基础医学与临床 ›› 2014, Vol. 34 ›› Issue (2): 229-234.

• 技术与方法 • 上一篇    下一篇

一种基于计算机的单核苷酸多态性位点检测方法

马磊,贾奇男,张俊,易青青,贺建峰,张琪   

  1. 昆明理工大学
  • 收稿日期:2013-06-14 修回日期:2013-09-25 出版日期:2014-02-05 发布日期:2014-01-13
  • 通讯作者: 马磊 E-mail:roy_murray@qq.com
  • 基金资助:
    国家自然科学基金(地区基金);云南应用基础研究基金;云南省教育厅科学研究基金

A novel computer based method for the selection of genetic loci with single nucleotide polymorphism

  • Received:2013-06-14 Revised:2013-09-25 Online:2014-02-05 Published:2014-01-13
  • Contact: Lei Ma E-mail:roy_murray@qq.com

摘要: 目的 探讨一种成本低廉、操作简便,并能在大量基因数据中筛选出单核苷酸多态性(SNP)位点的计算机方法。方法 通过提取特征属性值项,采用基于最优风险与预防模式的数学算法,从SNP位点的角度分析基因突变现象。并以HBV(乙肝病毒)的演化为例,应用所提出的方法研究急性乙型肝炎转化为慢性乙型肝炎再至肝硬化过程中病毒基因的突变现象。结果 实验共检测出18处急性转慢性候选SNPs位点,其中4处属于碱基替换突变,1处属于碱基缺失突变,该5处已有报道,另外13处是新发现的候选SNP位点。同时检测出3处新发现的慢性转肝硬化候选SNPs位点,其中2处属于碱基替换突变,1处属于碱基缺失突变。结论 该方法操作简便,所需软硬件设备容易配置,在检测的便捷性和检出率方面都具有一定优势,将对乙型肝炎及其他疾病的临床诊断和研究起到有益的参考作用。

关键词: 最优风险与预防模型, SNP位点, 乙型肝炎病毒

Abstract: Objective In this paper, a computer based method that could select the genetic loci with single nucleotide polymorphism (SNP) from amount of gene data with relative low costs and simple operations is proposed. Methods The algorithm with optimal risk and preventive pattern is applied to analyse the mutation of gene based on SNP loci after the extraction of feature property. The evolution of HBV (Hepatitis B Virus) is studied as an example to discover the phenomena of mutation during the transition from Acute to Chronic carrier, then to Cirrhosis. Results The computing experiment releases 18 potential SNPs locus that demonstrate the transition from Acute to Chronic, five of them have been reported by previous research, the remaining 13 are potential locus. In addition, 3 potential SNPs locus that demonstrate the transition to Cirrhosis are uncovered. Conclusion The proposed method can be used to select SNP locus from large number of gene data effectively and inexpensively, which may possibly be applied to the clinic diagnosis and basic research of HBV or other virus caused disease.

Key words: optimal risk and preventive pattern, genetic loci with SNP, HBV

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