Establishment of Bioinformatics Platforms for SNP ID Retrieval and SNP-SNP Interaction

• Main Authors: Cheng-Hao Wen, 温政浩
• Other Authors: Hsueh-Wei Chang
• Format: Others
• Language: zh-TW
• Online Access: http://ndltd.ncl.edu.tw/handle/74377834838473243832

碩士 === 高雄醫學大學 === 生物醫學暨環境生物學研究所碩士班 === 95 === Coupling molecular techniques with bioinformatics make the complicated biological science research become more quickly and easily than before. The purpose of this study is to combine the development of bioinformatics software and molecular biological study. We tried to develop the SNP (Single Nucleotide Polymorphism) ID retrieval and SNP interaction analysis platform to analyze the asociation study of oral cancer. In molecular biological experiment, we used TRIzol reagent to isolate the RNA, DNA and protein separately from single sample to save the usage of sample and provide the fruitful information of molecular level. In bioinformatics view, we developed the platform to discuss the SNP ID retrieval, the primer design software for SNPs and the genetic algorithm of SNP interaction. The results and discussions were followed. (1) Using real-time PCR to elucidate down-regulated genes of oal cancer, and futher discuss the methylation of these genes. Here we biulfite-treated DNA and TA cloning technique to discovery the promoter methylatio of Cyclin G2. (2) Development of SNP ID retrieval platfom to solve the problems form association study reference. We supplied users to input gene name, DNA sequence, cytogenetic band range and chromosome contig position in ePCR-independent platform, including SNPosition, SNPsearch and SNP fasta. About the SNP-ePCR platform, we could predict the whole PCR product length and sequence by inputting primer sequence from reference. And then through the SNPosition platform, the information of exact SNPs consisted in PCR product and flanking SNPs would be supplied to users. (3) The development of SNP-dependent primer design software, Prim-SNPing and restriction enzyme-independent primer design, PCR-CTPP (polymerase chain reaction with confronting two-pair primers). (4) Using genetic algorithm to discuss the gene-gene interaction of oral cancer model. Here we discussed the oral cancer associated gene, XRCC1, XRCC2, XRCC3 and XRCC4 with the contribution to oral cancer, called pseudo-haplotype. We found that the specific pseudo-haplotype combination were highly associated with oral cancer. Conclusion: we had developed the combination of bioinformatics platform and molecular biological experiment to discuss the system biology of oral cancer model.