s (FEV1) in 6- to 18-year-old children. A patient was defined as a responder if an improvement was observed after treatment and the predictive probability of such improvement in absence of intervention was less than 0.01. An FEV1 response was considered clinically relevant if it corresponded to an increase of more than 8%.ResultsThe key endpoint of a clinical trial using this model is the rate of response. The power of the study is based on the posterior probability that the rate of response observed is greater than the rate of response that would be observed in the absence of treatment predicted based on the individual patient's previous natural history. In order to appropriately control for Type 1 error, the threshold probability by which the difference in response rates exceeds zero was adapted to 91%, ensuring a 5% overall Type 1 error rate for the trial.ConclusionsBayesian statistical analysis of natural history data allowed us to reliably simulate the evolution of symptoms for individual patients over time and to probabilistically compare these simulated trajectories to actual observed post-treatment outcomes. The proposed model adequately predicted the natural evolution of patients over the duration of the study and will facilitate a sufficiently powerful trial design that can cope with the disease's rarity. Further research and ongoing dialog with regulatory authorities are needed to allow for more applications of Bayesian statistics in orphan disease research.

Project description:BackgroundClinical trial enrollment and completion is challenging, with nearly half of all trials not being completed or not completed on time. In 2014, the National Institutes of Health StrokeNet in collaboration with stroke epidemiologists from GCNKSS (Greater Cincinnati/Northern Kentucky Stroke Study) began providing proposed clinical trials with formal trial feasibility assessments. Herein, we describe the process of prospective feasibility analyses using epidemiological data that can be used to improve enrollment and increase the likelihood a trial is completed.MethodsIn 2014, DEFUSE 3 (Endovascular Therapy Following Imaging Evaluation for Ischemic Stroke 3) trialists, National Institutes of Health StrokeNet, and stroke epidemiologists from GCNKSS collaborated to evaluate the initial inclusion/exclusion criteria for the DEFUSE 3 study. Trial criteria were discussed and an assessment was completed to evaluate the percent of the stroke population that might be eligible for the study. The DEFUSE 3 trial was stopped early with the publication of DAWN (Thrombectomy 6 to 24 Hours After Stroke With a Mismatch Between Deficit and Infarct), and the Wilcoxon rank-sum statistic was used to analyze whether the trial would have been stopped had the proposed changes not been made, following the DEFUSE 3 statistical analysis plan.ResultsAfter initial epidemiological analysis, 2.4% of patients with acute stroke in the GCNKSS population would have been predicted to be eligible for the study. After discussion with primary investigators and modifying 4 key exclusion criteria (upper limit of age increased to 90 years, baseline modified Rankin Scale broadened to 0-2, time since last well expanded to 16 hours, and decreased lower limit of National Institutes of Health Stroke Scale score to <6), the number predicted to be eligible for the trial increased to 4%. At the time of trial conclusion, 57% of the enrolled patients qualified only by the modified criteria, and the trial was stopped at an interim analysis that demonstrated efficacy. We estimated that the Wilcoxon rank-sum value for the unadjusted predicted enrollment would not have crossed the threshold for efficacy and the trial not stopped.ConclusionsObjectively assessing trial inclusion/exclusion criteria using a population-based resource in a collaborative and iterative process including epidemiologists can lead to improved recruitment and can increase the likelihood of successful trial completion.

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Project description:Overly restrictive eligibility criteria for clinical trials may limit the generalizability of the trial results to their target real-world patient populations. We developed a novel machine learning approach using large collections of real-world data (RWD) to better inform clinical trial eligibility criteria design. We extracted patients' clinical events from electronic health records (EHRs), which include demographics, diagnoses, and drugs, and assumed certain compositions of these clinical events within an individual's EHRs can determine the subphenotypes-homogeneous clusters of patients, where patients within each subgroup share similar clinical characteristics. We introduced an outcome-guided probabilistic model to identify those subphenotypes, such that the patients within the same subgroup not only share similar clinical characteristics but also at similar risk levels of encountering severe adverse events (SAEs). We evaluated our algorithm on two previously conducted clinical trials with EHRs from the OneFlorida+ Clinical Research Consortium. Our model can clearly identify the patient subgroups who are more likely to suffer or not suffer from SAEs as subphenotypes in a transparent and interpretable way. Our approach identified a set of clinical topics and derived novel patient representations based on them. Each clinical topic represents a certain clinical event composition pattern learned from the patient EHRs. Tested on both trials, patient subgroup (#SAE=0) and patient subgroup (#SAE>0) can be well-separated by k-means clustering using the inferred topics. The inferred topics characterized as likely to align with the patient subgroup (#SAE>0) revealed meaningful combinations of clinical features and can provide data-driven recommendations for refining the exclusion criteria of clinical trials. The proposed supervised topic modeling approach can infer the clinical topics from the subphenotypes with or without SAEs. The potential rules for describing the patient subgroups with SAEs can be further derived to inform the design of clinical trial eligibility criteria.

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Bayesian clinical trial design using historical data that inform the treatment effect.

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Bayesian clinical trial design using historical data that inform the treatment effect.

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