Iida Naoko, Yamao Fumiaki, Nakamura Yasukazu, Iida Tetsushi
Genome Informatics Laboratory, National Institute of Genetics, Mishima, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan.
Genes Cells. 2014 Jun;19(6):517-27. doi: 10.1111/gtc.12151. Epub 2014 Apr 28.
In forward genetics, identification of mutations is a time-consuming and laborious process. Modern whole-genome sequencing, coupled with bioinformatics analysis, has enabled fast and cost-effective mutation identification. However, for many experimental researchers, bioinformatics analysis is still a difficult aspect of whole-genome sequencing. To address this issue, we developed a browser-accessible and easy-to-use bioinformatics tool called Mutation discovery (Mudi; http://naoii.nig.ac.jp/mudi_top.html), which enables 'one-click' identification of causative mutations from whole-genome sequence data. In this study, we optimized Mudi for pooled-linkage analysis aimed at identifying mutants in yeast model systems. After raw sequencing data are uploaded, Mudi performs sequential analysis, including mapping, detection of variant alleles, filtering and removal of background polymorphisms, prioritization, and annotation. In an example study of suppressor mutants of ptr1-1 in the fission yeast Schizosaccharomyces pombe, pooled-linkage analysis with Mudi identified mip1(+) , a component of Target of Rapamycin Complex 1 (TORC1), as a novel component involved in RNA interference (RNAi)-related cell-cycle control. The accessibility of Mudi will accelerate systematic mutation analysis in forward genetics.
在正向遗传学中，突变的鉴定是一个耗时且费力的过程。现代全基因组测序结合生物信息学分析，实现了快速且经济高效的突变鉴定。然而，对于许多实验研究人员来说，生物信息学分析仍是全基因组测序中困难的一环。为解决这一问题，我们开发了一种名为突变发现（Mudi；http://naoii.nig.ac.jp/mudi_top.html）的可通过浏览器访问且易于使用的生物信息学工具，它能够从全基因组序列数据中“一键式”鉴定致病突变。在本研究中，我们针对旨在鉴定酵母模型系统中突变体的混合连锁分析对Mudi进行了优化。上传原始测序数据后，Mudi会进行一系列分析，包括映射、变异等位基因检测、背景多态性的过滤和去除、优先级排序以及注释。在对裂殖酵母粟酒裂殖酵母中ptr1-1抑制突变体的一项实例研究中，使用Mudi进行的混合连锁分析鉴定出雷帕霉素靶蛋白复合物1（TORC1）的一个组分mip1(+)，它是参与RNA干扰（RNAi）相关细胞周期调控的一个新组分。Mudi的易用性将加速正向遗传学中的系统突变分析。
