Chemical Pattern Recognition Genotyping of STR Locus Based on Nearinfrared Spectroscopy Combined with Support Vector Machine
摘 要
利用近红外光谱(NIRS)结合支持向量机(SVM)模式识别原理建立了微卫星(短串联重复序列,STR)的分型方法.以D16S539基因座的10-10、10-11和11-11 3种不同基因型为例,研究了包含该多态性位点的脱氧核糖核酸(DNA)片段的聚合酶链反应(PCR)扩增条件和NIRS检测条件,建立了标准化扩增条件和检测条件,以此条件获得了基因分型的标准物及其标准NIRS.以标准光谱为识别变量,建立该3类基因型的SVM判别模型,有效地克服了光谱共线性,并对少样本数表现出良好的稳定性,模型预测率100%.该方法不需任何检测前处理,而只需一步PCR扩增和NIRS检测即可实现STR分型,具有简单、快速、低成本等优点.
Abstract
By using the near-infrared spectra of short tandem repeats (STR′s) and applying the principle of support vector machine (SVM) chemical pattern recognition,model for distingushing STRs of different genotypes was established.Taking 3 kinds of genotype,i.e.,10-10,10-11 and 11-11,of the Locus D16S539 as examples,conditions of NIRS detection and amplification of polyenzyme chain reaction (PCR) of DNA fragment containing polymorphism sites were studied,resulting the establishment of standardized conditions of amplification and detection,as well as obtaining standard materials and their standard NIR spectra for genotyping.By taking the NIR spectra as identifying variables,model for distiguishing STR′s of the 3 genotypes mentioned above was established,thus the spectral collinearity was effectively overcome,and good stability was obtained for small number of samples,attaining the model prediction rate of 100%.The present method was proved to have the advantage of achieving the STR genotyping by merely the PCR amplification and NIRS detection,in a simple rapid and economic way,without the necessity of any pretreatment in the detection.
中图分类号 O657.33
所属栏目 试验与研究
基金项目 国家大学生创新性实验计划项目资助(SG315865)
收稿日期 2009/10/12
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备注郭莉萍(1962-),女,重庆市人,主要研究方向为化学合成、分离与分析.
引用该论文: GUO Li-ping,XU Rong,REN Li,HE Xiao-li,YAO Min,HE Hua-lan,XIE Hong-ping. Chemical Pattern Recognition Genotyping of STR Locus Based on Nearinfrared Spectroscopy Combined with Support Vector Machine[J]. Physical Testing and Chemical Analysis part B:Chemical Analysis, 2010, 46(7): 728~731
郭莉萍,徐容,任丽,何晓丽,姚敏,贺华兰,谢洪平. 近红外光谱结合支持向量机对STR基因座的化学模式识别分型[J]. 理化检验-化学分册, 2010, 46(7): 728~731
被引情况:
【1】张斌,鲁辉,汪雪娇,胡海燕,刘玲,谢洪平,顾炳仁, "基于主判别变量法的近红外光谱STR基因分型专家系统",理化检验-化学分册 48, 516-520(2012)
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参考文献
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【2】EDWARDS A,CIVITELLO A,HAMMOND H A,et al.DNA typing and genetic mapping with trimeric and tetrameric tandem repeats[J].Am J Hum Genet,1991,49(4):746-756.
【3】HAMMOND H A,JIN L,ZHONG Y,et al.Evaluation of 13 short tandem repeat loci for use in personal identification applications[J].Am J Hum Genet,1994,55(1):175-189.
【4】ALFORD R L,HAMMOND H A,COTO I,et al.Rapid and efficient resolution of parentage by amplification of short tandem repeats[J].Am J Hum Genet,1994,55(1):190-195.
【5】BUTLER J M.Short tandem repeat typing technologies used in human identity testing[J].Biotechniques,2007,43(4):2-5.
【6】ANDREA M,MONIKA D A.Assay for single-nucleotide polymorphism genotyping and gene copy number evaluation[J].Methods Mol Biol,2006,335:173-186.
【7】PARK B,ABBOTT J A,LEE K J,et al.Near-infrared diffuse reflectance for quantitative and qualitative measurement of soluble solids and firmness of delicious and gala apples[J].Transactions of the ASAE,2003,46(6):1721-1731.
【8】叶美盈,汪晓东.混沌光学系统辨识的支持向量机方法[J].光学学报,2004,24(7):953-956.
【9】赵杰文,呼怀平,邹小波.支持向量机在苹果分类的近红外光谱模型中的应用[J].农业工程学报,2007,23(4):149-152.
【10】马群,郝贵奇,乔延江,等.近红外光谱法结合支持向量机测定天然牛黄粉中人工牛黄的掺入量[J].光谱学与光谱分析,2006,26(10):1842-1845.
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