The determination for the three genotypes of D16S539 locus based on near-infrared spectroscopy and chemical pattern recognition.

ABSTRACT

The paper has established an approach of typing short tandem repeats (STRs) based on the near-infrared spectroscopy (NIRS)-chemical pattern recognition. Taking the three genotypes 9-9, 9-11 and 11-11 of D16S539 locus as example, which have a middle degree of difference, DNA fragments containing the polymorphism sites were amplified by a pair of primers to obtain three genotypes samples; these samples were tested by the NIRS directly; using their spectra as recognition variables, the chemical pattern recognition models of the three genotypes were respectively established by using the principal discriminant variate (PDV) and support vector machine (SVM). The two models have a good fitting ability and strong prediction (i.e. the predicting accuracy was 100%). They are robust for these strong collinear spectra and the small number of the calibration samples. Without any preprocessing for the analyzed samples after PCR, the three genotypes of D16S539 locus could be indirectly determined by using the NIRS-s of the samples with the help of the models. This method is simple, rapid and low cost.