Studies on short tandem repeat genotyping and its expert system based on ultraviolet spectroscopy-principal discriminant variate

The paper has presented a method which could be used to detect short tandem repeat (STR) rapidly, simply and low-costly based on ultraviolet spectroscopy combined with principal discriminant variate (PDV) of chemical pattern recognition. Genotypes 10-11, 11-11 and 10-12 of STR locus D16S539 which was commonly used in forensic medicine were used to establish two-classified PDV genotyping models. The conditions of polymerase chain reaction (PCR) and ultraviolet spectral detection were optimized. Based on the optimal PCR conditions, each genotype was amplified twice in parallel. For the PDV model of 10-11 and 11-11, the prediction samples were all distributed in the scope of calibration samples, the between-class distances were big enough and the prediction accuracy was up to 100%, which indicated that the established PDV model could be used to discriminate genotypes with only one core repeat unit difference. Then the PDV model for genotypes 11-11 and 10-12 whose difference was even smaller (the total numbers of the two genotypes were both 22) was established. The model displayed the same classified characteristics as the above-mentioned one. Therefore, we assumed that the ultraviolet spectrum (UVS)-PDV method could be used to discriminate the genotypes with various degrees of differences. Subsequently, the expert system for six genotypes of the D16S539 locus was constructed based on their difference in the total number of core repeat unit. The 5 two-classified PDV models in the expert system all displayed satisfactory robustness and the discrimination ratios of the prediction samples were all 100%. The result indicated that the expert system based on the UVS-PDV method could be used to discriminate multi-genotypes of STR locus. Based on UVS, the paper achieved the detection of STR genotypes rapidly, simply and low-costly.