NeuroCure Clinical Research Centre, Charité - Universitätsmedizin Berlin, Charitéplatz 1, D-10117 Berlin, Germany.
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W516-20. doi: 10.1093/nar/gks487. Epub 2012 Jun 4.
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 http://www.homozygositymapper.org/.
单体型作图是在近亲家庭中定位隐性特征的常用方法。为了便于这些分析，我们开发了 HomozygosityMapper，这是一种用于单体型作图的基于网络的方法。HomozygosityMapper 允许研究人员直接上传主要基因分型平台产生的基因型文件以及深度测序数据。它可以检测受影响个体共有的纯合子区域，并以图形方式显示出来。用户可以交互式地检查潜在的基因型，手动细化这些区域，并最终将其提交给我们的候选基因搜索引擎 GeneDistiller，以确定最有前途的候选基因。在这里，我们介绍了 HomozygosityMapper 的新版本。最显著的新功能是支持下一代测序 *.vcf 文件作为输入。应用户要求，我们已经实现了对常见实验动物和重要农场动物的分析。此外，我们还扩展了单一家系和杂合性丢失研究的选项。另一个新功能是为深度测序策略的潜在疾病区域的靶向富集导出 *.bed 文件。HomozygosityMapper 还生成用于常规连锁分析的文件，这些文件已经局限于可能的疾病区域，因此取代了 CPU 密集型的全基因组分析。HomozygosityMapper 可在 http://www.homozygositymapper.org/ 免费获得。
