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G-scores: A method for identifying disease-causing pathogens with application to lower respiratory tract infections
Zhang, Peng1; Peng, Peichao2; Wang, Lu3; Kang, Yu4
关键词Change Point Gibbs Sampling Loop-mediated Isothermal Amplification Markov Chain Monte Carlo Tobit Model Zero-inflated Models
刊名STATISTICS IN MEDICINE
2014-07-20
DOI10.1002/sim.6129
33期:16页:2814-2829
收录类别SCI
文章类型Article
WOS标题词Science & Technology
类目[WOS]Mathematical & Computational Biology ; Public, Environmental & Occupational Health ; Medical Informatics ; Medicine, Research & Experimental ; Statistics & Probability
研究领域[WOS]Mathematical & Computational Biology ; Public, Environmental & Occupational Health ; Medical Informatics ; Research & Experimental Medicine ; Mathematics
关键词[WOS]MEDIATED ISOTHERMAL AMPLIFICATION ; COUNT DATA ; REGRESSION ; MODELS ; LAMP ; DNA ; ISSUES ; TESTS
英文摘要

Lower respiratory tract infections (LRTIs) are well known for the lack of a good diagnostic method. The main difficulty lies in the fact that there are a variety of pathogens causing LRTIs, and their management and treatment are quite different. The development of quantitative real-time loop-mediated isothermal amplification (qrt-LAMP) made it possible to rapidly amplify and quantify multiple pathogens simultaneously. The question that remains to be answered is how accurate and reliable is this method? More importantly, how are qrt-LAMP measurements utilized to inform/suggest medical decisions? When does a pathogen start to grow out of control and cause infection? Answers to these questions are crucial to advise treatment guidance for LRTIs and also helpful to design phase I/II trials or adaptive treatment strategies. In this article, our main contributions include the following two aspects. First, we utilize zero-inflated mixture models to provide statistical evidence for the validity of qrt-LAMP being used in detecting pathogens for LRTIs without the presence of a gold standard test. Our results on qrt-LAMP suggest that it provides reliable measurements on pathogens of interest. Second, we propose a novel statistical approach to identify disease-causing pathogens, that is, distinguish the pathogens that colonize without causing problems from those that rapidly grow and cause infection. We achieve this by combining information from absolute quantities of pathogens and their symbiosis information to form G-scores. Change-point detection methods are utilized on these G-scores to detect the three phases of bacterial growth-lag phase, log phase, and stationary phase. Copyright (C) 2014 John Wiley & Sons, Ltd.

语种英语
WOS记录号WOS:000339071500008
引用统计
文献类型期刊论文
条目标识符http://ir.bjmu.edu.cn/handle/400002259/55079
专题北京大学第二临床医学院
作者单位1.Univ Penn, Dept Stat, Philadelphia, PA 19104 USA
2.Univ Michigan, Dept Surg, Ann Arbor, MI 48109 USA
3.Univ Michigan, Dept Biostat, Ann Arbor, MI 48109 USA
4.Peking Univ, Peoples Hosp, Dept Resp & Crit Care Med, Beijing 100044, Peoples R China
推荐引用方式
GB/T 7714
Zhang, Peng,Peng, Peichao,Wang, Lu,et al. G-scores: A method for identifying disease-causing pathogens with application to lower respiratory tract infections[J]. STATISTICS IN MEDICINE,2014,33(16):2814-2829.
APA Zhang, Peng,Peng, Peichao,Wang, Lu,&Kang, Yu.(2014).G-scores: A method for identifying disease-causing pathogens with application to lower respiratory tract infections.STATISTICS IN MEDICINE,33(16),2814-2829.
MLA Zhang, Peng,et al."G-scores: A method for identifying disease-causing pathogens with application to lower respiratory tract infections".STATISTICS IN MEDICINE 33.16(2014):2814-2829.
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