title: A Bayesian hierarchical model for quantitative real-time PCR data.
abstract: We present a Bayesian hierarchical model for quantitative real-time polymerase chain reaction (PCR) data, aiming at relative quantification of DNA copy number in different biological samples. The model is specified in terms of a hidden Markov model for fluorescence intensities measured at successive cycles of the polymerase chain reaction. The efficiency of the reaction is assumed to depend on the abundance of the target DNA through fluorescence intensities, and the relationship is specified based on the kinetics of the reaction. The model incorporates the intrinsic random nature of the process as well as measurement error. Taking a Bayesian inferential approach, marginal posterior distributions of the quantities of interest are estimated using Markov chain Monte Carlo. The method is applied to simulated data and an experimental data set.
authors.affiliation: Norwegian University of Science and Technology. turid.follestad@sintef.no
authors.forename: Turid
authors.initials: T
authors.lastname: Follestad
authors.forename: Tommy S
authors.initials: TS
authors.lastname: Jørstad
authors.forename: Sten E
authors.initials: SE
authors.lastname: Erlandsen
authors.forename: Arne K
authors.initials: AK
authors.lastname: Sandvik
authors.forename: Atle M
authors.initials: AM
authors.lastname: Bones
authors.forename: Mette
authors.initials: M
authors.lastname: Langaas
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D001499:Bayes Theorem; D056808:Biostatistics; D004247:DNA / Q000032:analysis / Q000235:genetics; D017931:DNA Primers / Q000235:genetics; D003627:Data Interpretation, Statistical; D005260:Female; D015870:Gene Expression / Q000187:drug effects; D000090062:Kruppel-Like Factor 4; D051741:Kruppel-Like Transcription Factors / Q000235:genetics; D008390:Markov Chains; D015233:Models, Statistical; D009010:Monte Carlo Method; D015282:Octreotide / Q000494:pharmacology; D016133:Polymerase Chain Reaction / Q000706:statistics & numerical data*; D051381:Rats; D017207:Rats, Sprague-Dawley; D013269:Stochastic Processes
chemical_list: D017931:DNA Primers; D000090062:Kruppel-Like Factor 4; D051741:Kruppel-Like Transcription Factors; D004247:DNA; D015282:Octreotide