Likelihood-Based Inference for Multi-Color Optical Mapping

Tong Liping, Mets Laurens and McPeek Mary Sara
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Tong Liping: University of Washington
Mets Laurens: University of Chicago
McPeek Mary Sara: University of Chicago

Statistical Applications in Genetics and Molecular Biology, 2007, vol. 6, issue 1, 32

Abstract: Multi-color optical mapping is a new technique being developed to obtain detailed physical maps (indicating relative positions of various recognition sites) of DNA molecules. We consider a study design in which the data consist of noisy observations of multiple copies of a DNA molecule marked with colors at recognition sites. The primary goal is to estimate a physical map. A secondary goal is to estimate error rates associated with the experiment, which are potentially useful for analysis and refinement of the biochemical steps in the mapping procedure. We propose statistical models for various sources of error and use maximum likelihood estimation (MLE) to construct a physical map and estimate error rates. To overcome difficulties arising in the maximization process, a latent-variable Markov chain version of the model is proposed, and the EM algorithm is used for maximization. In addition, a simulated annealing procedure is applied to maximize the profile likelihood over the discrete space of sequences of colors. We apply the methods to simulated data on the bacteriophage lambda genome.

Keywords: optical mapping; maximum likelihood estimation; hidden Markov model; simulated annealing (search for similar items in EconPapers)
Date: 2007
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DOI: 10.2202/1544-6115.1266

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