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sequenceLDhot: Detecting Recombination Hotspots.

Fearnhead, Paul (2006) sequenceLDhot: Detecting Recombination Hotspots. Bioinformatics, 22 (24). pp. 3061-3066. ISSN 1460-2059

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    Abstract

    Motivation: There is much local variation in recombination rates across the human genome—with the majority of recombination occuring in recombination hotspots—short regions of around ~2 kb in length that have much higher recombination rates than neighbouring regions. Knowledge of this local variation is important, e.g. in the design and analysis of association studies for disease genes. Population genetic data, such as that generated by the HapMap project, can be used to infer the location of these hotspots. We present a new, efficient and powerful method for detecting recombination hotspots from population data. Results: We compare our method with four current methods for detecting hotspots. It is orders of magnitude quicker, and has greater power, than two related approaches. It appears to be more powerful than HotspotFisher, though less accurate at inferring the precise positions of the hotspot. It was also more powerful than LDhot in some situations: particularly for weaker hotspots (10–40 times the background rate) when SNP density is lower (< 1/kb). Availability: Program, data sets, and full details of results are available at: http://www.maths.lancs.ac.uk/~fearnhea/Hotspot.

    Item Type: Article
    Journal or Publication Title: Bioinformatics
    Subjects: Q Science > QA Mathematics
    Departments: Faculty of Science and Technology > Mathematics and Statistics
    ID Code: 8186
    Deposited By: Prof Paul Fearnhead
    Deposited On: 15 Apr 2008 11:25
    Refereed?: Yes
    Published?: Published
    Last Modified: 09 Oct 2013 15:41
    Identification Number:
    URI: http://eprints.lancs.ac.uk/id/eprint/8186

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