A quantitative approach for polymerase chain reactions based on a hidden Markov model
Journal article, 2009

Polymerase chain reaction (PCR) is a major DNA amplification technology from molecular biology. The quantitative analysis of PCR aims at determining the initial amount of the DNA molecules from the observation of typically several PCR amplifications curves. The mainstream observation scheme of the DNA amplification during PCR involves fluorescence intensity measurements. Under the classical assumption that the measured fluorescence intensity is proportional to the amount of present DNA molecules, and under the assumption that these measurements are corrupted by an additive Gaussian noise, we analyze a single amplification curve using a hidden Markov model(HMM). The unknown parameters of the HMM may be separated into two parts. On the one hand, the parameters from the amplification process are the initial number of the DNA molecules and the replication efficiency, which is the probability of one molecule to be duplicated. On the other hand, the parameters from the observational scheme are the scale parameter allowing to convert the fluorescence intensity into the number of DNA molecules and the mean and variance characterizing the Gaussian noise. We use the maximum likelihood estimation procedure to infer the unknown parameters of the model from the exponential phase of a single amplification curve, the main parameter of interest for quantitative PCR being the initial amount of the DNA molecules. An illustrative example is provided.

Hidden Markov model

Monte Carlo


Data analysis



em algorithm


Polymerase chain reaction

expectation maximization algorithm

Molecular biology

real-time pcr



maximum-likelihood estimator



Nadia Lalam

University of Gothenburg

Chalmers, Mathematical Sciences, Mathematical Statistics

Journal of Mathematical Biology

0303-6812 (ISSN) 1432-1416 (eISSN)

Vol. 59 4 517-533

Subject Categories

Computational Mathematics



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