arXiv subjects

Thomas Jaki

Publications and source records attributed to Thomas Jaki.

At least 37 records · Page 2Linked to original sources

arXiv2024

Bayesian Model Averaging for Partial Ordering Continual Reassessment Methods

Phase I clinical trials are essential to bringing novel therapies from chemical development to widespread use. Traditional approaches to dose-finding in Phase I trials, such as the '3+3' method and the Continual Reassessment Method (CRM), provide a principled approach for escalating across dose levels. However, these methods lack the ability to incorporate uncertainty regarding the dose-toxicity ordering as found in combination drug trials. Under this setting, dose-levels vary across multiple drugs simultaneously, leading to multiple possible dose-toxicity orderings. The Partial Ordering CRM (POCRM) extends to these settings by allowing for multiple dose-toxicity orderings. In this work, it is shown that the POCRM is vulnerable to 'estimation incoherency' whereby toxicity estimates shift in an illogical way, threatening patient safety and undermining clinician trust in dose-finding models. To this end, the Bayesian model averaged POCRM (BMA-POCRM) is proposed. BMA-POCRM uses Bayesian model averaging to take into account all possible orderings simultaneously, reducing the frequency of estimation incoherencies. The effectiveness of BMA-POCRM in drug combination settings is demonstrated through a specific instance of estimate incoherency of POCRM and simulation studies. The results highlight the improved safety, accuracy and reduced occurrence of estimate incoherency in trials applying the BMA-POCRM relative to the POCRM model.

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arXiv2024

Adaptive enrichment trial designs using joint modeling of longitudinal and time-to-event data

Adaptive enrichment allows for pre-defined patient subgroups of interest to be investigated throughout the course of a clinical trial. Many trials which measure a long-term time-to-event endpoint often also routinely collect repeated measures on biomarkers which may be predictive of the primary endpoint. Although these data may not be leveraged directly to support subgroup selection decisions and early stopping decisions, we aim to make greater use of these data to increase efficiency and improve interim decision making. In this work, we present a joint model for longitudinal and time-to-event data and two methods for creating standardised statistics based on this joint model. We can use the estimates to define enrichment rules and efficacy and futility early stopping rules for a flexible efficient clinical trial with possible enrichment. Under this framework, we show asymptotically that the familywise error rate is protected in the strong sense. To assess the results, we consider a trial for the treatment of metastatic breast cancer where repeated ctDNA measurements are available and the subgroup criteria is defined by patients' ER and HER2 status. Using simulation, we show that incorporating biomarker information leads to accurate subgroup identification and increases in power.

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arXiv2023

Design of platform trials with a change in the control treatment arm

Platform trials are a more efficient way of testing multiple treatments compared to running separate trials. In this paper we consider platform trials where, if a treatment is found to be superior to the control, it will become the new standard of care (and the control in the platform). The remaining treatments are then tested against this new control. In such a setting, one can either keep the information on both the new standard of care and the other active treatments before the control is changed or one could discard this information when testing for benefit of the remaining treatments. We will show analytically and numerically that retaining the information collected before the change in control can be detrimental to the power of the study. Specifically, we consider the overall power, the probability that the active treatment with the greatest treatment effect is found during the trial. We also consider the conditional power of the active treatments, the probability a given treatment can be found superior against the current control. We prove when, in a multi-arm multi-stage trial where no arms are added, retaining the information is detrimental to both overall and conditional power of the remaining treatments. This loss of power is studied for a motivating example. We then discuss the effect on platform trials in which arms are added later. On the basis of these observations we discuss different aspects to consider when deciding whether to run a continuous platform trial or whether one may be better running a new trial.

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arXiv2023

A preplanned multi-stage platform trial for discovering multiple superior treatments with control of FWER and power

There is a growing interest in the implementation of platform trials, which provide the flexibility to incorporate new treatment arms during the trial and the ability to halt treatments early based on lack of benefit or observed superiority. In such trials, it can be important to ensure that error rates are controlled. This paper introduces a multi-stage design that enables the addition of new treatment arms, at any point, in a pre-planned manner within a platform trial, while still maintaining control over the family-wise error rate. This paper focuses on finding the required sample size to achieve a desired level of statistical power when treatments are continued to be tested even after a superior treatment has already been found. This may be of interest if there are other sponsors treatments which are also superior to the current control or multiple doses being tested. The calculations to determine the expected sample size is given. A motivating trial is presented in which the sample size of different configurations is studied. Additionally the approach is compared to running multiple separate trials and it is shown that in many scenarios if family wise error rate control is needed there may not be benefit in using a platform trial when comparing the sample size of the trial.

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arXiv2022

Point estimation for adaptive trial designs I: a methodological review

Recent FDA guidance on adaptive clinical trial designs defines bias as "a systematic tendency for the estimate of treatment effect to deviate from its true value", and states that it is desirable to obtain and report estimates of treatment effects that reduce or remove this bias. The conventional end-of-trial point estimates of the treatment effects are prone to bias in many adaptive designs, because they do not take into account the potential and realised trial adaptations. While much of the methodological developments on adaptive designs have tended to focus on control of type I error rates and power considerations, in contrast the question of biased estimation has received relatively less attention. This paper is the first in a two-part series that studies the issue of potential bias in point estimation for adaptive trials. Part I provides a comprehensive review of the methods to remove or reduce the potential bias in point estimation of treatment effects for adaptive designs, while part II illustrates how to implement these in practice and proposes a set of guidelines for trial statisticians. The methods reviewed in this paper can be broadly classified into unbiased and bias-reduced estimation, and we also provide a classification of estimators by the type of adaptive design. We compare the proposed methods, highlight available software and code, and discuss potential methodological gaps in the literature.

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arXiv2022

Point estimation for adaptive trial designs II: practical considerations and guidance

In adaptive clinical trials, the conventional end-of-trial point estimate of a treatment effect is prone to bias, that is, a systematic tendency to deviate from its true value. As stated in recent FDA guidance on adaptive designs, it is desirable to report estimates of treatment effects that reduce or remove this bias. However, it may be unclear which of the available estimators are preferable, and their use remains rare in practice. This paper is the second in a two-part series that studies the issue of bias in point estimation for adaptive trials. Part I provided a methodological review of approaches to remove or reduce the potential bias in point estimation for adaptive designs. In part II, we discuss how bias can affect standard estimators and assess the negative impact this can have. We review current practice for reporting point estimates and illustrate the computation of different estimators using a real adaptive trial example (including code), which we use as a basis for a simulation study. We show that while on average the values of these estimators can be similar, for a particular trial realisation they can give noticeably different values for the estimated treatment effect. Finally, we propose guidelines for researchers around the choice of estimators and the reporting of estimates following an adaptive design. The issue of bias should be considered throughout the whole lifecycle of an adaptive design, with the estimation strategy pre-specified in the statistical analysis plan. When available, unbiased or bias-reduced estimates are to be preferred.

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arXiv2022

Bayesian sample size determination in basket trials borrowing information between subsets

Basket trials are increasingly used for the simultaneous evaluation of a new treatment in various patient subgroups under one overarching protocol. We propose a Bayesian approach to sample size determination in basket trials that permit borrowing of information between commensurate subsets. Specifically, we consider a randomised basket trial design where patients are randomly assigned to the new treatment or a control within each trial subset (`subtrial' for short). Closed-form sample size formulae are derived to ensure each subtrial has a specified chance of correctly deciding whether the new treatment is superior to or not better than the control by some clinically relevant difference. Given pre-specified levels of pairwise (in)commensurability, the subtrial sample sizes are solved simultaneously. The proposed Bayesian approach resembles the frequentist formulation of the problem in yielding comparable sample sizes for circumstances of no borrowing. When borrowing is enabled between commensurate subtrials, a considerably smaller trial sample size is required compared to the widely implemented approach of no borrowing. We illustrate the use of our sample size formulae with two examples based on real basket trials. A comprehensive simulation study further shows that the proposed methodology can maintain the true positive and false positive rates at desired levels.

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arXiv2022

Backfilling Cohorts in Phase I Dose-Escalation Studies

The use of `backfilling', assigning additional patients to doses deemed safe, in phase I dose-escalation studies has been used in practice to collect additional information on the safety profile, pharmacokinetics and activity of a drug. These additional patients help ensure that the Maximum Tolerated Dose (MTD) is reliably estimated and give additional information in order to determine the recommended phase II dose (RP2D). In this paper, we study the effect of employing backfilling in a phase I trial on the estimation of the MTD and the duration of the study. We consider the situation where only one cycle of follow-up is used for escalation as well as the case where there may be delayed onset toxicities. We find that, over a range of scenarios, there is an increase in the proportion of correct selections and a notable reduction in the trial duration at the cost of more patients required in the study.

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arXiv2022

Dose Finding Studies for Therapies with Late-Onset Safety and Efficacy Outcomes

In Phase I/II dose-finding trials, the objective is to find the Optimal Biological Dose (OBD), a dose that is both safe and efficacious that maximises some optimality criterion based on safety and efficacy. This is further complicated when the investigated treatment consists of multiple cycles of therapy, and both toxicity and efficacy outcomes may occur at any point throughout the follow up of multiple cycles. In this work we present the Joint TITE-CRM, a model-based design for late onset toxicities and efficacies based on the well-known TITE-CRM. It is found to be superior to both currently available alternative designs that account for late onset bivariate outcomes; a model-assisted method and a bivariate survival design, as well as being both intuitive and computationally feasible.

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arXiv2022

Online error control for platform trials

Platform trials evaluate multiple experimental treatments under a single master protocol, where new treatment arms are added to the trial over time. Given the multiple treatment comparisons, there is the potential for inflation of the overall type I error rate, which is complicated by the fact that the hypotheses are tested at different times and are not all necessarily pre-specified. Online error control methodology provides a possible solution to the problem of multiplicity for platform trials where a relatively large number of hypotheses are expected to be tested over time. In the online testing framework, hypotheses are tested in a sequential manner, where at each time-step an analyst decides whether to reject the current null hypothesis without knowledge of future tests but based solely on past decisions. Methodology has recently been developed for online control of the false discovery rate as well as the familywise error rate (FWER). In this paper, we describe how to apply online error control to the platform trial setting, present extensive simulation results, and give some recommendations for the use of this new methodology in practice. We show that the algorithms for online error rate control can have a substantially lower FWER than uncorrected testing, while still achieving noticeable gains in power when compared with the use of a Bonferroni procedure. We also illustrate how online error control would have impacted a currently ongoing platform trial.

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arXiv2021

A multi-arm multi-stage platform design that allows pre-planned addition of arms while still controlling the family-wise error

There is growing interest in platform trials that allow for adding of new treatment arms as the trial progresses as well as being able to stop treatments part way through the trial for either lack of benefit/futility or for superiority. In some situations, platform trials need to guarantee that error rates are controlled. This paper presents a multi-stage design that allows additional arms to be added in a platform trial in a pre-planned fashion, while still controlling the family wise error rate. A method is given to compute the sample size required to achieve a desired level of power and we show how the distribution of the sample size and the expected sample size can be found. A motivating trial is presented which focuses on two settings, with the first being a set number of stages per active treatment arm and the second being a set total number of stages, with treatments that are added later getting fewer stages. Through this example we show that the proposed method results in a smaller sample size while still controlling the errors compared to running multiple separate trials.

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arXiv2021

Adding experimental treatment arms to Multi-Arm Multi-Stage platform trials in progress

Multi-Arm Multi-Stage (MAMS) platform trials are an efficient tool for the comparison of several treatments. Suppose we wish to add a treatment to a trial already in progress, to access the benefits of a MAMS design. How should this be done? The MAMS framework requires pre-planned options for how the trial proceeds at each stage in order to control the family-wise error rate. Thus, it is difficult to make both planned and unplanned design modifications. The conditional error approach is a tool that allows unplanned design modifications while maintaining the overall error rate. In this work, we use the conditional error approach to allow adding new arms to a MAMS trial in progress. We demonstrate the principles of incorporating additional hypotheses into the testing structure. Using this framework, we show how to update the testing procedure for a MAMS trial in progress to incorporate additional treatment arms. Simulations illustrate the possible operating characteristics of such procedures using a fixed rule for how and when the design modification is made.

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arXiv2021

A Comparison of Model-Free Phase I Dose Escalation Designs for Dual-Agent Combination Therapies

It is increasingly common for therapies in oncology to be given in combination. In some cases, patients can benefit from the interaction between two drugs, although often at the risk of higher toxicity. A large number of designs to conduct phase I trials in this setting are available, where the objective is to select the maximum tolerated dose combination (MTC). Recently, a number of model-free (also called model-assisted) designs have provoked interest, providing several practical advantages over the more conventional approaches of rule-based or model-based designs. In this paper, we demonstrate a novel calibration procedure for model-free designs to determine their most desirable parameters. Under the calibration procedure, we compare the behaviour of model-free designs to a model-based approach in a comprehensive simulation study, covering a number of clinically plausible scenarios. It is found that model-free designs are competitive with the model-based design in terms of the proportion of correct selections of the MTC. However, there are a number of scenarios in which model-free designs offer a safer alternative. This is also illustrated in the application of the designs to a case study using data from a phase I oncology trial.

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arXiv2021

Dose Finding Studies for Therapies with Late-Onset Toxicities: A Comparison Study of Designs

An objective of phase I dose-finding trials is to find the maximum tolerated dose; the dose with a particular risk of toxicity. Frequently, this risk is assessed across the first cycle of therapy. However, in oncology, a course of treatment frequently consists of multiple cycles of therapy. In many cases, the overall risk of toxicity for a given treatment is not fully encapsulated by observations from the first cycle, and hence it is advantageous to include toxicity outcomes from later cycles in phase I trials. Extending the follow up period in a trial naturally extends the total length of the trial which is undesirable. We present a comparison of eight methods that incorporate late onset toxicities whilst not extensively extending the trial length. We conduct simulation studies over a number of scenarios and in two settings; the first setting with minimal stopping rules and the second setting with a full set of standard stopping rules expected in such a dose finding study. We find that the model-based approaches in general outperform the model-assisted approaches, with an Interval Censored approach and a modified version of the Time-to-Event Continual Reassessment Method giving the most promising overall performance in terms of correct selections and trial length. Further recommendations are made for the implementation of such methods.

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arXiv2020

A Novel Statistical Test for Treatment Differences in Clinical Trials using a Response Adaptive Forward Looking Gittins Index Rule

The most common objective for response adaptive clinical trials is to seek to ensure that patients within a trial have a high chance of receiving the best treatment available by altering the chance of allocation on the basis of accumulating data. Approaches which yield good patient benefit properties suffer from low power from a frequentist perspective when testing for a treatment difference at the end of the study due to the high imbalance in treatment allocations. In this work we develop an alternative pairwise test for treatment difference on the basis of allocation probabilities of the covariate-adjusted response-adaptive randomization with forward looking Gittins index rule (CARA-FLGI). The performance of the novel test is evaluated in simulations for two-armed studies and then its applications to multi-armed studies is illustrated. The proposed test has markedly improved power over the traditional Fisher exact test when this class of non-myopic response adaptation is used. We also find that the test's power is close to the power of a Fisher exact test under equal randomization.

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arXiv2020

Bayesian sample size determination using commensurate priors to leverage pre-experimental data

This paper develops Bayesian sample size formulae for experiments comparing two groups. We assume the experimental data will be analysed in the Bayesian framework, where pre-experimental information from multiple sources can be represented into robust priors. In particular, such robust priors account for preliminary belief about the pairwise commensurability between parameters that underpin the historical and new experiments, to permit flexible borrowing of information. Averaged over the probability space of the new experimental data, appropriate sample sizes are found according to criteria that control certain aspects of the posterior distribution, such as the coverage probability or length of a defined density region. Our Bayesian methodology can be applied to circumstances where the common variance in the new experiment is known or unknown. Exact solutions are available based on most of the criteria considered for Bayesian sample size determination, while a search procedure is described in cases for which there are no closed-form expressions. We illustrate the application of our Bayesian sample size formulae in the setting of designing a clinical trial. Hypothetical data examples, motivated by a rare-disease trial with elicitation of expert prior opinion, and a comprehensive performance evaluation of the proposed methodology are presented.

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arXiv2020

A Seamless Phase I/II Platform Design with a Time-To-Event Efficacy Endpoint for Potential COVID-19 Therapies

In the search for effective treatments for COVID-19, initial emphasis has been on re-purposed treatments. To maximise the chances of finding successful treatments, novel treatments that have been developed for this disease in particular, are needed. In this manuscript we describe and evaluate the statistical design of the AGILE platform, an adaptive randomized seamless Phase I/II trial platform that seeks to quickly establish a safe range of doses and investigates treatments for potential efficacy using a Bayesian sequential trial design. Both single agent and combination treatments are considered. We find that the design can identify potential treatments that are safe and efficacious reliably with small to moderate sample sizes.

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arXiv2020

Adding flexibility to clinical trial designs: an example-based guide to the practical use of adaptive designs

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.

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