HCV基因分型生物芯片探针设计的探讨  

New strategy for design of probes on genechip: application in hepatitis C virus genotyping

作　　者：甄国亮[1] 齐名[1] 陈亚利[1] 熊华[1] 王艾丽[1] 李保仝[1] 武建国[1] 

机构地区：[1]南京军区南京总医院,南京210002

出　　处：《临床检验杂志》2005年第2期84-87,共4页Chinese Journal of Clinical Laboratory Science

基　　金：江苏省社会发展科技基金(BS2000025)

摘　　要：目的　探讨适用于临床实验室的丙型肝炎病毒(hepatictisCvirus,HCV)基因分型诊断芯片的探针设计方案。方法　用TaxonomyBrowser和BLAST工具搜索GenBank中所有已登录的HCV序列,用Clustal.W算法进行序列连配与比对,用生物信息学方法获得 5′非编码区(5′UTR)和核心蛋白区(C区)的比对文件,根据探针设计的原则和要求,确定探针在序列中的位置。用Oligo6. 0和PrimerPremier5. 0软件设计探针。设计芯片上 6×6的探针阵列模式。结果　从 778个HCV序列中获得 5′UTR和C区序列变异比对文件,发现 7个存在活跃共突变的区域。根据序列分析数据设计了 5′UTR27个探针和C区 9个探针。设计了由不同的探针组合构成的 33种杂交阵列模式。结论　采用 5′UTR和C区多探针联合检测的基因芯片技术可简化HCV分型方法,提高检测结果的特异性。Objective To explore a new strategy for design of probes immobilized on genechip to identify the genotype of hepatitis C virus (HCV).Methods All the HCV sequences logging in GenBank were searched and retrieved by Taxonomy Browser and BLAST tools.Clustal.W software was used for match and alignment of the download sequences.The alignment documents of 5′untranslated region (UTR) and core region of HCV were obtained by bioinformatics methods.The position of probes in the sequences of HCV genome was ascertained according to the principles of probe design.The probes were designed by Oligo 6.0 and Primer Premier 5.0 softwares.The array patterns of six by sixon genechip were designed and formed.Results The alignment documents of variation from 778 HCV sequence were obtained and 7 active covariant regions were discovered.The probes,27 for 5′UTR and 9 for C region,were designed in accordance with the data of sequence analysis.Thirty-three array patterns composed by various probes were designed for hybridization. Conclusion The application of genechip constructed by multiple probes from 5′UTR and C region may simplify the protocol of HCV genotyping and improve the specificity of experimental results.

关 键 词：HCV 探针 基因分型 比对 核心蛋白 丙型肝炎病毒 基因芯片技术 文件 5.0软件 登录 

分 类 号：R512[医药卫生—内科学] R446[医药卫生—临床医学]