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Comment on” Estimands and their Estimators for Clinical Trials Impacted by the COVID-19 Pandemic: A Report from the NISS Ingram Olkin Forum Series on Unplanned Clinical Trial Disruptions” 评论“新冠肺炎大流行影响的临床试验的估计及其估计:NISS Ingram Olkin论坛系列关于计划外临床试验中断的报告”
IF 1.8 4区 医学 Q3 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2023-01-02 DOI: 10.1080/19466315.2022.2128405
S. Vansteelandt
I would like to thank the editor, Prof. Hamasaki, for the opportunity to comment on the thought-provoking work by the NISS working group on unplanned clinical trial disruptions (Van Lancker et al. 2022). The working group’s proposals focus on two basic problems relevant to clinical trials affected by the COVID19 pandemic. The first problem is that, due to the pandemic, the patient population may change systematically over the course of the trial. This raises questions over what is the relevant patient population for which the effect is of interest. The second problem, which receives the major focus in the paper, relates to problems of intercurrent events fueled by the pandemic. The solutions proposed by the working group are interesting and useful. In this commentary, I will nonetheless raise two conceptual shortcomings, which I will attempt to resolve by making more explicit use of methods from causal inference (as opposed to missing data analysis). First, the data collected in a randomized clinical trial are so precious that it is generally difficult to justify ignoring the data collected before or after the start of the pandemic. Those data will often still carry useful information about treatment efficacy, and should ideally be used. Second, whenever possible, analyses of randomized clinical trials should protect the null hypothesis of no treatment effect in the sense that rejection rates should be no larger than the nominal (5%) rate, even when the adopted assumptions fail. Intercurrent events 6 and 7 appear such that they will occur with equal rates in both arms of the trial. If this is so, then this suggests that standard analyses that target the treatment policy estimand, thus ignoring intercurrent events, will protect the null hypothesis of no treatment effect; indeed, the treatment policy estimand then reduces to the balanced estimand of Michiels et al. (2021), which expresses what the treatment effect had been had intercurrent events occurred at “equal rates” in both arms. In this light, analyses that invoke Missing At Random (MAR) assumptions must be taken with caution, as they may be biased whenever the MAR assumption fails. More importantly, analyses that explicitly combine biased and unbiased estimators, as in
我要感谢编辑滨崎步教授给我机会对NISS工作组关于计划外临床试验中断的发人深省的工作发表评论(Van Lancker等人,2022)。工作组的建议集中在与受新冠肺炎疫情影响的临床试验相关的两个基本问题上。第一个问题是,由于大流行,患者群体可能会在试验过程中发生系统性变化。这就提出了一个问题,即感兴趣的相关患者群体是什么。论文主要关注的第二个问题与疫情引发的并发事件有关。工作组提出的解决方案是令人感兴趣和有用的。然而,在这篇评论中,我将提出两个概念上的缺陷,我将试图通过更明确地使用因果推断的方法(而不是缺失的数据分析)来解决这两个缺陷。首先,随机临床试验中收集的数据非常宝贵,通常很难证明忽视在大流行开始之前或之后收集的数据是合理的。这些数据通常仍然会包含有关治疗效果的有用信息,并且应该在理想情况下使用。其次,在可能的情况下,随机临床试验的分析应保护无治疗效果的无效假设,即排斥率不应大于标称(5%),即使所采用的假设失败。并发事件6和7的出现使得它们在试验的两个阶段中的发生率相等。如果是这样的话,那么这表明针对治疗政策估计的标准分析,从而忽略并发事件,将保护没有治疗效果的无效假设;事实上,治疗政策的估计需求随后减少到Michiels等人的平衡估计需求。(2021),它表达了如果两组同时发生的事件以“相等的比率”发生,治疗效果是什么。有鉴于此,必须谨慎对待援引随机缺失(MAR)假设的分析,因为每当MAR假设失败时,这些分析可能会有偏差。更重要的是,明确结合有偏和无偏估计量的分析,如
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引用次数: 0
Estimands and their Estimators for Clinical Trials Impacted by the COVID-19 Pandemic: A Report from the NISS Ingram Olkin Forum Series on Unplanned Clinical Trial Disruptions 受COVID-19大流行影响的临床试验的估计及其估计:NISS英格拉姆奥尔金论坛系列关于计划外临床试验中断的报告
IF 1.8 4区 医学 Q3 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2023-01-02 DOI: 10.1080/19466315.2022.2094459
Kelly Van Lancker, S. Tarima, J. Bartlett, M. Bauer, Bharani Bharani-Dharan, F. Bretz, N. Flournoy, Hege Michiels, Camila Olarte Parra, J. L. Rosenberger, S. Cro
Abstract The COVID-19 pandemic continues to affect the conduct of clinical trials globally. Complications may arise from pandemic-related operational challenges such as site closures, travel limitations and interruptions to the supply chain for the investigational product, or from health-related challenges such as COVID-19 infections. Some of these complications lead to unforeseen intercurrent events in the sense that they affect either the interpretation or the existence of the measurements associated with the clinical question of interest. In this article, we demonstrate how the ICH E9(R1) Addendum on estimands and sensitivity analyses provides a rigorous basis to discuss potential pandemic-related trial disruptions and to embed these disruptions in the context of study objectives and design elements. We introduce several hypothetical estimand strategies and review various causal inference and missing data methods, as well as a statistical method that combines unbiased and possibly biased estimators for estimation. To illustrate, we describe the features of a stylized trial, and how it may have been impacted by the pandemic. This stylized trial will then be revisited by discussing the changes to the estimand and the estimator to account for pandemic disruptions. Finally, we outline considerations for designing future trials in the context of unforeseen disruptions.
摘要新冠肺炎大流行继续影响全球临床试验的进行。并发症可能源于与流行病相关的操作挑战,如研究产品的现场关闭、旅行限制和供应链中断,或与健康相关的挑战,如新冠肺炎感染。其中一些并发症会导致不可预见的并发事件,因为它们会影响与感兴趣的临床问题相关的测量的解释或存在。在这篇文章中,我们展示了ICH E9(R1)关于估计和敏感性分析的附录如何为讨论潜在的与大流行相关的试验中断提供了严格的基础,并将这些中断嵌入研究目标和设计元素的背景中。我们介绍了几种假设的估计策略,并回顾了各种因果推断和缺失数据方法,以及一种结合无偏和可能有偏估计量进行估计的统计方法。为了说明这一点,我们描述了程式化试验的特点,以及它可能如何受到疫情的影响。然后,将通过讨论估计需求和估计量的变化来重新审视这一程式化试验,以解释疫情的干扰。最后,我们概述了在不可预见的中断情况下设计未来试验的考虑因素。
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引用次数: 7
Good Data Science Practice: Moving toward a Code of Practice for Drug Development (Rejoinder) 良好数据科学实践:迈向药物开发实践规范(复辩状)
IF 1.8 4区 医学 Q3 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2023-01-02 DOI: 10.1080/19466315.2022.2128402
Mark Baillie, Conor Moloney, Carsten Philipp Mueller, Jonas Dorn, J. Branson, D. Ohlssen
Fang and He ask why we focus on exploratory (cite “[...] 26 times exploratory [...] only 3 times confirmatory [/.]”) over confirmatory activities and if as a consequence our data science definition is limited in scope. They also ask if the definition of data science should be more specific, with a focus on treatment effectiveness: “exploratory activities are insufficient for the purpose of establishing the existence and estimating the magnitude of treatment effects, which is confirmatory in nature.”
方和何问,为什么我们把重点放在探索性活动上(引用“[…]26次探索性[…]只有3次验证性[/.]”),而不是验证性活动,因此,我们的数据科学定义范围是否有限。他们还询问,数据科学的定义是否应该更具体,重点关注治疗效果:“探索性活动不足以确定治疗效果的存在性和估计治疗效果的大小,这在本质上是证实性的。”
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引用次数: 0
Editor’s Note: Special Section on a Collection of Articles on Opportunities and Challenges in Utilizing Real-World Data for Clinical Trials and Medical Product Development 编者注:关于利用真实世界数据进行临床试验和医疗产品开发的机遇和挑战的文章集合的特别部分
IF 1.8 4区 医学 Q3 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2023-01-02 DOI: 10.1080/19466315.2022.2162291
T. Hamasaki
There have been increasing discussions on how real-world data (RWD) and real-world evidence (RWE) can play a role in health care decisions, particularly in medical product regulation, where RWD are the data relating to patient health status and/or the delivery of health care routinely collected from a variety of sources (e.g., observational studies, electronic health records, product, and disease registries, etc.), and RWE is the clinical evidence regarding the usage and potential benefits or risks of a medical product derived from analysis of RWD (Food and Drug Administration (FDA) 2017). Unitizing external data sources in the design and analysis of clinical trials or medical product development is not a new idea. In assessing clinical trial feasibility of a medical product, external data sources have often been used to find new hypotheses/findings, characterizing relevant patient populations and subpopulations, understanding unmet need, identifying important assumptions about the impact of potential eligibility criteria on trial feasibility. At the protocol development of the clinical trials, they have been used to estimate the expected effect size of the medical products, to calculate the sample size, and to support patient recruitment, and during the trial conduct, they might be used to change or modify the trial protocol or designs, or sometimes to stop the trial. At the end of the development of the medical product, in general, comprehensive integrated analysis of the efficacy and safety has been conducted, including other sources of information relevant to efficacy and safety of the product. Furthermore, in Japan, there is a very unique regulatory decision-making framework for evaluating off-label use of unapproved medical products, so called “Public KnowledgeBased Applications” (“Kochi Shinsei” in Japanese) (Ministry of Health and Welfare (MHLW) 1980). A sponsor is able to submit an application without conducting (additional) clinical trials, if efficacy and safety for a new indication of the medical product are recognized to be well known in the medical and pharmacological field through publications. This framework is a great practice of regulatory decision-making based on RWD/RWE. What is happening right now? What is different from current practice? Due to the latest advanced technologies, it is much easier to gather and store huge amounts of health-related data in “real time.” It is expected that RWD/RWE can be used into
关于真实世界数据(RWD)和真实世界证据(RWE)如何在医疗保健决策中发挥作用,特别是在医疗产品监管中,RWD是从各种来源(例如,观察性研究、电子健康记录、产品和疾病登记等)常规收集的与患者健康状况和/或医疗保健提供有关的数据,RWE是关于RWD分析得出的医疗产品的使用和潜在益处或风险的临床证据(美国食品药品监督管理局(FDA)2017)。在临床试验或医疗产品开发的设计和分析中统一外部数据源并不是一个新想法。在评估医疗产品的临床试验可行性时,经常使用外部数据源来寻找新的假设/发现,表征相关患者群体和亚群体,了解未满足的需求,确定关于潜在资格标准对试验可行性影响的重要假设。在临床试验的方案制定过程中,它们被用于估计医疗产品的预期效果大小,计算样本量,并支持患者招募,在试验进行过程中,可能被用于更改或修改试验方案或设计,有时甚至停止试验。在医疗产品开发结束时,通常会对疗效和安全性进行全面的综合分析,包括与产品疗效和安全相关的其他信息来源。此外,在日本,有一个非常独特的监管决策框架来评估未经批准的医疗产品的标签外使用,即所谓的“基于公共知识的应用”(日语为“Kochi Shinsei”)(卫生福利部(MHLW)1980)。如果通过出版物确认医疗产品新适应症的疗效和安全性在医学和药理学领域众所周知,赞助商可以在不进行(额外)临床试验的情况下提交申请。该框架是基于RWD/RWE的监管决策的一个伟大实践。现在发生了什么?与目前的做法有什么不同?由于最新的先进技术,可以更容易地“实时”收集和存储大量与健康相关的数据。预计RWD/RWE可以用于
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引用次数: 0
Comment on “Estimands and Their Estimators for Clinical Trials Impacted by the COVID-19 Pandemic: A Report from the NISS Ingram Olkin Forum Series on Unplanned Clinical Trial Disruptions” 对“受COVID-19大流行影响的临床试验的估计及其估计量:NISS英格拉姆奥尔金论坛系列关于计划外临床试验中断的报告”的评论
IF 1.8 4区 医学 Q3 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2023-01-02 DOI: 10.1080/19466315.2022.2151507
M. Akacha, Tianmeng Lyu
We
我们
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引用次数: 1
Comparative Effectiveness Research using Bayesian Adaptive Designs for Rare Diseases: Response Adaptive Randomization Reusing Participants. 利用贝叶斯自适应设计进行罕见病比较效益研究:响应自适应随机化重复使用参与者。
IF 1.8 4区 医学 Q3 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2023-01-01 Epub Date: 2021-08-31 DOI: 10.1080/19466315.2021.1961854
Fengming Tang, Byron J Gajewski

Slow accrual rate is a major challenge in clinical trials for rare diseases and is identified as the most frequent reason for clinical trials to fail. This challenge is amplified in comparative effectiveness research where multiple treatments are compared to identify the best treatment. Novel efficient clinical trial designs are in urgent need in these areas. Our proposed response adaptive randomization (RAR) reusing participants trial design mimics the real-world clinical practice that allows patients to switch treatments when desired outcome is not achieved. The proposed design increases efficiency by two strategies: 1) Allowing participants to switch treatments so that each participant can have more than one observation and hence it is possible to control for participant specific variability to increase statistical power; and 2) Utilizing RAR to allocate more participants to the promising arms such that ethical and efficient studies will be achieved. Extensive simulations were conducted and showed that, compared with trials where each participant receives one treatment, the proposed participants reusing RAR design can achieve comparable power with a smaller sample size and a shorter trial duration, especially when the accrual rate is low. The efficiency gain decreases as the accrual rate increases.

累积率低是罕见病临床试验的一大挑战,也是临床试验失败的最常见原因。在比较有效性研究中,这一挑战更为严峻,因为在这种研究中,需要对多种治疗方法进行比较,以确定最佳治疗方法。这些领域迫切需要新的高效临床试验设计。我们提出的反应自适应随机化(RAR)重复使用参与者试验设计模拟了现实世界中的临床实践,允许患者在未达到预期结果时更换治疗方法。拟议的设计通过两种策略提高效率:1)允许参与者转换治疗方法,这样每个参与者可以有不止一次的观察机会,从而有可能控制参与者的特定变异性,提高统计功率;以及 2)利用 RAR 将更多参与者分配到有希望的臂中,从而实现道德和高效的研究。我们进行了大量的模拟试验,结果表明,与每个参与者接受一种治疗的试验相比,拟议的参与者重复使用 RAR 设计能以较小的样本量和较短的试验持续时间达到相当的功率,尤其是在应计率较低的情况下。效率增益随着应计率的增加而降低。
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引用次数: 0
Power and Sample Size Calculations for the Restricted Mean Time Analysis of Prioritized Composite Endpoints. 优先复合端点限制平均时间分析的功率和样本量计算。
IF 1.8 4区 医学 Q3 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2023-01-01 DOI: 10.1080/19466315.2022.2110936
Lu Mao

As a new way of reporting treatment effect, the restricted mean time in favor (RMT-IF) of treatment measures the net average time the treated have had a less serious outcome than the untreated over a specified time window. With multiple outcomes of differing severity, this offers a more interpretable and data-efficient alternative to the prototypical restricted mean (event-free) survival time. To facilitate its adoption in actual trials, we develop simple approaches to power and sample size calculations and implement them in user-friendly R programs. In doing so we model the bivariate outcomes of death and a nonfatal event using a Gumbel-Hougaard copula with component-wise proportional hazards structures, under which the RMT-IF estimand is derived in closed form. In a standard set-up for censoring, the variance of the nonparametric effect-size estimator is simplified and computed via a hybrid of numerical and Monte Carlo integrations, allowing us to compute the power and sample size as functions of component-wise hazard ratios. Simulation studies show that these formulas provide accurate approximations in realistic settings. To illustrate our methods, we consider designing a new trial to evaluate treatment effect on the composite outcomes of death and cancer relapse in lymph node-positive breast cancer patients, with baseline parameters calculated from a previous study.

作为一种报告治疗效果的新方法,治疗的限制平均有利时间(RMT-IF)衡量的是在指定的时间窗口内,治疗组比未治疗组预后较轻的净平均时间。对于不同严重程度的多种结果,这为典型的受限平均(无事件)生存时间提供了更可解释和数据效率更高的替代方案。为了便于在实际试验中采用,我们开发了简单的方法来计算功率和样本量,并在用户友好的R程序中实现它们。在这样做的过程中,我们使用Gumbel-Hougaard copula和成分比例风险结构来模拟死亡和非致命事件的双变量结果,在这种情况下,RMT-IF估计以封闭形式导出。在审查的标准设置中,非参数效应大小估计量的方差通过数值和蒙特卡罗积分的混合进行简化和计算,使我们能够计算功率和样本量作为成分风险比的函数。仿真研究表明,这些公式在实际情况下提供了准确的近似值。为了说明我们的方法,我们考虑设计一项新的试验来评估治疗对淋巴结阳性乳腺癌患者死亡和癌症复发的复合结局的影响,基线参数从先前的研究中计算出来。
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引用次数: 2
Hypothetical Estimands in Clinical Trials: A Unification of Causal Inference and Missing Data Methods. 临床试验中的假设估计:因果推断和缺失数据方法的统一。
IF 1.8 4区 医学 Q3 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2023-01-01 DOI: 10.1080/19466315.2022.2081599
Camila Olarte Parra, Rhian M Daniel, Jonathan W Bartlett

The ICH E9 addendum introduces the term intercurrent event to refer to events that happen after treatment initiation and that can either preclude observation of the outcome of interest or affect its interpretation. It proposes five strategies for handling intercurrent events to form an estimand but does not suggest statistical methods for estimation. In this article we focus on the hypothetical strategy, where the treatment effect is defined under the hypothetical scenario in which the intercurrent event is prevented. For its estimation, we consider causal inference and missing data methods. We establish that certain "causal inference estimators" are identical to certain "missing data estimators." These links may help those familiar with one set of methods but not the other. Moreover, using potential outcome notation allows us to state more clearly the assumptions on which missing data methods rely to estimate hypothetical estimands. This helps to indicate whether estimating a hypothetical estimand is reasonable, and what data should be used in the analysis. We show that hypothetical estimands can be estimated by exploiting data after intercurrent event occurrence, which is typically not used. Supplementary materials for this article are available online.

ICH E9附录引入了“并发事件”一词,指的是在治疗开始后发生的事件,这些事件可能会妨碍对目标结果的观察或影响其解释。它提出了五种策略来处理并发事件以形成估计,但没有提出估计的统计方法。在本文中,我们关注的是假设策略,其中治疗效果是在假设的情况下定义的,在这种情况下,并发事件被阻止了。对于其估计,我们考虑了因果推理和缺失数据方法。我们建立了某些“因果推理估计量”与某些“缺失数据估计量”相同。这些链接可能对那些熟悉其中一组方法而不熟悉另一组方法的人有所帮助。此外,使用潜在结果表示法使我们能够更清楚地陈述缺失数据方法所依赖的假设,以估计假设的估计。这有助于表明估计假设估计是否合理,以及应该在分析中使用哪些数据。我们表明,假设的估计可以通过利用交互事件发生后的数据来估计,这通常是不使用的。本文的补充材料可在网上获得。
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引用次数: 11
A flexible analytical framework for reference-based imputation, delta adjustment and tipping-point stress-testing 一个灵活的分析框架,用于基于参考的imputation, delta调整和临界点压力测试
IF 1.8 4区 医学 Q3 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2022-12-08 DOI: 10.1080/19466315.2022.2151506
Alberto García-Hernandez, T. Pérez, M. Pardo, D. Rizopoulos
Abstract This article addresses the challenge of implementing the treatment policy strategy when subjects are not followed up after treatment discontinuation. This problem can be addressed using reference-based imputation, delta adjustment, and tipping-point analysis. Our new framework tackles this problem analytically. We characterize the process that measures the response regardless of drug discontinuation, Z(t), using its association with two observable processes: time to drug dropout , and the variable representing the response in a hypothetical world without drug discontinuation Y(t). We define the intervention discontinuation effect (IDE) as the unobservable process that quantifies the difference between Y(t) and Z(t) after . We express various well-known imputation rules as forms of the IDE. We model Y using mixed models and with the Royston-Parmar model. We build estimators for the marginal mean of Z given the estimated parameters for Y and T . We demonstrate that this simple estimator building suits all studied rules and provide guidance to extend this methodology. With the proposed framework, we can analytically resolve a broad range of imputation rules and have right-censored treatment discontinuation. This methodology is more efficient and computationally faster than multiple imputation and, unlike Rubin’s variance estimator, presents no standard error over-estimation.
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引用次数: 1
A closer look at the kernels generated by the decision and regression tree ensembles 仔细查看由决策树和回归树集成生成的核
IF 1.8 4区 医学 Q3 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2022-12-08 DOI: 10.1080/19466315.2022.2150680
Dai Feng, R. Baumgartner
Abstract Tree ensembles can be interpreted as implicit kernel generators, where the ensuing proximity matrix represents the data-driven tree ensemble kernel. Focus of our work is the utility of tree based ensembles as kernel generators that (in conjunction with a regularized linear model) enable kernel learning. We elucidate the performance of the tree based random forest (RF) and gradient boosted tree (GBT) kernels in a comprehensive simulation study comprising of continuous and binary targets. We show that for continuous targets (regression), this kernel learning approach is competitive to the respective tree ensemble in higher dimensional scenarios, particularly in cases with larger number of noisy features. For the binary target (classification), the tree ensemble based kernels and their respective ensembles exhibit comparable performance. We provide the results from several real life datasets for regression and classification relevant for biopharmaceutical and biomedical applications, that are in line with the simulations to show how these insights may be leveraged in practice. We discuss general applicability and extensions of the tree ensemble based kernels for survival targets and interpretable landmarking in classification and regression. Finally, we outline future research for kernel learning due to feature space partitionings.
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引用次数: 1
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Statistics in Biopharmaceutical Research
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