基于主判别变量法的近红外光谱STR基因分型专家系统
Genotyping-Dendrogram of D16S539 Locus Based on Near-infrared Spectroscopy and Principal Discriminate Variate
摘 要
基于近红外光谱结合主判别变量算法对短串联重复序列(STR)基因分型专家系统进行研究。选择STR基因座D16S539中6种总核心重复串数不同且出现频率较高的基因型9-9、9-11、9-12、10-10、10-11和11-11作为研究对象。6种基因型样本分别通过两次聚合酶链反应(PCR)平行扩增,以扩增产物的近红外光谱作为判别变量建立判别模型。最后,基于该基因座6种基因型的总核心重复序列数的差异来构建其基因分型专家系统。结果表明:方法适用于不同差异程度的基因型分型,预测准确率高且稳健性好,这为建立其他基因座的分型专家系统提供了可行性。
近红外光谱
主判别变量
基因分型专家系统
Short tandem repeats
Near-infrared spectroscopy
Principal discriminate variate
Genotyping-dendrogram
Abstract
The genotyping-dendrogram of short tandem repeat (STR) has been established based on near-infrared spectroscopy in combination with the principal discriminate variate method. Six genotypes 9-9, 9-11, 9-12, 10-10, 10-11 and 11-11 of D16S539 locus, which had different total number of core-repeat units and the high frequencies of occurrence, were selected as the research objects. The samples of 6 genotypes were obtained by polymerase chain reaction (PCR) in twice. Discriminate models with the near-infrared spectrum of each PCR product as discriminating variable were built. Based on the differences of total number of the core-repeat units, the genotyping-dendrogram was established. It was shown that these models in the dendrogram were appropriate for discriminating the genotypes of all the samples and the method was of good stability and predicting ability. It provided potential to establish expert system for genotyping of other STR loci.
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(编号111028537)
收稿日期 2011/5/2
修改稿日期
网络出版日期
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备注张斌(1985-),男,江苏苏州人,研究方向为药物质量控制。
引用该论文: ZHANG Bin,LU Hui,WANG Xue-jiao,HU Hai-yan,LIU Ling,XIE Hong-ping,GU Bing-ren. Genotyping-Dendrogram of D16S539 Locus Based on Near-infrared Spectroscopy and Principal Discriminate Variate[J]. Physical Testing and Chemical Analysis part B:Chemical Analysis, 2012, 48(5): 516～520
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[J]. 理化检验－化学分册, 2012, 48(5): 516～520
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【4】DEFORCE D L, MILLECAMPS R E, VAN H D, et al. Comparison of slab gel electrophoresis and capillary electrophoresis for the detection of the fluorescently labeled polymerase chain reaction products of short tandem repeat fragments［J］. J Chromatogr A, 1998,806(1):149-155.
【5】SCHMALZING D, KOUTNY L, CHISHOLM D, et al. Two-color multiplexed analysis of eight short tandem repeat loci with an electrophoretic microdevice［J］. Anal Biochem, 1999,270(1):148-152.
【6】MITNIK L, CAREY L, BURGER R, et al. High-speed analysis of multiplexed short tandem repeats with an electrophoretic microdevice［J］. Electrophoresis, 2002,23(5):719-726.
【7】ROSS P L, BELGRADER P. Analysis of short tandem repeat polymorphisms in human DNA by matrix-assisted laser desorption/ionization mass spectrometry［J］. Anal Chem, 1997,69:3966-3972.
【8】OBERACHER H, PARSON W, MUHLMANN R, et al. Analysis of polymerase chain reaction products by on-line liquid chromatography-mass spectrometry for genotyping of polymorphic short tandem repeat loci［J］. Anal Chem, 2001,73(21):5109-5115.
【9】NULL A P, HANNIS J C, MUDDIMAN D C. Genotyping of simple and compound short tandem repeat loci using electrospray ionization fourier transform ion cyclotron resonance mass spectrometry［J］. Anal Chem, 2001,73(18):4514-4521.
【10】郭莉萍,徐容,任丽,等.近红外光谱结合支持向量机对STR基因型的化学模型识别分型［J］.理化检验-化学分册, 2010,46(7):728-731.
【11】SWEET D, LORENTE M, VALENZUELA A, et al. Increasing DNA extraction yield from saliva stains with a modified chelex method［J］. Forensic Sci Int, 1996,83(3):167-177.
【12】MARINO M A, DEVANEY J M, SMITH J K, et al. Sequencing using capillary electrophoresis of short tandem repeat alleles separated and purified by high performance liquid chromatography［J］. Electrophoresis, 1998,19(1):108-118.
【13】DEVANEY J M, GIRARD J E, MARINO M A. DNA microsatellite analysis using ion-pair reversed-phase high-performance liquid chromatography［J］. Anal Chem, 2000,72(4):858-864.
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