Yuan Hsiang-Yu, Chiou Jen-Jie, Tseng Wen-Hsien, Liu Chia-Hung, Liu Chuan-Kun, Lin Yi-Jung, Wang Hui-Hung, Yao Adam, Chen Yuan-Tsong, Hsu Chun-Nan
Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W635-41. doi: 10.1093/nar/gkl236.
Single nucleotide polymorphism (SNP) prioritization based on the phenotypic risk is essential for association studies. Assessment of the risk requires access to a variety of heterogeneous biological databases and analytical tools. FASTSNP (function analysis and selection tool for single nucleotide polymorphisms) is a web server that allows users to efficiently identify and prioritize high-risk SNPs according to their phenotypic risks and putative functional effects. A unique feature of FASTSNP is that the functional effect information used for SNP prioritization is always up-to-date, because FASTSNP extracts the information from 11 external web servers at query time using a team of web wrapper agents. Moreover, FASTSNP is extendable by simply deploying more Web wrapper agents. To validate the results of our prioritization, we analyzed 1569 SNPs from the SNP500Cancer database. The results show that SNPs with a high predicted risk exhibit low allele frequencies for the minor alleles, consistent with a well-known finding that a strong selective pressure exists for functional polymorphisms. We have been using FASTSNP for 2 years and FASTSNP enables us to discover a novel promoter polymorphism. FASTSNP is available at http://fastsnp.ibms.sinica.edu.tw.
基于表型风险对单核苷酸多态性（SNP）进行优先级排序对于关联研究至关重要。风险评估需要访问各种异质生物数据库和分析工具。FASTSNP（单核苷酸多态性功能分析与选择工具）是一个网络服务器，它允许用户根据SNP的表型风险和假定的功能效应有效地识别高风险SNP并对其进行优先级排序。FASTSNP的一个独特功能是用于SNP优先级排序的功能效应信息始终是最新的，因为FASTSNP在查询时使用一组网络包装代理从11个外部网络服务器提取信息。此外，只需部署更多网络包装代理，FASTSNP就可扩展。为了验证我们优先级排序的结果，我们分析了来自SNP500Cancer数据库的1569个SNP。结果表明，预测风险高的SNP次要等位基因的等位基因频率较低，这与一个众所周知的发现一致，即功能多态性存在强大的选择压力。我们使用FASTSNP已有两年，FASTSNP使我们能够发现一种新的启动子多态性。可通过http://fastsnp.ibms.sinica.edu.tw访问FASTSNP。
