Chemical Pattern Recognition Genotyping of STR Locus Based on Nearinfrared Spectroscopy Combined with Support Vector Machine

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.