An integrated graphical user platform of high-throughput SNP data analysis for disease gene mapping

• Main Authors: Chih-Cheng Huang, 黃志成
• Other Authors: Ming-Wei Lin
• Format: Others
• Language: zh-TW
• Published: 2008
• Online Access: http://ndltd.ncl.edu.tw/handle/12049083429914163259

碩士 === 國立陽明大學 === 生物醫學資訊研究所 === 96 === Background：Single nucleotide polymorphisms (SNPs) became the most common used markers in current human genetic studies. Researchers usually need to select a set of SNPs from an enormous amount of SNP of candidate genes or regions. Moreover, current platforms of high-throughput SNP genotyping will produce huge amounts of genotyping data with different output format. It is a trivial and time-consuming work to pick up SNPs and process different kinds of data format for specific linkage or association analysis program. Material and Methods：We generated a graphical user platform named “AutoSNP” by using Perl language to ease the task of managing high-throughput SNPs data from two main platforms - Illumina and Affymetrix assays. In this platform, users can select SNP data source and then convert SNP genotyping data into appropriate format for specific genetic analysis program. We integrated both linkage analysis programs (ALLEGRO, GENEHUNTER, LINKAGE, MERLIN, SUPERLINK and SIMWALK2) and association analysis programs (FBAT, PLINK, Haploview, PHASE, and WHAP) in this platform. Moreover, this platform also provides users to connect to Ensembl database, NCBI SNP database, and the TAMAL (Technology And Money Are Limiting) database to query information from their SNPs list. Results：In AutoSNP，the Convert Data function provides high-throughput SNP genotyping data conversion for specific linkage or association analysis format. The Check Data function provides data checking including allele frequency, Hardy-Weinberg equilibrium, Mendelian error, and Sex status. The Query Data function provides the connection of three databases for querying SNP related information by using a SNP list or specific SNP rs ID. All these five association software are integrated in a graphical user interface. Finally, the GeneFinding function provides connection of Ensembl and NCBI dbSNP database to query disease susceptibility gene information from the output results. Conclusion：Our platform provides analysis software data format convertion, association analysis software operation (graphical user interface), and database connection from output results to get gene information. This platform can accelerate the discovery of disease susceptibility variant and provide useful gene information for further genetic studies.