Specifications of a continual reassessment method design for phase I trials of combined drugs

In studies of combinations of agents in phase I oncology trials, the dose–toxicity relationship may not be monotone for all combinations, in which case the toxicity probabilities follow a partial order. The continual reassessment method for partial orders (PO‐CRM) is a design for phase I trials of combinations that leans upon identifying possible complete orders associated with the partial order. This article addresses some practical design considerations not previously undertaken when describing the PO‐CRM. We describe an approach in choosing a proper subset of possible orderings, formulated according to the known toxicity relationships within a matrix of combination therapies. Other design issues, such as working model selection and stopping rules, are also discussed. We demonstrate the practical ability of PO‐CRM as a phase I design for combinations through its use in a recent trial designed at the University of Virginia Cancer Center. Copyright © 2013 John Wiley & Sons, Ltd.     

Improvements to the Escalation with Overdose Control design and a comparison with the restricted Continual Reassessment Method

The Escalation with Overdose Control (EWOC) design for cancer dose finding clinical trials is a variation of the Continual Reassessment Method (CRM) that was proposed to overcome the limitation of the original CRM of exposing patients to high toxic doses. The properties of EWOC have been studied to some extent, but some aspects of the design are not well studied, and its performance is not fully understood. Comparisons of the EWOC design to the most commonly used modified CRM designs have not yet been performed, and the advantages of EWOC over the modified CRM designs are unclear. In this paper, we assess the properties of the EWOC design and of the restricted CRM and some variations of these designs. We show that EWOC has several weaknesses that CRM does not have that make it impractical to use in its original formulation. We propose modified EWOC designs that address some of the weaknesses and that have some desirable statistical properties compared with the original EWOC design, the restricted CRM design, and the 3 + 3 design. However, their statistical properties are sensitive to correct specification of the prior distribution of their parameters and hence nevertheless will need to be used with some caution. The restricted CRM design is shown to have more stable performance across a wider family of dose‐toxicity curves than EWOC and therefore may be a preferable general choice in cancer clinical research.     

Incorporating historical information to improve phase I clinical trials

Incorporating historical data has a great potential to improve the efficiency of phase I clinical trials and to accelerate drug development. For model-based designs, such as the continuous reassessment method (CRM), this can be conveniently carried out by specifying a “skeleton,” that is, the prior estimate of dose limiting toxicity (DLT) probability at each dose. In contrast, little work has been done to incorporate historical data into model-assisted designs, such as the Bayesian optimal interval (BOIN), Keyboard, and modified toxicity probability interval (mTPI) designs. This has led to the misconception that model-assisted designs cannot incorporate prior information. In this paper, we propose a unified framework that allows for incorporating historical data into model-assisted designs. The proposed approach uses the well-established “skeleton” approach, combined with the concept of prior effective sample size, thus it is easy to understand and use. More importantly, our approach maintains the hallmark of model-assisted designs: simplicity—the dose escalation/de-escalation rule can be tabulated prior to the trial conduct. Extensive simulation studies show that the proposed method can effectively incorporate prior information to improve the operating characteristics of model-assisted designs, similarly to model-based designs.     

Dynamic ordering design for dose finding in drug-combination trials

Drug-combination studies have become increasingly popular in oncology. One of the critical concerns in phase I drug-combination trials is the uncertainty in toxicity evaluation. Most of the existing phase I designs aim to identify the maximum tolerated dose (MTD) by reducing the two-dimensional searching space to one dimension via a prespecified model or splitting the two-dimensional space into multiple one-dimensional subspaces based on the partially known toxicity order. Nevertheless, both strategies often lead to complicated trials which may either be sensitive to model assumptions or induce longer trial durations due to subtrial split. We develop two versions of dynamic ordering design (DOD) for dose finding in drug-combination trials, where the dose-finding problem is cast in the Bayesian model selection framework. The toxicity order of dose combinations is continuously updated via a two-dimensional pool-adjacent-violators algorithm, and then the dose assignment for each incoming cohort is selected based on the optimal model under the dynamic toxicity order. We conduct extensive simulation studies to evaluate the performance of DOD in comparison with four other commonly used designs under various scenarios. Simulation results show that the two versions of DOD possess competitive performances in terms of correct MTD selection as well as safety, and we apply both versions of DOD to two real oncology trials for illustration.     

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.     

Unifying CRM and EWOC designs for phase I cancer clinical trials

The main goal of phase I cancer clinical trials is to determine the highest dose of a new therapy associated with an acceptable level of toxicity for the use in a subsequent phase II trial. The continual reassessment method (CRM) [O’Quigley, J., Pepe, M., Fisher, L., 1990. Continual reassessment method: a practical design for phase I clinical trials in cancer. Biometrics 46, 33–48] and escalation with overdose control (EWOC) [Babb, J., Rogatko, A., Zacks, S., 1998. Cancer phase I clinical trials: efficient dose escalation with overdose control. Statist. Med. 17 (10), 1103–1120] are two model-based designs used for phase I cancer clinical trials. A few modifications of the (original) CRM and EWOC have been made by many authors. In this paper, we show how CRM and EWOC can be unified and present a hybrid design. We study the characteristics of the approach of the hybrid design. The comparisons of the three designs (CRM, EWOC, and the hybrid design) are presented by convergence rates and overdose proportions. The simulation results show that the hybrid design generally has faster convergence rates than EWOC and smaller overdose proportions than CRM, especially when the true maximum tolerated dose (MTD) is above the mid-level of the dose range considered. The performance of these three designs is also evaluated in terms of sensitivity to outliers.     

Time-to-event calibration-free odds design: A robust efficient design for phase I trials with late-onset outcomes

Compared with most of the existing phase I designs, the recently proposed calibration-free odds (CFO) design has been demonstrated to be robust, model-free, and easy to use in practice. However, the original CFO design cannot handle late-onset toxicities, which have been commonly encountered in phase I oncology dose-finding trials with targeted agents or immunotherapies. To account for late-onset outcomes, we extend the CFO design to its time-to-event (TITE) version, which inherits the calibration-free and model-free properties. One salient feature of CFO-type designs is to adopt game theory by competing three doses at a time, including the current dose and the two neighboring doses, while interval-based designs only use the data at the current dose and is thus less efficient. We conduct comprehensive numerical studies for the TITE-CFO design under both fixed and randomly generated scenarios. TITE-CFO shows robust and efficient performances compared with interval-based and model-based counterparts. As a conclusion, the TITE-CFO design provides robust, efficient, and easy-to-use alternatives for phase I trials when the toxicity outcome is late-onset.     

Phase I trial design for drug combinations with Bayesian model averaging

Various statistical models have been proposed for two‐dimensional dose finding in drug‐combination trials. However, it is often a dilemma to decide which model to use when conducting a particular drug‐combination trial. We make a comprehensive comparison of four dose‐finding methods, and for fairness, we apply the same dose‐finding algorithm under the four model structures. Through extensive simulation studies, we compare the operating characteristics of these methods in various practical scenarios. The results show that different models may lead to different design properties and that no single model performs uniformly better in all scenarios. As a result, we propose using Bayesian model averaging to overcome the arbitrariness of the model specification and enhance the robustness of the design. We assign a discrete probability mass to each model as the prior model probability and then estimate the toxicity probabilities of combined doses in the Bayesian model averaging framework. During the trial, we adaptively allocated each new cohort of patients to the most appropriate dose combination by comparing the posterior estimates of the toxicity probabilities with the prespecified toxicity target. The simulation results demonstrate that the Bayesian model averaging approach is robust under various scenarios. Copyright © 2015 John Wiley & Sons, Ltd.     

Performance of phase-I dose finding designs with and without a run-in intra-patient dose escalation stage

Dose-finding designs for phase-I trials aim to determine the recommended phase-II dose (RP2D) for further phase-II drug development. If the trial includes patients for whom several lines of standard therapy failed or if the toxicity of the investigated agent does not necessarily increase with dose, optimal dose-finding designs should limit the frequency of treatment with suboptimal doses. We propose a two-stage design strategy with a run-in intra-patient dose escalation part followed by a more traditional dose-finding design. We conduct simulation studies to compare the 3 + 3 design, the Bayesian Optimal Interval Design (BOIN) and the Continual Reassessment Method (CRM) with and without intra-patient dose escalation. The endpoints are accuracy, sample size, safety, and therapeutic efficiency. For scenarios where the correct RP2D is the highest dose, inclusion of an intra-patient dose escalation stage generally increases accuracy and therapeutic efficiency. However, for scenarios where the correct RP2D is below the highest dose, intra-patient dose escalation designs lead to increased risk of overdosing and an overestimation of RP2D. The magnitude of the change in operating characteristics after including an intra-patient stage is largest for the 3 + 3 design, decreases for the BOIN and is smallest for the CRM.     

Designs foe phase i cancer clinical trials with differentiation of graded toxicity

For phase I cancer clinical trials, toxicity is a major concern. Commonly, toxicity is categorized to five levels of severity. In addition to the traditional standard dose-escaiation design, the Continual Reassessment Method (CRM) provides a promising alternative to estimate the maximum tolerated dose of a drug. However, in both standard design (STD) and CRM, the severity level of toxicity on grade 3/4 of a previous patient's response would not be a differentiated factor for the next dose level assignment. In this study, we extend the procedure incorporating the idea of unequal weights on the assessments of grade 3 and grade 4 toxicity in the dose escalation. The simulation results show that the proposed extended procedures by taking the impact of grade 4 toxicity into account, both for STD and CRM, reduce the chance of recommendation to the higher dose levels. Similar trends are observed for patient allocation to the higher levels. Additionally, for CRM which performs more accurately on the estimation of maximum tolerated dose (MTD), the proposed extended CRM maintains the same characteristic.     

Bayesian optimization design for dose-finding based on toxicity and efficacy outcomes in phase I/II clinical trials

In phase I trials, the main goal is to identify a maximum tolerated dose under an assumption of monotonicity in dose–response relationships. On the other hand, such monotonicity is no longer applied to biologic agents because a different mode of action from that of cytotoxic agents potentially draws unimodal or flat dose–efficacy curves. Therefore, biologic agents require an optimal dose that provides a sufficient efficacy rate under an acceptable toxicity rate instead of a maximum tolerated dose. Many trials incorporate both toxicity and efficacy data, and drugs with a variety of modes of actions are increasingly being developed; thus, optimal dose estimation designs have been receiving increased attention. Although numerous authors have introduced parametric model-based designs, it is not always appropriate to apply strong assumptions in dose–response relationships. We propose a new design based on a Bayesian optimization framework for identifying optimal doses for biologic agents in phase I/II trials. Our proposed design models dose–response relationships via nonparametric models utilizing a Gaussian process prior, and the uncertainty of estimates is considered in the dose selection process. We compared the operating characteristics of our proposed design against those of three other designs through simulation studies. These include an expansion of Bayesian optimal interval design, the parametric model-based EffTox design, and the isotonic design. In simulations, our proposed design performed well and provided results that were more stable than those from the other designs, in terms of the accuracy of optimal dose estimations and the percentage of correct recommendations.     

Logistic retainment interval dose exploration design for Phase I clinical trials of cytotoxic agents

Phase I studies of a cytotoxic agent often aim to identify the dose that provides an investigator specified target dose-limiting toxicity (DLT) probability. In practice, an initial cohort receives a dose with a putative low DLT probability, and subsequent dosing follows by consecutively deciding whether to retain the current dose, escalate to the adjacent higher dose, or de-escalate to the adjacent lower dose. This article proposes a Phase I design derived using a Bayesian decision-theoretic approach to this sequential decision-making process. The design consecutively chooses the action that minimizes posterior expected loss where the loss reflects the distance on the log-odds scale between the target and the DLT probability of the dose that would be given to the next cohort under the corresponding action. A logistic model is assumed for the log odds of a DLT at the current dose with a weakly informative t-distribution prior centered at the target. The key design parameters are the pre-specified odds ratios for the DLT probabilities at the adjacent higher and lower doses. Dosing rules may be pre-tabulated, as these only depend on the outcomes at the current dose, which greatly facilitates implementation. The recommended default version of the proposed design improves dose selection relative to many established designs across a variety of scenarios.     

TITE‐BOIN‐ET: Time‐to‐event Bayesian optimal interval design to accelerate dose‐finding based on both efficacy and toxicity outcomes

One of the primary purposes of an oncology dose‐finding trial is to identify an optimal dose (OD) that is both tolerable and has an indication of therapeutic benefit for subjects in subsequent clinical trials. In addition, it is quite important to accelerate early stage trials to shorten the entire period of drug development. However, it is often challenging to make adaptive decisions of dose escalation and de‐escalation in a timely manner because of the fast accrual rate, the difference of outcome evaluation periods for efficacy and toxicity and the late‐onset outcomes. To solve these issues, we propose the time‐to‐event Bayesian optimal interval design to accelerate dose‐finding based on cumulative and pending data of both efficacy and toxicity. The new design, named “TITE‐BOIN‐ET” design, is nonparametric and a model‐assisted design. Thus, it is robust, much simpler, and easier to implement in actual oncology dose‐finding trials compared with the model‐based approaches. These characteristics are quite useful from a practical point of view. A simulation study shows that the TITE‐BOIN‐ET design has advantages compared with the model‐based approaches in both the percentage of correct OD selection and the average number of patients allocated to the ODs across a variety of realistic settings. In addition, the TITE‐BOIN‐ET design significantly shortens the trial duration compared with the designs without sequential enrollment and therefore has the potential to accelerate early stage dose‐finding trials.     

An alternative phase II/III design for continuous endpoints

The success rate of drug development has been declined dramatically in recent years and the current paradigm of drug development is no longer functioning. It requires a major undertaking on breakthrough strategies and methodology for designs to minimize sample sizes and to shorten duration of the development. We propose an alternative phase II/III design based on continuous efficacy endpoints, which consists of two stages: a selection stage and a confirmation stage. For the selection stage, a randomized parallel design with several doses with a placebo group is employed for selection of doses. After the best dose is chosen, the patients of the selected dose group and placebo group continue to enter the confirmation stage. New patients will also be recruited and randomized to receive the selected dose or placebo group. The final analysis is performed with the cumulative data of patients from both stages. With the pre‐specified probabilities of rejecting the drug at each stage, sample sizes and critical values for both stages can be determined. As it is a single trial with controlling overall type I and II error rates, the proposed phase II/III adaptive design may not only reduce the sample size but also improve the success rate. An example illustrates the applications of the proposed phase II/III adaptive design. Copyright © 2010 John Wiley & Sons, Ltd.     

Three-level main-effects designs exploiting prior information about model uncertainty

To explore the projection efficiency of a design, Tsai, et al [2000. Projective three-level main effects designs robust to model uncertainty. Biometrika 87, 467–475] introduced the Q criterion to compare three-level main-effects designs for quantitative factors that allow the consideration of interactions in addition to main effects. In this paper, we extend their method and focus on the case in which experimenters have some prior knowledge, in advance of running the experiment, about the probabilities of effects being non-negligible. A criterion which incorporates experimenters’ prior beliefs about the importance of each effect is introduced to compare orthogonal, or nearly orthogonal, main effects designs with robustness to interactions as a secondary consideration. We show that this criterion, exploiting prior information about model uncertainty, can lead to more appropriate designs reflecting experimenters’ prior beliefs.     

A Bayesian phase I/II design to determine subgroup-specific optimal dose for immunotherapy sequentially combined with radiotherapy

Sequential administration of immunotherapy following radiotherapy (immunoRT) has attracted much attention in cancer research. Due to its unique feature that radiotherapy upregulates the expression of a predictive biomarker for immunotherapy, novel clinical trial designs are needed for immunoRT to identify patient subgroups and the optimal dose for each subgroup. In this article, we propose a Bayesian phase I/II design for immunotherapy administered after standard-dose radiotherapy for this purpose. We construct a latent subgroup membership variable and model it as a function of the baseline and pre-post radiotherapy change in the predictive biomarker measurements. Conditional on the latent subgroup membership of each patient, we jointly model the continuous immune response and the binary efficacy outcome using plateau models, and model toxicity using the equivalent toxicity score approach to account for toxicity grades. During the trial, based on accumulating data, we continuously update model estimates and adaptively randomize patients to admissible doses. Simulation studies and an illustrative trial application show that our design has good operating characteristics in terms of identifying both patient subgroups and the optimal dose for each subgroup.     

Application of Bayesian hierarchical models for phase I/II clinical trials in oncology

Treatment during cancer clinical trials sometimes involves the combination of multiple drugs. In addition, in recent years there has been a trend toward phase I/II trials in which a phase I and a phase II trial are combined into a single trial to accelerate drug development. Methods for the seamless combination of phases I and II parts are currently under investigation. In the phase II part, adaptive randomization on the basis of patient efficacy outcomes allocates more patients to the dose combinations considered to have higher efficacy. Patient toxicity outcomes are used for determining admissibility to each dose combination and are not used for selection of the dose combination itself. In cases where the objective is not to find the optimum dose combination solely for efficacy but regarding both toxicity and efficacy, the need exists to allocate patients to dose combinations with consideration of the balance of existing trade‐offs between toxicity and efficacy. We propose a Bayesian hierarchical model and an adaptive randomization with consideration for the relationship with toxicity and efficacy. Using the toxicity and efficacy outcomes of patients, the Bayesian hierarchical model is used to estimate the toxicity probability and efficacy probability in each of the dose combinations. Here, we use Bayesian moving‐reference adaptive randomization on the basis of desirability computed from the obtained estimator. Computer simulations suggest that the proposed method will likely recommend a higher percentage of target dose combinations than a previously proposed method.     

Optimal designs for the power logistic model

We investigate non-sequential designs for estimating model parameters in a power logistic model when the power is assumed to be approximately known and only the ranges for the other two parameters are available. The sensitivity of these designs to nominal values of all the three parameters are studied and our proposed optimal designs are shown to be reasonably robust under moderate deviation from the assumed model. An application to a toxicity experiment involving adult beetles is discussed, including the benefits of using an optimal design.     

On Robust and Efficient Designs for Risk Estimation in Epidemiological Studies

Abstract.  We consider the design problem for the estimation of several scalar measures suggested in the epidemiological literature for comparing the success rate in two samples. The designs considered so far in the literature are local in the sense that they depend on the unknown probabilities of success in the two groups and are not necessarily robust with respect to their misspecification. A maximin approach is proposed to obtain efficient and robust designs for the estimation of the relative risk, attributable risk and odds ratio, whenever a range for the success rates can be specified by the experimenter. It is demonstrated that the designs obtained by this method are usually more efficient than the commonly used uniform design, which allocates equal sample sizes to the two groups.     

Using adaptive line-transect sampling in airborne geophysics studies

We introduce a design that combines elements from distance and adaptive cluster sampling designs. We propose a line-transect sampling method, where the sample-strips are selected by unequal selection probabilities, detectability of clusters is assumed imperfect and detectability of sample units belonging to each detected cluster is assumed perfect. Here, the application of distance sampling is broaden to airborne geophysics studies. We introduce efficient estimators for this new sample design. Also, we conduct two simulation studies. One of the populations is Sar Cheshmeh Copper mine with data from an airborne geophysics study and the other is an artificial population.