BiostatisticsPub Date : 2023-12-15DOI: 10.1093/biostatistics/kxac040
Marta Bofill Roig, Guadalupe Gómez Melis, Martin Posch, Franz Koenig
{"title":"Adaptive clinical trial designs with blinded selection of binary composite endpoints and sample size reassessment.","authors":"Marta Bofill Roig, Guadalupe Gómez Melis, Martin Posch, Franz Koenig","doi":"10.1093/biostatistics/kxac040","DOIUrl":"10.1093/biostatistics/kxac040","url":null,"abstract":"<p><p>For randomized clinical trials where a single, primary, binary endpoint would require unfeasibly large sample sizes, composite endpoints (CEs) are widely chosen as the primary endpoint. Despite being commonly used, CEs entail challenges in designing and interpreting results. Given that the components may be of different relevance and have different effect sizes, the choice of components must be made carefully. Especially, sample size calculations for composite binary endpoints depend not only on the anticipated effect sizes and event probabilities of the composite components but also on the correlation between them. However, information on the correlation between endpoints is usually not reported in the literature which can be an obstacle for designing future sound trials. We consider two-arm randomized controlled trials with a primary composite binary endpoint and an endpoint that consists only of the clinically more important component of the CE. We propose a trial design that allows an adaptive modification of the primary endpoint based on blinded information obtained at an interim analysis. Especially, we consider a decision rule to select between a CE and its most relevant component as primary endpoint. The decision rule chooses the endpoint with the lower estimated required sample size. Additionally, the sample size is reassessed using the estimated event probabilities and correlation, and the expected effect sizes of the composite components. We investigate the statistical power and significance level under the proposed design through simulations. We show that the adaptive design is equally or more powerful than designs without adaptive modification on the primary endpoint. Besides, the targeted power is achieved even if the correlation is misspecified at the planning stage while maintaining the type 1 error. All the computations are implemented in R and illustrated by means of a peritoneal dialysis trial.</p>","PeriodicalId":55357,"journal":{"name":"Biostatistics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2023-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10939415/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33479811","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
BiostatisticsPub Date : 2023-12-15DOI: 10.1093/biostatistics/kxac044
Quentin Le Coënt, Catherine Legrand, Virginie Rondeau
{"title":"Time-to-event surrogate endpoint validation using mediation analysis and meta-analytic data.","authors":"Quentin Le Coënt, Catherine Legrand, Virginie Rondeau","doi":"10.1093/biostatistics/kxac044","DOIUrl":"10.1093/biostatistics/kxac044","url":null,"abstract":"<p><p>With the ongoing development of treatments and the resulting increase in survival in oncology, clinical trials based on endpoints such as overall survival may require long follow-up periods to observe sufficient events and ensure adequate statistical power. This increase in follow-up time may compromise the feasibility of the study. The use of surrogate endpoints instead of final endpoints may be attractive for these studies. However, before a surrogate can be used in a clinical trial, it must be statistically validated. In this article, we propose an approach to validate surrogates when both the surrogate and final endpoints are censored event times. This approach is developed for meta-analytic data and uses a mediation analysis to decompose the total effect of the treatment on the final endpoint as a direct effect and an indirect effect through the surrogate. The meta-analytic nature of the data is accounted for in a joint model with random effects at the trial level. The proportion of the indirect effect over the total effect of the treatment on the final endpoint can be computed from the parameters of the model and used as a measure of surrogacy. We applied this method to investigate time-to-relapse as a surrogate endpoint for overall survival in resectable gastric cancer.</p>","PeriodicalId":55357,"journal":{"name":"Biostatistics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2023-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40498295","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
BiostatisticsPub Date : 2023-12-15DOI: 10.1093/biostatistics/kxac038
Joseph Antonelli, Ander Wilson, Brent A Coull
{"title":"Multiple exposure distributed lag models with variable selection.","authors":"Joseph Antonelli, Ander Wilson, Brent A Coull","doi":"10.1093/biostatistics/kxac038","DOIUrl":"10.1093/biostatistics/kxac038","url":null,"abstract":"<p><p>Distributed lag models are useful in environmental epidemiology as they allow the user to investigate critical windows of exposure, defined as the time periods during which exposure to a pollutant adversely affects health outcomes. Recent studies have focused on estimating the health effects of a large number of environmental exposures, or an environmental mixture, on health outcomes. In such settings, it is important to understand which environmental exposures affect a particular outcome, while acknowledging the possibility that different exposures have different critical windows. Further, in studies of environmental mixtures, it is important to identify interactions among exposures and to account for the fact that this interaction may occur between two exposures having different critical windows. Exposure to one exposure early in time could cause an individual to be more or less susceptible to another exposure later in time. We propose a Bayesian model to estimate the temporal effects of a large number of exposures on an outcome. We use spike-and-slab priors and semiparametric distributed lag curves to identify important exposures and exposure interactions and discuss extensions with improved power to detect harmful exposures. We then apply these methods to estimate the effects of exposure to multiple air pollutants during pregnancy on birthweight from vital records in Colorado.</p>","PeriodicalId":55357,"journal":{"name":"Biostatistics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2023-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10724118/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33448924","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
BiostatisticsPub Date : 2023-12-15DOI: 10.1093/biostatistics/kxac053
Michael C Sachs, Erin E Gabriel, Alessio Crippa, Michael J Daniels
{"title":"Flexible evaluation of surrogacy in platform studies.","authors":"Michael C Sachs, Erin E Gabriel, Alessio Crippa, Michael J Daniels","doi":"10.1093/biostatistics/kxac053","DOIUrl":"10.1093/biostatistics/kxac053","url":null,"abstract":"<p><p>Trial-level surrogates are useful tools for improving the speed and cost effectiveness of trials but surrogates that have not been properly evaluated can cause misleading results. The evaluation procedure is often contextual and depends on the type of trial setting. There have been many proposed methods for trial-level surrogate evaluation, but none, to our knowledge, for the specific setting of platform studies. As platform studies are becoming more popular, methods for surrogate evaluation using them are needed. These studies also offer a rich data resource for surrogate evaluation that would not normally be possible. However, they also offer a set of statistical issues including heterogeneity of the study population, treatments, implementation, and even potentially the quality of the surrogate. We propose the use of a hierarchical Bayesian semiparametric model for the evaluation of potential surrogates using nonparametric priors for the distribution of true effects based on Dirichlet process mixtures. The motivation for this approach is to flexibly model relationships between the treatment effect on the surrogate and the treatment effect on the outcome and also to identify potential clusters with differential surrogate value in a data-driven manner so that treatment effects on the surrogate can be used to reliably predict treatment effects on the clinical outcome. In simulations, we find that our proposed method is superior to a simple, but fairly standard, hierarchical Bayesian method. We demonstrate how our method can be used in a simulated illustrative example (based on the ProBio trial), in which we are able to identify clusters where the surrogate is, and is not useful. We plan to apply our method to the ProBio trial, once it is completed.</p>","PeriodicalId":55357,"journal":{"name":"Biostatistics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2023-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10939396/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10843733","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
BiostatisticsPub Date : 2023-12-15DOI: 10.1093/biostatistics/kxad002
Xiao Wu, Kate R Weinberger, Gregory A Wellenius, Francesca Dominici, Danielle Braun
{"title":"Assessing the causal effects of a stochastic intervention in time series data: are heat alerts effective in preventing deaths and hospitalizations?","authors":"Xiao Wu, Kate R Weinberger, Gregory A Wellenius, Francesca Dominici, Danielle Braun","doi":"10.1093/biostatistics/kxad002","DOIUrl":"10.1093/biostatistics/kxad002","url":null,"abstract":"<p><p>The methodological development of this article is motivated by the need to address the following scientific question: does the issuance of heat alerts prevent adverse health effects? Our goal is to address this question within a causal inference framework in the context of time series data. A key challenge is that causal inference methods require the overlap assumption to hold: each unit (i.e., a day) must have a positive probability of receiving the treatment (i.e., issuing a heat alert on that day). In our motivating example, the overlap assumption is often violated: the probability of issuing a heat alert on a cooler day is near zero. To overcome this challenge, we propose a stochastic intervention for time series data which is implemented via an incremental time-varying propensity score (ItvPS). The ItvPS intervention is executed by multiplying the probability of issuing a heat alert on day $t$-conditional on past information up to day $t$-by an odds ratio $delta_t$. First, we introduce a new class of causal estimands, which relies on the ItvPS intervention. We provide theoretical results to show that these causal estimands can be identified and estimated under a weaker version of the overlap assumption. Second, we propose nonparametric estimators based on the ItvPS and derive an upper bound for the variances of these estimators. Third, we extend this framework to multisite time series using a spatial meta-analysis approach. Fourth, we show that the proposed estimators perform well in terms of bias and root mean squared error via simulations. Finally, we apply our proposed approach to estimate the causal effects of increasing the probability of issuing heat alerts on each warm-season day in reducing deaths and hospitalizations among Medicare enrollees in 2837 US counties.</p>","PeriodicalId":55357,"journal":{"name":"Biostatistics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2023-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11032723/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10816841","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
BiostatisticsPub Date : 2023-12-15DOI: 10.1093/biostatistics/kxac041
Daniel Gomon, Hein Putter, Rob G H H Nelissen, Stéphanie Van Der Pas
{"title":"CGR-CUSUM: a continuous time generalized rapid response cumulative sum chart.","authors":"Daniel Gomon, Hein Putter, Rob G H H Nelissen, Stéphanie Van Der Pas","doi":"10.1093/biostatistics/kxac041","DOIUrl":"10.1093/biostatistics/kxac041","url":null,"abstract":"<p><p>Rapidly detecting problems in the quality of care is of utmost importance for the well-being of patients. Without proper inspection schemes, such problems can go undetected for years. Cumulative sum (CUSUM) charts have proven to be useful for quality control, yet available methodology for survival outcomes is limited. The few available continuous time inspection charts usually require the researcher to specify an expected increase in the failure rate in advance, thereby requiring prior knowledge about the problem at hand. Misspecifying parameters can lead to false positive alerts and large detection delays. To solve this problem, we take a more general approach to derive the new Continuous time Generalized Rapid response CUSUM (CGR-CUSUM) chart. We find an expression for the approximate average run length (average time to detection) and illustrate the possible gain in detection speed by using the CGR-CUSUM over other commonly used monitoring schemes on a real-life data set from the Dutch Arthroplasty Register as well as in simulation studies. Besides the inspection of medical procedures, the CGR-CUSUM can also be used for other real-time inspection schemes such as industrial production lines and quality control of services.</p>","PeriodicalId":55357,"journal":{"name":"Biostatistics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2023-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10939399/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40372006","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
BiostatisticsPub Date : 2023-12-15DOI: 10.1093/biostatistics/kxac034
Saskia Comess, Howard H Chang, Joshua L Warren
{"title":"A Bayesian framework for incorporating exposure uncertainty into health analyses with application to air pollution and stillbirth.","authors":"Saskia Comess, Howard H Chang, Joshua L Warren","doi":"10.1093/biostatistics/kxac034","DOIUrl":"10.1093/biostatistics/kxac034","url":null,"abstract":"<p><p>Studies of the relationships between environmental exposures and adverse health outcomes often rely on a two-stage statistical modeling approach, where exposure is modeled/predicted in the first stage and used as input to a separately fit health outcome analysis in the second stage. Uncertainty in these predictions is frequently ignored, or accounted for in an overly simplistic manner when estimating the associations of interest. Working in the Bayesian setting, we propose a flexible kernel density estimation (KDE) approach for fully utilizing posterior output from the first stage modeling/prediction to make accurate inference on the association between exposure and health in the second stage, derive the full conditional distributions needed for efficient model fitting, detail its connections with existing approaches, and compare its performance through simulation. Our KDE approach is shown to generally have improved performance across several settings and model comparison metrics. Using competing approaches, we investigate the association between lagged daily ambient fine particulate matter levels and stillbirth counts in New Jersey (2011-2015), observing an increase in risk with elevated exposure 3 days prior to delivery. The newly developed methods are available in the R package KDExp.</p>","PeriodicalId":55357,"journal":{"name":"Biostatistics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2023-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10724312/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10841925","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
BiostatisticsPub Date : 2023-12-15DOI: 10.1093/biostatistics/kxac039
Aliasghar Tarkhan, Noah Simon
{"title":"An online framework for survival analysis: reframing Cox proportional hazards model for large data sets and neural networks.","authors":"Aliasghar Tarkhan, Noah Simon","doi":"10.1093/biostatistics/kxac039","DOIUrl":"10.1093/biostatistics/kxac039","url":null,"abstract":"<p><p>In many biomedical applications, outcome is measured as a \"time-to-event\" (e.g., disease progression or death). To assess the connection between features of a patient and this outcome, it is common to assume a proportional hazards model and fit a proportional hazards regression (or Cox regression). To fit this model, a log-concave objective function known as the \"partial likelihood\" is maximized. For moderate-sized data sets, an efficient Newton-Raphson algorithm that leverages the structure of the objective function can be employed. However, in large data sets this approach has two issues: (i) The computational tricks that leverage structure can also lead to computational instability; (ii) The objective function does not naturally decouple: Thus, if the data set does not fit in memory, the model can be computationally expensive to fit. This additionally means that the objective is not directly amenable to stochastic gradient-based optimization methods. To overcome these issues, we propose a simple, new framing of proportional hazards regression: This results in an objective function that is amenable to stochastic gradient descent. We show that this simple modification allows us to efficiently fit survival models with very large data sets. This also facilitates training complex, for example, neural-network-based, models with survival data.</p>","PeriodicalId":55357,"journal":{"name":"Biostatistics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2023-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10724274/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47211901","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
BiostatisticsPub Date : 2023-12-15DOI: 10.1093/biostatistics/kxac032
Danni Tu, Bridget Mahony, Tyler M Moore, Maxwell A Bertolero, Aaron F Alexander-Bloch, Ruben Gur, Dani S Bassett, Theodore D Satterthwaite, Armin Raznahan, Russell T Shinohara
{"title":"CoCoA: conditional correlation models with association size.","authors":"Danni Tu, Bridget Mahony, Tyler M Moore, Maxwell A Bertolero, Aaron F Alexander-Bloch, Ruben Gur, Dani S Bassett, Theodore D Satterthwaite, Armin Raznahan, Russell T Shinohara","doi":"10.1093/biostatistics/kxac032","DOIUrl":"10.1093/biostatistics/kxac032","url":null,"abstract":"<p><p>Many scientific questions can be formulated as hypotheses about conditional correlations. For instance, in tests of cognitive and physical performance, the trade-off between speed and accuracy motivates study of the two variables together. A natural question is whether speed-accuracy coupling depends on other variables, such as sustained attention. Classical regression techniques, which posit models in terms of covariates and outcomes, are insufficient to investigate the effect of a third variable on the symmetric relationship between speed and accuracy. In response, we propose a conditional correlation model with association size, a likelihood-based statistical framework to estimate the conditional correlation between speed and accuracy as a function of additional variables. We propose novel measures of the association size, which are analogous to effect sizes on the correlation scale while adjusting for confound variables. In simulation studies, we compare likelihood-based estimators of conditional correlation to semiparametric estimators adapted from genomic studies and find that the former achieves lower bias and variance under both ideal settings and model assumption misspecification. Using neurocognitive data from the Philadelphia Neurodevelopmental Cohort, we demonstrate that greater sustained attention is associated with stronger speed-accuracy coupling in a complex reasoning task while controlling for age. By highlighting conditional correlations as the outcome of interest, our model provides complementary insights to traditional regression modeling and partitioned correlation analyses.</p>","PeriodicalId":55357,"journal":{"name":"Biostatistics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2023-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10724258/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9993653","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
BiostatisticsPub Date : 2023-10-18DOI: 10.1093/biostatistics/kxac025
Jiawei Xu, Matthew A Psioda, Joseph G Ibrahim
{"title":"Bayesian design of clinical trials using joint models for recurrent and terminating events.","authors":"Jiawei Xu, Matthew A Psioda, Joseph G Ibrahim","doi":"10.1093/biostatistics/kxac025","DOIUrl":"10.1093/biostatistics/kxac025","url":null,"abstract":"<p><p>Joint models for recurrent event and terminating event data are increasingly used for the analysis of clinical trials. However, few methods have been proposed for designing clinical trials using these models. In this article, we develop a Bayesian clinical trial design methodology focused on evaluating the effect of an investigational product (IP) on both recurrent event and terminating event processes considered as multiple primary endpoints, using a multifrailty joint model. Dependence between the recurrent and terminating event processes is accounted for using a shared frailty. Inferences for the multiple primary outcomes are based on posterior model probabilities corresponding to mutually exclusive hypotheses regarding the benefit of IP with respect to the recurrent and terminating event processes. We propose an approach for sample size determination to ensure the trial design has a high power and a well-controlled type I error rate, with both operating characteristics defined from a Bayesian perspective. We also consider a generalization of the proposed parametric model that uses a nonparametric mixture of Dirichlet processes to model the frailty distributions and compare its performance to the proposed approach. We demonstrate the methodology by designing a colorectal cancer clinical trial with a goal of demonstrating that the IP causes a favorable effect on at least one of the two outcomes but no harm on either.</p>","PeriodicalId":55357,"journal":{"name":"Biostatistics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2023-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40605886","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}