NRE: a tool for exploring neutral loci in the human genome
NRE: a tool for exploring neutral loci in the human genome
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DOI：
10.1186/1471-2105-13-301
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发表时间：
2012-11-14
影响因子：
3
通讯作者：
Keinan, Alon
中科院分区：
文献类型：
--
作者：
Arbiza, Leonardo;Zhong, Elaine;Keinan, Alon
背景：分析基因组中遗传变异不受自然选择混杂影响的区域对于许多群体遗传学研究至关重要。最近对人类的几项研究强调了自然选择对相关中性位点的巨大影响，并表明对假定中性区域的选择可以对人口统计历史的估计产生显着影响。结果：NRE（中性区域浏览器）提供了一种从人类基因组中轻松提取和分析近中性区域的机制。它可以组合许多基因组过滤器，包括选择过滤器、重组率、到最近基因的遗传距离、与注释区域的重叠百分比以及用户提供的基因座。该程序实现了两步过滤过程，以实现更大的多功能性，允许用户编制一组基本的中立标准，探索其效果，并使用这些知识来完善过滤。结果可以立即以标准格式下载，以及摘要和排名统计数据，或导出到基因组浏览器，例如来自 1000 Genomes 和 UCSC 的浏览器。通过使用不同的中性区域选择策略估计X染色体与常染色体有效群体大小之比的实例，证明了NRE的适用性和价值。结论：NRE的综合特征使得群体遗传学研究日益要求的灵活、严格的中性位点挖掘和分析成为可能。 NRE 可在 http://nre.cb.bscb.cornell.edu 获取。
Background: Analyzing regions of the genome where genetic variation is free from the confounding effects of natural selection is essential for many population genetic studies. Several recent studies in humans have stressed the large effect of natural selection at linked neutral sites and have shown that the choice of putatively neutral regions can have a marked effect on estimates of demographic history.Results: NRE (Neutral Region Explorer) provides a mechanism for the easy extraction and analysis of nearly neutral regions from the human genome. It can combine many genomic filters, including filters for selection, recombination rate, genetic distance to the nearest gene, percent overlap with annotated regions, and user-provided loci. The program implements a two-step filtering process for greater versatility, allowing users to compile a basic set of neutrality criteria, explore their effect, and use this knowledge to refine filtering. Results can be instantly downloaded in standard formats, along with summary and ranking statistics, or exported to genome browsers such as those from the 1000 Genomes and UCSC. The applicability and value of NRE are demonstrated through an example in the estimation of the ratio of chromosome X-to-autosomal effective population size using different strategies for the selection of neutral regions.Conclusions: The combined features of NRE make possible the sort of flexible, rigorous mining and analysis of neutral loci increasingly demanded by population genetic studies. NRE is available at http://nre.cb.bscb.cornell.edu.