title: Bayesian latent variable models for hierarchical clustered count outcomes with repeated measures in microbiome studies.
abstract: Motivated by the multivariate nature of microbiome data with hierarchical taxonomic clusters, counts that are often skewed and zero inflated, and repeated measures, we propose a Bayesian latent variable methodology to jointly model multiple operational taxonomic units within a single taxonomic cluster. This novel method can incorporate both negative binomial and zero-inflated negative binomial responses, and can account for serial and familial correlations. We develop a Markov chain Monte Carlo algorithm that is built on a data augmentation scheme using Pólya-Gamma random variables. Hierarchical centering and parameter expansion techniques are also used to improve the convergence of the Markov chain. We evaluate the performance of our proposed method through extensive simulations. We also apply our method to a human microbiome study.
authors.affiliation: Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.
authors.forename: Lizhen
authors.initials: L
authors.lastname: Xu
authors.affiliation: Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.|Dalla Lana School of Public Health, University of Toronto, ON, M5T 3M7, Canada.
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Paterson
authors.affiliation: Dalla Lana School of Public Health, University of Toronto, ON, M5T 3M7, Canada.|Department of Biostatistics, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada.
authors.forename: Wei
authors.initials: W
authors.lastname: Xu
mesh_terms: D000293:Adolescent; D000328:Adult; D000367:Age Factors; D000368:Aged; D000465:Algorithms; D001499:Bayes Theorem; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000235:genetics*; D005243:Feces / Q000382:microbiology; D005260:Female; D006801:Humans; D008390:Markov Chains; D064307:Microbiota / Q000235:genetics*; D008875:Middle Aged; D008957:Models, Genetic; D015233:Models, Statistical; D009010:Monte Carlo Method; D009765:Obesity / Q000235:genetics; D012107:Research Design; D013851:Thinness / Q000235:genetics; D018433:Twin Studies as Topic; D055815:Young Adult
chemical_list: D004269:DNA, Bacterial
keywords: Bayesian latent variable model; microbiome; multivariate model; repeated measures; zero-inflated count outcomes