HomozygosityMapper2012-bridging the gap between homozygosity mapping and deep sequencing
HomozygosityMapper2012-bridging the gap between homozygosity mapping and deep sequencing
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DOI：
10.1093/nar/gks487
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发表时间：
2012-07-01
影响因子：
14.9
通讯作者：
Schuelke, Markus
中科院分区：
文献类型：
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作者：
Seelow, Dominik;Schuelke, Markus
纯合性作图是绘制近亲家庭隐性性状的常用方法。为了促进这些分析，我们开发了 HomozygosityMapper，这是一种基于网络的纯合性映射方法。 HomozygosityMapper 允许研究人员直接上传主要基因分型平台生成的基因型文件以及深度测序数据。它检测受影响个体共享的纯合性延伸并以图形方式显示它们。用户可以交互式地检查潜在的基因型，手动细化这些区域，并最终将它们提交给我们的候选基因搜索引擎 GeneDistiller，以识别最有希望的候选基因。在这里，我们介绍新版本的 HomozygosityMapper。最引人注目的新功能是支持下一代测序 *.vcf 文件作为输入。根据用户的要求，我们对常见的实验啮齿动物以及重要的农场动物进行了分析。此外，我们还扩大了单亲家庭和杂合性缺失研究的选择范围。另一个新功能是导出 *.bed 文件，用于有针对性地富集潜在疾病区域，以实现深度测序策略。 HomozygosityMapper 还生成用于传统连锁分析的文件，这些文件已经限制在可能的疾病区域，因此取代了 CPU 密集型全基因组分析。 HomozygosityMapper 可在 http://www.homozygositymapper.org/ 上免费获得。
Homozygosity mapping is a common method to map recessive traits in consanguineous families. To facilitate these analyses, we have developed HomozygosityMapper, a web-based approach to homozygosity mapping. HomozygosityMapper allows researchers to directly upload the genotype files produced by the major genotyping platforms as well as deep sequencing data. It detects stretches of homozygosity shared by the affected individuals and displays them graphically. Users can interactively inspect the underlying genotypes, manually refine these regions and eventually submit them to our candidate gene search engine GeneDistiller to identify the most promising candidate genes. Here, we present the new version of HomozygosityMapper. The most striking new feature is the support of Next Generation Sequencing *.vcf files as input. Upon users' requests, we have implemented the analysis of common experimental rodents as well as of important farm animals. Furthermore, we have extended the options for single families and loss of heterozygosity studies. Another new feature is the export of *.bed files for targeted enrichment of the potential disease regions for deep sequencing strategies. HomozygosityMapper also generates files for conventional linkage analyses which are already restricted to the possible disease regions, hence superseding CPU-intensive genome-wide analyses. HomozygosityMapper is freely available at n http://www.homozygositymapper.org/.