Biometrical Journal最新文献_第10页

Robust incorporation of historical information with known type I error rate inflation 在已知 I 类错误率膨胀的情况下稳健地纳入历史信息

IF 1.7 3区生物学

Biometrical Journal Pub Date : 2023-12-08 DOI: 10.1002/bimj.202200322

Silvia Calderazzo, Manuel Wiesenfarth, Annette Kopp-Schneider

{"title":"Robust incorporation of historical information with known type I error rate inflation","authors":"Silvia Calderazzo, Manuel Wiesenfarth, Annette Kopp-Schneider","doi":"10.1002/bimj.202200322","DOIUrl":"10.1002/bimj.202200322","url":null,"abstract":"Bayesian clinical trials can benefit from available historical information through the specification of informative prior distributions. Concerns are however often raised about the potential for prior-data conflict and the impact of Bayes test decisions on frequentist operating characteristics, with particular attention being assigned to inflation of type I error (TIE) rates. This motivates the development of principled borrowing mechanisms, that strike a balance between frequentist and Bayesian decisions. Ideally, the trust assigned to historical information defines the degree of robustness to prior-data conflict one is willing to sacrifice. However, such relationship is often not directly available when explicitly considering inflation of TIE rates. We build on available literature relating frequentist and Bayesian test decisions, and investigate a rationale for inflation of TIE rate which explicitly and linearly relates the amount of borrowing and the amount of TIE rate inflation in one-arm studies. A novel dynamic borrowing mechanism tailored to hypothesis testing is additionally proposed. We show that, while dynamic borrowing prevents the possibility to obtain a simple closed-form TIE rate computation, an explicit upper bound can still be enforced. Connections with the robust mixture prior approach, particularly in relation to the choice of the mixture weight and robust component, are made. Simulations are performed to show the properties of the approach for normal and binomial outcomes, and an exemplary application is demonstrated in a case study.","PeriodicalId":55360,"journal":{"name":"Biometrical Journal","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2023-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bimj.202200322","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138562993","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Bayesian optimal stepped wedge design 贝叶斯优化阶梯式楔形设计。

IF 1.7 3区生物学

Biometrical Journal Pub Date : 2023-12-06 DOI: 10.1002/bimj.202300168

Satya Prakash Singh

引用次数: 0

Bayesian dose escalation with overdose and underdose control utilizing all toxicities in Phase I/II clinical trials 在I/II期临床试验中，贝叶斯剂量递增与剂量过量和剂量不足控制。

IF 1.7 3区生物学

Biometrical Journal Pub Date : 2023-12-04 DOI: 10.1002/bimj.202200189

Jieqi Tu, Zhengjia Chen

{"title":"Bayesian dose escalation with overdose and underdose control utilizing all toxicities in Phase I/II clinical trials","authors":"Jieqi Tu, Zhengjia Chen","doi":"10.1002/bimj.202200189","DOIUrl":"10.1002/bimj.202200189","url":null,"abstract":"Escalation with overdose control (EWOC) is a commonly used Bayesian adaptive design, which controls overdosing risk while estimating maximum tolerated dose (MTD) in cancer Phase I clinical trials. In 2010, Chen and his colleagues proposed a novel toxicity scoring system to fully utilize patients’ toxicity information by using a normalized equivalent toxicity score (NETS) in the range 0 to 1 instead of a binary indicator of dose limiting toxicity (DLT). Later in 2015, by adding underdosing control into EWOC, escalation with overdose and underdose control (EWOUC) design was proposed to guarantee patients the minimum therapeutic effect of drug in Phase I/II clinical trials. In this paper, the EWOUC-NETS design is developed by integrating the advantages of EWOUC and NETS in a Bayesian context. Moreover, both toxicity response and efficacy are treated as continuous variables to maximize trial efficiency. The dose escalation decision is based on the posterior distribution of both toxicity and efficacy outcomes, which are recursively updated with accumulated data. We compare the operation characteristics of EWOUC-NETS and existing methods through simulation studies under five scenarios. The study results show that EWOUC-NETS design treating toxicity and efficacy outcomes as continuous variables can increase accuracy in identifying the optimized utility dose (OUD) and provide better therapeutic effects.","PeriodicalId":55360,"journal":{"name":"Biometrical Journal","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2023-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138479358","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Drug combinations screening using a Bayesian ranking approach based on dose–response models 使用基于剂量-反应模型的贝叶斯排序方法筛选药物组合。

IF 1.7 3区生物学

Biometrical Journal Pub Date : 2023-11-20 DOI: 10.1002/bimj.202200332

Luana Boumendil, Morgane Fontaine, Vincent Lévy, Kim Pacchiardi, Raphaël Itzykson, Lucie Biard

{"title":"Drug combinations screening using a Bayesian ranking approach based on dose–response models","authors":"Luana Boumendil, Morgane Fontaine, Vincent Lévy, Kim Pacchiardi, Raphaël Itzykson, Lucie Biard","doi":"10.1002/bimj.202200332","DOIUrl":"10.1002/bimj.202200332","url":null,"abstract":"Drug combinations have been of increasing interest in recent years for the treatment of complex diseases such as cancer, as they could reduce the risk of drug resistance. Moreover, in oncology, combining drugs may allow tackling tumor heterogeneity. Identifying potent combinations can be an arduous task since exploring the full dose–response matrix of candidate combinations over a large number of drugs is costly and sometimes unfeasible, as the quantity of available biological material is limited and may vary across patients. Our objective was to develop a rank-based screening approach for drug combinations in the setting of limited biological resources. A hierarchical Bayesian 4-parameter log-logistic (4PLL) model was used to estimate dose–response curves of dose–candidate combinations based on a parsimonious experimental design. We computed various activity ranking metrics, such as the area under the dose–response curve and Bliss synergy score, and we used the posterior distributions of ranks and the surface under the cumulative ranking curve to obtain a comprehensive final ranking of combinations. Based on simulations, our proposed method achieved good operating characteristics to identifying the most promising treatments in various scenarios with limited sample sizes and interpatient variability. We illustrate the proposed approach on real data from a combination screening experiment in acute myeloid leukemia.","PeriodicalId":55360,"journal":{"name":"Biometrical Journal","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2023-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bimj.202200332","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138178002","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Multivariate joint model under competing risks to predict death of hospitalized patients for SARS-CoV-2 infection 竞争风险下的多变量联合模型预测严重急性呼吸系统综合征冠状病毒2型感染住院患者的死亡。

IF 1.7 3区生物学

Biometrical Journal Pub Date : 2023-11-01 DOI: 10.1002/bimj.202300049

Alexandra Lavalley-Morelle, Nathan Peiffer-Smadja, Simon B. Gressens, Bérénice Souhail, Alexandre Lahens, Agathe Bounhiol, François-Xavier Lescure, France Mentré, Jimmy Mullaert

{"title":"Multivariate joint model under competing risks to predict death of hospitalized patients for SARS-CoV-2 infection","authors":"Alexandra Lavalley-Morelle, Nathan Peiffer-Smadja, Simon B. Gressens, Bérénice Souhail, Alexandre Lahens, Agathe Bounhiol, François-Xavier Lescure, France Mentré, Jimmy Mullaert","doi":"10.1002/bimj.202300049","DOIUrl":"10.1002/bimj.202300049","url":null,"abstract":"During the coronavirus disease 2019 (COVID-19) pandemic, several clinical prognostic scores have been proposed and evaluated in hospitalized patients, relying on variables available at admission. However, capturing data collected from the longitudinal follow-up of patients during hospitalization may improve prediction accuracy of a clinical outcome. To answer this question, 327 patients diagnosed with COVID-19 and hospitalized in an academic French hospital between January and July 2020 are included in the analysis. Up to 59 biomarkers were measured from the patient admission to the time to death or discharge from hospital. We consider a joint model with multiple linear or nonlinear mixed-effects models for biomarkers evolution, and a competing risks model involving subdistribution hazard functions for the risks of death and discharge. The links are modeled by shared random effects, and the selection of the biomarkers is mainly based on the significance of the link between the longitudinal and survival parts. Three biomarkers are retained: the blood neutrophil counts, the arterial pH, and the C-reactive protein. The predictive performances of the model are evaluated with the time-dependent area under the curve (AUC) for different landmark and horizon times, and compared with those obtained from a baseline model that considers only information available at admission. The joint modeling approach helps to improve predictions when sufficient information is available. For landmark 6 days and horizon of 30 days, we obtain AUC [95% CI] 0.73 [0.65, 0.81] and 0.81 [0.73, 0.89] for the baseline and joint model, respectively (p = 0.04). Statistical inference is validated through a simulation study.","PeriodicalId":55360,"journal":{"name":"Biometrical Journal","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71429417","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Incorporation of healthy volunteers data on receptor occupancy into a phase II proof-of-concept trial using a Bayesian dynamic borrowing design 使用贝叶斯动态借用设计将健康志愿者的受体占用数据纳入II期概念验证试验。

IF 1.7 3区生物学

Biometrical Journal Pub Date : 2023-10-27 DOI: 10.1002/bimj.202200305

Fulvio Di Stefano, Christelle Rodrigues, Stephanie Galtier, Sandrine Guilleminot, Veronique Robert, Mauro Gasparini, Gaelle Saint-Hilary

{"title":"Incorporation of healthy volunteers data on receptor occupancy into a phase II proof-of-concept trial using a Bayesian dynamic borrowing design","authors":"Fulvio Di Stefano, Christelle Rodrigues, Stephanie Galtier, Sandrine Guilleminot, Veronique Robert, Mauro Gasparini, Gaelle Saint-Hilary","doi":"10.1002/bimj.202200305","DOIUrl":"10.1002/bimj.202200305","url":null,"abstract":"Receptor occupancy in targeted tissues measures the proportion of receptors occupied by a drug at equilibrium and is sometimes used as a surrogate of drug efficacy to inform dose selection in clinical trials. We propose to incorporate data on receptor occupancy from a phase I study in healthy volunteers into a phase II proof-of-concept study in patients, with the objective of using all the available evidence to make informed decisions. A minimal physiologically based pharmacokinetic modeling is used to model receptor occupancy in healthy volunteers and to predict it in the patients of a phase II proof-of-concept study, taking into account the variability of the population parameters and the specific differences arising from the pathological condition compared to healthy volunteers. Then, given an estimated relationship between receptor occupancy and the clinical endpoint, an informative prior distribution is derived for the clinical endpoint in both the treatment and control arms of the phase II study. These distributions are incorporated into a Bayesian dynamic borrowing design to supplement concurrent phase II trial data. A simulation study in immuno-inflammation demonstrates that the proposed design increases the power of the study while maintaining a type I error at acceptable levels for realistic values of the clinical endpoint.","PeriodicalId":55360,"journal":{"name":"Biometrical Journal","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2023-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54232411","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A scalable approach for short-term disease forecasting in high spatial resolution areal data 在高空间分辨率区域数据中进行短期疾病预测的可扩展方法。

IF 1.7 3区生物学

Biometrical Journal Pub Date : 2023-10-27 DOI: 10.1002/bimj.202300096

Erick Orozco-Acosta, Andrea Riebler, Aritz Adin, Maria D. Ugarte

引用次数: 0

Multiple testing of composite null hypotheses for discrete data using randomized p-values 使用随机p值对离散数据的复合零假设进行多重测试。

IF 1.7 3区生物学

Biometrical Journal Pub Date : 2023-10-19 DOI: 10.1002/bimj.202300077

Daniel Ochieng, Anh-Tuan Hoang, Thorsten Dickhaus

{"title":"Multiple testing of composite null hypotheses for discrete data using randomized p-values","authors":"Daniel Ochieng, Anh-Tuan Hoang, Thorsten Dickhaus","doi":"10.1002/bimj.202300077","DOIUrl":"10.1002/bimj.202300077","url":null,"abstract":"P-values that are derived from continuously distributed test statistics are typically uniformly distributed on (0,1) under least favorable parameter configurations (LFCs) in the null hypothesis. Conservativeness of a p-value P (meaning that P is under the null hypothesis stochastically larger than uniform on (0,1)) can occur if the test statistic from which P is derived is discrete, or if the true parameter value under the null is not an LFC. To deal with both of these sources of conservativeness, we present two approaches utilizing randomized p-values. We illustrate their effectiveness for testing a composite null hypothesis under a binomial model. We also give an example of how the proposed p-values can be used to test a composite null in group testing designs. We find that the proposed randomized p-values are less conservative compared to nonrandomized p-values under the null hypothesis, but that they are stochastically not smaller under the alternative. The problem of establishing the validity of randomized p-values has received attention in previous literature. We show that our proposed randomized p-values are valid under various discrete statistical models, which are such that the distribution of the corresponding test statistic belongs to an exponential family. The behavior of the power function for the tests based on the proposed randomized p-values as a function of the sample size is also investigated. Simulations and a real data example are used to compare the different considered p-values.","PeriodicalId":55360,"journal":{"name":"Biometrical Journal","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2023-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bimj.202300077","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49685340","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A Bayesian approach for mixed effects state-space models under skewness and heavy tails 偏态和重尾下混合效应状态空间模型的贝叶斯方法。

IF 1.7 3区生物学

Biometrical Journal Pub Date : 2023-10-18 DOI: 10.1002/bimj.202100302

Lina L. Hernandez-Velasco, Carlos A. Abanto-Valle, Dipak K. Dey, Luis M. Castro

{"title":"A Bayesian approach for mixed effects state-space models under skewness and heavy tails","authors":"Lina L. Hernandez-Velasco, Carlos A. Abanto-Valle, Dipak K. Dey, Luis M. Castro","doi":"10.1002/bimj.202100302","DOIUrl":"10.1002/bimj.202100302","url":null,"abstract":"Human immunodeficiency virus (HIV) dynamics have been the focus of epidemiological and biostatistical research during the past decades to understand the progression of acquired immunodeficiency syndrome (AIDS) in the population. Although there are several approaches for modeling HIV dynamics, one of the most popular is based on Gaussian mixed-effects models because of its simplicity from the implementation and interpretation viewpoints. However, in some situations, Gaussian mixed-effects models cannot (a) capture serial correlation existing in longitudinal data, (b) deal with missing observations properly, and (c) accommodate skewness and heavy tails frequently presented in patients' profiles. For those cases, mixed-effects state-space models (MESSM) become a powerful tool for modeling correlated observations, including HIV dynamics, because of their flexibility in modeling the unobserved states and the observations in a simple way. Consequently, our proposal considers an MESSM where the observations' error distribution is a skew-t. This new approach is more flexible and can accommodate data sets exhibiting skewness and heavy tails. Under the Bayesian paradigm, an efficient Markov chain Monte Carlo algorithm is implemented. To evaluate the properties of the proposed models, we carried out some exciting simulation studies, including missing data in the generated data sets. Finally, we illustrate our approach with an application in the AIDS Clinical Trial Group Study 315 (ACTG-315) clinical trial data set.","PeriodicalId":55360,"journal":{"name":"Biometrical Journal","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2023-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49685339","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Comment on Oberman & Vink: Should we fix or simulate the complete data in simulation studies evaluating missing data methods? Oberman&Vink评论：我们应该在评估缺失数据方法的模拟研究中修复或模拟完整的数据吗？

IF 1.7 3区生物学

Biometrical Journal Pub Date : 2023-10-12 DOI: 10.1002/bimj.202300085

Tim P. Morris, Ian R. White, Suzie Cro, Jonathan W. Bartlett, James R. Carpenter, Tra My Pham

引用次数: 0