SequenceLDhot: detecting recombination hotspots
SequenceLDhot: detecting recombination hotspots
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DOI：
10.1093/bioinformatics/btl540
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发表时间：
2006-12-15
期刊：
影响因子：
5.8
通讯作者：
Fearnhead, Paul
中科院分区：
文献类型：
--
作者：
Fearnhead, Paul
动机：在人类基因组中，重组率存在很大的局部差异，大多数重组发生在重组热点，即长度约为2kb的短区域，其重组率比相邻区域高得多。这种局部变异的知识是重要的，例如在疾病基因关联研究的设计和分析中。群体遗传数据，如人类基因组单体型图项目产生的数据，可以用来推断这些热点的位置。我们提出了一种新的，有效的和强大的方法来检测重组热点从populationdatas.Results：我们比较了我们的方法与目前的四种方法检测热点。它比两种相关的方法快几个数量级，并且具有更大的功率。它似乎比HotspotFisher更强大，尽管在推断热点的精确位置方面不太准确。在某些情况下，它也比LDhot更强大：特别是对于SNP密度较低（< 1/kb）的较弱热点（背景速率的10-40倍）。可用性：程序，数据集和结果的完整细节可在：http://www.maths.lancs.ac.uk/similar到fearnhea/Hotspot。联系方式：p. lancs.ac.uk
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 similar to 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/similar to fearnhea/Hotspot.Contact: p.fearnhead@lancs.ac.uk