José L Jiménez, Isobel Barrott, Francesca Gasperoni, Dominic Magirr
{"title":"Visualizing hypothesis tests in survival analysis under anticipated delayed effects.","authors":"José L Jiménez, Isobel Barrott, Francesca Gasperoni, Dominic Magirr","doi":"10.1002/pst.2393","DOIUrl":"10.1002/pst.2393","url":null,"abstract":"<p><p>What can be considered an appropriate statistical method for the primary analysis of a randomized clinical trial (RCT) with a time-to-event endpoint when we anticipate non-proportional hazards owing to a delayed effect? This question has been the subject of much recent debate. The standard approach is a log-rank test and/or a Cox proportional hazards model. Alternative methods have been explored in the statistical literature, such as weighted log-rank tests and tests based on the Restricted Mean Survival Time (RMST). While weighted log-rank tests can achieve high power compared to the standard log-rank test, some choices of weights may lead to type-I error inflation under particular conditions. In addition, they are not linked to a mathematically unambiguous summary measure. Test statistics based on the RMST, on the other hand, allow one to investigate the average difference between two survival curves up to a pre-specified time point <math><mrow><mi>τ</mi></mrow> </math> -a mathematically unambiguous summary measure. However, by emphasizing differences prior to <math><mrow><mi>τ</mi></mrow> </math> , such test statistics may not fully capture the benefit of a new treatment in terms of long-term survival. In this article, we introduce a graphical approach for direct comparison of weighted log-rank tests and tests based on the RMST. This new perspective allows a more informed choice of the analysis method, going beyond power and type I error comparison.</p>","PeriodicalId":19934,"journal":{"name":"Pharmaceutical Statistics","volume":" ","pages":"870-883"},"PeriodicalIF":1.3,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140859909","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Using an early outcome as the sole source of information of interim decisions regarding treatment effect on a long-term endpoint: The non-Gaussian case.","authors":"Leandro Garcia Barrado, Tomasz Burzykowski","doi":"10.1002/pst.2398","DOIUrl":"10.1002/pst.2398","url":null,"abstract":"<p><p>In randomized clinical trials that use a long-term efficacy endpoint, the follow-up time necessary to observe the endpoint may be substantial. In such trials, an attractive option is to consider an interim analysis based solely on an early outcome that could be used to expedite the evaluation of treatment's efficacy. Garcia Barrado et al. (Pharm Stat. 2022; 21: 209-219) developed a methodology that allows introducing such an early interim analysis for the case when both the early outcome and the long-term endpoint are normally-distributed, continuous variables. We extend the methodology to any combination of the early-outcome and long-term-endpoint types. As an example, we consider the case of a binary outcome and a time-to-event endpoint. We further evaluate the potential gain in operating characteristics (power, expected trial duration, and expected sample size) of a trial with such an interim analysis in function of the properties of the early outcome as a surrogate for the long-term endpoint.</p>","PeriodicalId":19934,"journal":{"name":"Pharmaceutical Statistics","volume":" ","pages":"928-938"},"PeriodicalIF":1.3,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141261163","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A model-assisted design for partially or completely ordered groups.","authors":"Connor Celum, Mark Conaway","doi":"10.1002/pst.2396","DOIUrl":"10.1002/pst.2396","url":null,"abstract":"<p><p>This paper proposes a trial design for locating group-specific doses when groups are partially or completely ordered by dose sensitivity. Previous trial designs for partially ordered groups are model-based, whereas the proposed method is model-assisted, providing clinicians with a design that is simpler. The proposed method performs similarly to model-based methods, providing simplicity without losing accuracy. Additionally, to the best of our knowledge, the proposed method is the first paper on dose-finding for partially ordered groups with convergence results. To generalize the proposed method, a framework is introduced that allows partial orders to be transferred to a grid format with a known ordering across rows but an unknown ordering within rows.</p>","PeriodicalId":19934,"journal":{"name":"Pharmaceutical Statistics","volume":" ","pages":"906-927"},"PeriodicalIF":1.3,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11602961/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141071600","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Variable Duration Trial as an Alternative Design for Continuous Endpoints.","authors":"Jitendra Ganju, Julie Guoguang Ma","doi":"10.1002/pst.2418","DOIUrl":"10.1002/pst.2418","url":null,"abstract":"<p><p>Clinical trials with continuous primary endpoints typically measure outcomes at baseline, at a fixed timepoint (denoted T <sub>min</sub>), and at intermediate timepoints. The analysis is commonly performed using the mixed model repeated measures method. It is sometimes expected that the effect size will be larger with follow-up longer than T <sub>min</sub>. But extending the follow-up for all patients delays trial completion. We propose an alternative trial design and analysis method that potentially increases statistical power without extending the trial duration or increasing the sample size. We propose following the last enrolled patient until T <sub>min</sub>, with earlier enrollees having variable follow-up durations up to a maximum of T <sub>max</sub>. The sample size at T <sub>max</sub> will be smaller than at T <sub>min</sub>, and due to staggered enrollment, data missing at T <sub>max</sub> will be missing completely at random. For analysis, we propose an alpha-adjusted procedure based on the smaller of the p values at T <sub>min</sub> and T <sub>max</sub>, termed <math> <semantics><mrow><mtext>minP</mtext></mrow> </semantics> </math> . This approach can provide the highest power when the powers at T <sub>min</sub> and T <sub>max</sub> are similar. If the power at T <sub>min</sub> and T <sub>max</sub> differ significantly, the power of <math> <semantics><mrow><mtext>minP</mtext></mrow> </semantics> </math> is modestly reduced compared with the larger of the two powers. Rare disease trials, due to the limited size of the patient population, may benefit the most with this design.</p>","PeriodicalId":19934,"journal":{"name":"Pharmaceutical Statistics","volume":" ","pages":"1059-1064"},"PeriodicalIF":1.3,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141591009","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Sample Size Estimation Using a Partially Clustered Frailty Model for Biomarker-Strategy Designs With Multiple Treatments.","authors":"Derek Dinart, Virginie Rondeau, Carine Bellera","doi":"10.1002/pst.2407","DOIUrl":"10.1002/pst.2407","url":null,"abstract":"<p><p>Biomarker-guided therapy is a growing area of research in medicine. To optimize the use of biomarkers, several study designs including the biomarker-strategy design (BSD) have been proposed. Unlike traditional designs, the emphasis here is on comparing treatment strategies and not on treatment molecules as such. Patients are assigned to either a biomarker-based strategy (BBS) arm, in which biomarker-positive patients receive an experimental treatment that targets the identified biomarker, or a non-biomarker-based strategy (NBBS) arm, in which patients receive treatment regardless of their biomarker status. We proposed a simulation method based on a partially clustered frailty model (PCFM) as well as an extension of Freidlin formula to estimate the sample size required for BSD with multiple targeted treatments. The sample size was mainly influenced by the heterogeneity of treatment effect, the proportion of biomarker-negative patients, and the randomization ratio. The PCFM is well suited for the data structure and offers an alternative to traditional methodologies.</p>","PeriodicalId":19934,"journal":{"name":"Pharmaceutical Statistics","volume":" ","pages":"1084-1094"},"PeriodicalIF":1.3,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141627249","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yun Wang, Wenda Tu, William Koh, James Travis, Robert Abugov, Kiya Hamilton, Mengjie Zheng, Roberto Crackel, Pablo Bonangelino, Mark Rothmann
{"title":"Bayesian Hierarchical Models for Subgroup Analysis.","authors":"Yun Wang, Wenda Tu, William Koh, James Travis, Robert Abugov, Kiya Hamilton, Mengjie Zheng, Roberto Crackel, Pablo Bonangelino, Mark Rothmann","doi":"10.1002/pst.2424","DOIUrl":"10.1002/pst.2424","url":null,"abstract":"<p><p>In conventional subgroup analyses, subgroup treatment effects are estimated using data from each subgroup separately without considering data from other subgroups in the same study. The subgroup treatment effects estimated this way may be heterogenous with high variability due to small sample sizes in some subgroups and much different from the treatment effect in the overall population. A Bayesian hierarchical model (BHM) can be used to derive more precise, and less heterogenous estimates of subgroup treatment effects that are closer to the treatment effect in the overall population. BHM assumes exchangeability in treatment effect across subgroups after adjusting for effect modifiers and other relevant covariates. In this article, we will discuss the technical details for applying one-way and multi-way BHM using summary-level statistics, and patient-level data for subgroup analysis. Four case studies based on four new drug applications are used to illustrate the application of these models in subgroup analyses for continuous, dichotomous, time-to-event, and count endpoints.</p>","PeriodicalId":19934,"journal":{"name":"Pharmaceutical Statistics","volume":" ","pages":"1065-1083"},"PeriodicalIF":1.3,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141620632","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yulia Dyachkova, Cornelia Dunger-Baldauf, Nathalie Barbier, Jenny Devenport, Stefan Franzén, Gbenga Kazeem, Thomas Künzel, Pierre Mancini, Giacomo Mordenti, Knut Richert, Antonia Ridolfi, Daniel Saure
{"title":"Do You Want to Stay Single? Considerations on Single-Arm Trials in Drug Development and the Postregulatory Space.","authors":"Yulia Dyachkova, Cornelia Dunger-Baldauf, Nathalie Barbier, Jenny Devenport, Stefan Franzén, Gbenga Kazeem, Thomas Künzel, Pierre Mancini, Giacomo Mordenti, Knut Richert, Antonia Ridolfi, Daniel Saure","doi":"10.1002/pst.2412","DOIUrl":"10.1002/pst.2412","url":null,"abstract":"<p><p>Single-arm trials (SATs), while not preferred, remain in use throughout the drug development cycle. They may be accepted by regulators in particular contexts (e.g., in oncology or rare diseases) when the potential effects of new treatments are very large and placebo treatment is unethical. However, in the postregulatory space, SATs are common, and perhaps even more poorly suited to address the questions of interest. In this manuscript, we review regulatory and HTA positions on SATs; challenges posed by SATs to address research questions beyond regulators, evolving statistical methods to provide context for SATs, case studies where SATs could and could not address questions of interest, and communication strategies to influence decision making and optimize study design to address evidence needs.</p>","PeriodicalId":19934,"journal":{"name":"Pharmaceutical Statistics","volume":" ","pages":"1206-1217"},"PeriodicalIF":1.3,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141458675","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Handling Partially Observed Trial Data After Treatment Withdrawal: Introducing Retrieved Dropout Reference-Base Centred Multiple Imputation.","authors":"Suzie Cro, James H Roger, James R Carpenter","doi":"10.1002/pst.2416","DOIUrl":"10.1002/pst.2416","url":null,"abstract":"<p><p>The ICH E9(R1) Addendum (International Council for Harmonization 2019) suggests treatment-policy as one of several strategies for addressing intercurrent events such as treatment withdrawal when defining an estimand. This strategy requires the monitoring of patients and collection of primary outcome data following termination of randomised treatment. However, when patients withdraw from a study early before completion this creates true missing data complicating the analysis. One possible way forward uses multiple imputation to replace the missing data based on a model for outcome on- and off-treatment prior to study withdrawal, often referred to as retrieved dropout multiple imputation. This article introduces a novel approach to parameterising this imputation model so that those parameters which may be difficult to estimate have mildly informative Bayesian priors applied during the imputation stage. A core reference-based model is combined with a retrieved dropout compliance model, using both on- and off-treatment data, to form an extended model for the purposes of imputation. This alleviates the problem of specifying a complex set of analysis rules to accommodate situations where parameters which influence the estimated value are not estimable, or are poorly estimated leading to unrealistically large standard errors in the resulting analysis. We refer to this new approach as retrieved dropout reference-base centred multiple imputation.</p>","PeriodicalId":19934,"journal":{"name":"Pharmaceutical Statistics","volume":" ","pages":"1095-1116"},"PeriodicalIF":1.3,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11602953/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141627325","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Exploring Stratification Strategies for Population- Versus Randomization-Based Inference.","authors":"Marco Novelli, William F Rosenberger","doi":"10.1002/pst.2419","DOIUrl":"10.1002/pst.2419","url":null,"abstract":"<p><p>Stratification on important variables is a common practice in clinical trials, since ensuring cosmetic balance on known baseline covariates is often deemed to be a crucial requirement for the credibility of the experimental results. However, the actual benefits of stratification are still debated in the literature. Other authors have shown that it does not improve efficiency in large samples and improves it only negligibly in smaller samples. This paper investigates different subgroup analysis strategies, with a particular focus on the potential benefits in terms of inferential precision of prestratification versus both poststratification and post hoc regression adjustment. For each of these approaches, the pros and cons of population-based versus randomization-based inference are discussed. The effects of the presence of a treatment-by-covariate interaction and the variability in the patient responses are also taken into account. Our results show that, in general, prestratifying does not provide substantial benefit. On the contrary, it may be deleterious, in particular for randomization-based procedures in the presence of a chronological bias. Even when there is treatment-by-covariate interaction, prestratification may backfire by considerably reducing the inferential precision.</p>","PeriodicalId":19934,"journal":{"name":"Pharmaceutical Statistics","volume":" ","pages":"1045-1058"},"PeriodicalIF":1.3,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11602877/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141580473","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Efficient Study Design and Analysis of Longitudinal Dose-Response Data Using Fractional Polynomials.","authors":"Benjamin F Hartley, Dave Lunn, Adrian P Mander","doi":"10.1002/pst.2425","DOIUrl":"10.1002/pst.2425","url":null,"abstract":"<p><p>Correctly characterising the dose-response relationship and taking the correct dose forward for further study is a critical part of the drug development process. We use optimal design theory to compare different designs and show that using longitudinal data from all available timepoints in a continuous-time dose-response model can substantially increase the efficiency of estimation of the dose-response compared to a single timepoint model. We give theoretical results to calculate the efficiency gains for a large class of these models. For example, a linearly growing Emax dose-response in a population with a between/within-patient variance ratio ranging from 0.1 to 1 measured at six visits can be estimated with between 1.43 and 2.22 times relative efficiency gain, or equivalently, with 30% to a 55% reduced sample size, compared to a single model of the final timepoint. Fractional polynomials are a flexible way to incorporate data from repeated measurements, increasing precision without imposing strong constraints. Longitudinal dose-response models using two fractional polynomial terms are robust to mis-specification of the true longitudinal process while maintaining, often large, efficiency gains. These models have applications for characterising the dose-response at interim or final analyses.</p>","PeriodicalId":19934,"journal":{"name":"Pharmaceutical Statistics","volume":" ","pages":"1128-1143"},"PeriodicalIF":1.3,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141788779","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}