基于紫外光谱-惩罚岭型线性判别对STR基因座分型研究

目的:结合紫外光谱(UV-s)和惩罚岭型线性判别(PRLDA)模式识别方法建立短串联重复序列(STR)的基因分型方法。方法:以D16S539基因座的9-9,12-13两种基因型为研究对象,研究包含该多态性位点的DNA片段的聚合酶链反应(PCR)扩增条件和紫外检测条件,建立标准化扩增条件和检测条件,以此获得基因分型的标准物及其标准UV-s。以标准光谱为识别变量,建立了9-9与12-13基因型的PRLDA判别模型。结果:所建立的PRLDA模型有较大的类间距和较小的类内距,表明模型具有良好的稳健性,且预测样本均分布在校正样本集的范围之内,对预测样本也表现出了极强的判别能力。结论:该方法不需任何检测前处理,而只需一步PCR扩增和UV-s检测即可实现STR的基因分型,具有简单、快速、低成本等优点。

Genotyping of STR Locus Based on Ultraviolet Spectroscopy and Penalized Ridge-type Linear Dicriminant Analysis

Objective： To establish an approach for genotyping of the STR locus based on the ultraviolet spectroscopy（UVS） and penalized ridge-type linear dicriminant analysis （PRLDA）.Methods： Taking the two different genotypes 9-9,12-13 of locus D16S539 as example,the conditions of PCR amplification and UVS detection for a DNA fragment containing the polymorphism sites were studied,and then the standardized amplification and detection conditions were established,under which standard samples and standard ultraviolet spectra （UV-s） were obtained.Using these standard spectra as identifying variables,the PRLDA model of the two genotypes was established.Results： The established PRLDA model was not only robust with short within-class distance and large between-class distance,but also had strong predictive power which could effectively overcome the spectral collinearity.Conclusion： Without any pretreatment for the analyzed samples after PCR amplification,the two genotypes of GD16S539 locus could be indirectly determined by using the UV-s of the samples,which had the advantages of being simple,rapid and low-cost.