arXiv subjects

Thomas Jaki

Publications and source records attributed to Thomas Jaki.

49 records · Page 3Linked to original sources

arXiv2020

Endpoints for randomized controlled clinical trials for COVID-19 treatments

Introduction: Endpoint choice for randomized controlled trials of treatments for COVID-19 is complex. A new disease brings many uncertainties, but trials must start rapidly. COVID-19 is heterogeneous, ranging from mild disease that improves within days to critical disease that can last weeks and can end in death. While improvement in mortality would provide unquestionable evidence about clinical significance of a treatment, sample sizes for a study evaluating mortality are large and may be impractical. Furthermore, patient states in between "cure" and "death" represent meaningful distinctions. Clinical severity scores have been proposed as an alternative. However, the appropriate summary measure for severity scores has been the subject of debate, particularly in relating to the uncertainty about the time-course of COVID-19. Outcomes measured at fixed time-points may risk missing the time of clinical benefit. An endpoint such as time-to-improvement (or recovery), avoids the timing problem. However, some have argued that power losses will result from reducing the ordinal scale to a binary state of "recovered" vs "not recovered." Methods: We evaluate statistical power for possible trial endpoints for COVID-19 treatment trials using simulation models and data from two recent COVID-19 treatment trials. Results: Power for fixed-time point methods depends heavily on the time selected for evaluation. Time-to-improvement (or recovery) analyses do not specify a time-point. Time-to-event approaches have reasonable statistical power, even when compared to a fixed time-point method evaluated at the optimal time. Discussion: Time-to-event analyses methods have advantages in the COVID-19 setting, unless the optimal time for evaluating treatment effect is known in advance. Even when the optimal time is known, a time-to-event approach may increase power for interim analyses.

stat.ME↗

arXiv2020

Efficient adaptive designs for clinical trials of interventions for COVID-19

The COVID-19 pandemic has led to an unprecedented response in terms of clinical research activity. An important part of this research has been focused on randomized controlled clinical trials to evaluate potential therapies for COVID-19. The results from this research need to be obtained as rapidly as possible. This presents a number of challenges associated with considerable uncertainty over the natural history of the disease and the number and characteristics of patients affected, and the emergence of new potential therapies. These challenges make adaptive designs for clinical trials a particularly attractive option. Such designs allow a trial to be modified on the basis of interim analysis data or stopped as soon as sufficiently strong evidence has been observed to answer the research question, without compromising the trial's scientific validity or integrity. In this paper we describe some of the adaptive design approaches that are available and discuss particular issues and challenges associated with their use in the pandemic setting. Our discussion is illustrated by details of four ongoing COVID-19 trials that have used adaptive designs.

q-bio.QM↗

arXiv2019

A Permutation Test for Assessing the Presence of Individual Differences in Treatment Effects

One size fits all approaches to medicine have become a thing of the past as the understanding of individual differences grows. The paper introduces a test for the presence of heterogeneity in treatment effects in a clinical trial. Heterogeneity is assessed on the basis of the predicted individual treatment effects (PITE) framework and a permutation test is utilized to establish if significant heterogeneity is present. We first use the novel test to show that heterogeneity in the effects of interventions exists in the Amyotrophic Lateral Sclerosis Clinical Trials. We then show, using two different predictive models (linear regression model and Random Forests) that the test has adequate type I error control. Next, we use the ALS data as the basis for simulations to demonstrate the ability of the permutation test to find heterogeneity in treatment effects as a function of both effect size and sample size. We find that the proposed test has good power to detected heterogeneity in treatment effects when the heterogeneity was due primarily to a single predictor, or when it was spread across the predictors. The predictive model, on the other hand is of secondary importance to detect heterogeneity. The non-parametric property of the permutation test can be applied with any predictive method and requires no additional assumptions to obtain PITEs.

stat.ME↗

arXiv2019

A Bayesian hierarchical model for bridging across patient subgroups in phase I clinical trials with animal data

Incorporating preclinical animal data, which can be regarded as a special kind of historical data, into phase I clinical trials can improve decision making when very little about human toxicity is known. In this paper, we develop a robust hierarchical modelling approach to leverage animal data into new phase I clinical trials, where we bridge across non-overlapping, potentially heterogeneous patient subgroups. Translation parameters are used to bring both historical and contemporary data onto a common dosing scale. This leads to feasible exchangeability assumptions that the parameter vectors, which underpin the dose-toxicity relationship per study, are assumed to be drawn from a common distribution. Moreover, human dose-toxicity parameter vectors are assumed to be exchangeable either with the standardised, animal study-specific parameter vectors, or between themselves. Possibility of non-exchangeability for each parameter vector is considered to avoid inferences for extreme subgroups being overly influenced by the other. We illustrate the proposed approach with several trial data examples, and evaluate the operating characteristics of our model compared with several alternatives in a simulation study. Numerical results show that our approach yields robust inferences in circumstances, where data from multiple sources are inconsistent and/or the bridging assumptions are incorrect.

stat.ME↗

arXiv2019

Estimation of treatment effects following a sequential trial of multiple treatments

When a clinical trial is subject to a series of interim analyses as a result of which the study may be terminated or modified, final frequentist analyses need to take account of the design used. Failure to do so may result in overstated levels of significance, biased effect estimates and confidence intervals with inadequate coverage probabilities. A wide variety of valid methods of frequentist analysis have been devised for sequential designs comparing a single experimental treatment with a single control treatment. It is less clear how to perform the final analysis of a sequential or adaptive design applied in a more complex setting, for example to determine which treatment or set of treatments amongst several candidates should be recommended. This paper has been motivated by consideration of a trial in which four treatments for sepsis are to be compared, with interim analyses allowing the dropping of treatments or termination of the trial to declare a single winner or to conclude that there is little difference between the treatments that remain. The approach taken is based on the method of Rao-Blackwellisation which enhances the accuracy of unbiased estimates available from the first interim analysis by taking their conditional expectations given final sufficient statistics. Analytic approaches to determine such expectations are difficult and specific to the details of the design, and instead "reverse simulations" are conducted to construct replicate realisations of the first interim analysis from the final test statistics. The method also provides approximate confidence intervals for the differences between treatments.

stat.ME↗

arXiv2019

Loss Functions in Restricted Parameter Spaces and Their Bayesian Applications

Squared error loss remains the most commonly used loss function for constructing a Bayes estimator of the parameter of interest. However, it can lead to sub-optimal solutions when a parameter is defined in a restricted space. It can also be an inappropriate choice in the context when an extreme overestimation and/or underestimation results in severe consequences and a more conservative estimator is preferred. We advocate a class of loss functions for parameters defined on restricted spaces which infinitely penalize boundary decisions like the squared error loss does on the real line. We also recall several properties of loss functions such as symmetry, convexity, and invariance. We propose generalizations of the squared error loss function for parameters defined on the positive real line and on an interval. We provide explicit solutions for corresponding Bayes estimators and discuss multivariate extensions. {Four} well-known Bayesian estimation problems are used to demonstrate inferential benefits the novel Bayes estimators can provide in the context of restricted estimation.

math.ST↗

arXiv2018

Improving Safety of the Continual Reassessment Method via a Modified Allocation Rule

This paper proposes a novel criterion for the allocation of patients in Phase~I dose-escalation clinical trials aiming to find the maximum tolerated dose (MTD). Conventionally, using a model-based approach the next patient is allocated to the dose with the toxicity estimate closest (in terms of the absolute or squared distance) to the maximum acceptable toxicity. This approach, however, ignores the uncertainty in point estimates and ethical concerns of assigning a lot of patients to overly toxic doses. Motivated by recent discussions in the theory of estimation in restricted parameter spaces, we propose a criterion which accounts for both of these issues. The criterion requires a specification of one additional parameter only which has a simple and intuitive interpretation. We incorporate the proposed criterion into the one-parameter Bayesian continual reassessment method (CRM) and show, using simulations, that it results in the same proportion of correct selections on average as the original design, but in fewer mean number of toxic responses. A comparison to other model-based dose-escalation designs demonstrates that the proposed design can result in either the same mean accuracy as alternatives but fewer number of toxic responses, or in a higher mean accuracy but the same number of toxic responses. We conclude that the new criterion makes the existing model-based designs more ethical without losing efficiency in the context of Phase I clinical trials.

stat.ME↗

arXiv2018

An information-theoretic Phase I/II design for molecularly targeted agents that does not require an assumption of monotonicity

For many years Phase I and Phase II clinical trials were conducted separately, but there was a recent shift to combine these Phases. While a variety of Phase~I/II model-based designs for cytotoxic agents were proposed in the literature, methods for molecularly targeted agents (TA) are just starting to develop. The main challenge of the TA setting is the unknown dose-efficacy relation that can have either an increasing, plateau or umbrella shape. To capture these, approaches with more parameters are needed to model the dose-efficacy relationship or, alternatively, more orderings of the dose-efficacy relationship are required to account for the uncertainty in the curve shape. As a result, designs for more complex clinical trials, for example, trials looking at schedules of a combination treatment involving TA, have not been extensively studied yet. We propose a novel regimen-finding design which is based on a derived efficacy-toxicity trade-off function. Due to its special properties, an accurate regimen selection can be achieved without any parametric or monotonicity assumptions. We illustrate how this design can be applied in the context of a complex combination-schedule clinical trial. We discuss practical and ethical issues such as coherence, delayed and missing efficacy responses, safety and futility constraints.

stat.ME↗

arXiv2018

An information-theoretic approach for selecting arms in clinical trials

The question of selecting the "best" amongst different choices is a common problem in statistics. In drug development, our motivating setting, the question becomes, for example: what is the dose that gives me a pre-specified risk of toxicity or which treatment gives the best response rate. Motivated by a recent development in the weighted information measures theory, we propose an experimental design based on a simple and intuitive criterion which governs arm selection in the experiment with multinomial outcomes. The criterion leads to accurate arm selection without any parametric or monotonicity assumption. The asymptotic properties of the design are studied for different allocation rules and the small sample size behaviour is evaluated in simulations in the context of Phase I and Phase II clinical trials with binary endpoints. We compare the proposed design to currently used alternatives and discuss its practical implementation.

math.ST↗

arXiv2018

A Benchmark for Dose Finding Studies with Continuous Outcomes

An important tool to evaluate the performance of any design is an optimal benchmark proposed by O'Quigley and others (2002, Biostatistics 3(1), 51-56) that provides an upper bound on the performance of a design under a given scenario. The original benchmark can be applied to dose finding studies with a binary endpoint only. However, there is a growing interest in dose finding studies involving continuous outcomes, but no benchmark for such studies has been developed. We show that the original benchmark and its extension by Cheung (2014, Biometrics 70(2), 389-397), when looked at from a different perspective, can be generalised to various settings with several discrete and continuous outcomes. We illustrate and compare the benchmark performance in the setting of a Phase I clinical trial with continuous toxicity endpoint and in the setting of a Phase I/II clinical trial with continuous efficacy outcome. We show that the proposed benchmark provides an accurate upper bound for model-based dose finding methods and serves as a powerful tool for evaluating designs.

math.ST↗

arXiv2018

A review of the deterministic and diffusion approximations for stochastic chemical reaction networks

This work reviews deterministic and diffusion approximations of the stochastic chemical reaction networks and explains their applications. We discuss the added value the diffusion approximation provides for systems with different phenomena, such as a deficiency and a bistability. It is advocated that the diffusion approximation can be considered as an alternative theoretical approach to study the reaction networks rather than a simulation shortcut. We discuss two examples in which the diffusion approximation is able to catch qualitative properties of reaction networks that the deterministic model misses. We provide an explicit construction of the original process and the diffusion approximation such that the distance between their trajectories is controlled and demonstrate this construction for the examples. We also discuss the limitations and potential directions of the developments.

math.PR↗

arXiv2014

Adaptive Survival Trials

Mid-study design modifications are becoming increasingly accepted in confirmatory clinical trials, so long as appropriate methods are applied such that error rates are controlled. It is therefore unfortunate that the important case of time-to-event endpoints is not easily handled by the standard theory. We analyze current methods that allow design modifications to be based on the full interim data, i.e., not only the observed event times but also secondary endpoint and safety data from patients who are yet to have an event. We show that the final test statistic may ignore a substantial subset of the observed event times. Since it is the data corresponding to the earliest recruited patients that is ignored, this neglect becomes egregious when there is specific interest in learning about long-term survival. An alternative test incorporating all event times is proposed, where a conservative assumption is made in order to guarantee type I error control. We examine the properties of our proposed approach using the example of a clinical trial comparing two cancer therapies.

stat.AP↗

arXiv2011

Recovering Direct Effects in Genetics: A Comparison

In genetics it is often of interest to discover single nucleotide polymorphisms (SNPs) that are directly related to a disease, rather than just being associated with it. Few methods exist, however, addressing this so-called `true sparsity recovery' issue. In a thorough simulation study, we show that for moderate or low correlation between predictors, lasso-based methods perform well at true sparsity recovery, despite not being specifically designed for this purpose. For large correlations, however, more specialised methods are needed. Stability selection and direct effect testing perform well in all situations, including when the correlation is large.

stat.AP↗