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Bayesian Analysis of Isochores.

Fearnhead, Paul and Vasilieou, Despina (2009) Bayesian Analysis of Isochores. Journal of the American Statistical Association, 485. pp. 132-141.

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    Abstract

    Statistical identification of isochore structure, the variation in large-scale GC composition (proportion of DNA bases that are G or C as opposed to A or T), of mammalian genomes is a necessary requirement for understanding both the evolution of base composition and the many genomic features such as mutation and recombination rates, which covary with base composition. We have developed a Bayesian method for isochore analysis that we demonstrate to be more accurate than the commonly used binary segmentation approach implemented within the program IsoFinder. The method accounts for both fine-scale and large-scale structure. We adapt direct simulation methods to allow for iid samples from the posterior distribution of our model, and provide an accurate approximation to this that can analyze data from a chromosome in a matter of seconds. We apply our method to human chromosome 1. The resulting estimate of how GC content varies across this region is shown to be a better predictor of local recombination rates than IsoFinder, and we are able to detect regions consistent with the classic definition of isochores that cover 85% of the chromosome. We also show a measure of relative GC content to be particularly predictive of local recombination rates.

    Item Type: Article
    Journal or Publication Title: Journal of the American Statistical Association
    Subjects: Q Science > QA Mathematics
    Departments: Faculty of Science and Technology > Mathematics and Statistics
    ID Code: 26253
    Deposited By: Prof Paul Fearnhead
    Deposited On: 27 Apr 2009 09:24
    Refereed?: Yes
    Published?: Published
    Last Modified: 09 Oct 2013 15:41
    Identification Number:
    URI: http://eprints.lancs.ac.uk/id/eprint/26253

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