The expert system of genotype discrimination for D5S818 locus based on near-infrared spectroscopy-principal discriminant variate

Abstract

This paper studied the expert system of genotype discrimination for the STR locus D5S818 based on near-infrared spectroscopy-principal discriminant variate (PDV). Six genotypes, i.e. genotypes 10-10, 10-11, 11-11, 11-12, 11-13 and 13-13, were selected as research subjects. Based on the optimum polymerase chain reaction (PCR) conditions, about 54 measuring samples for each genotype were obtained; these samples were tested by near-infrared spectroscopy directly. With differences between homozygote genotypes and heterozygote ones, and differences of the total number of core repeat units between the six genotypes, two types of genotyping-tree structure were constructed and their respective PDV models were studied using the near-infrared spectra of the samples as recognition variables. Finally, based on the classification ability of these two genotyping-tree structures, an optimum expert system of genotype discrimination was built using the PDV models. The result demonstrated that the built expert system had good discriminability and robustness; without any preprocessing for PCR products, the six genotypes studied could be discriminated rapidly and correctly. It provided a methodological support for establishing an expert system of genotype discrimination for all genotypes of locus D5S818 and other STR loci.

Keywords: Expert system; Genotyping-tree structure; Near-infrared spectroscopy; Principal discriminant variate; Short tandem repeat.

Figure 1

Agarose gel electrophoretograms of the samples of the six different genotypes of the locus D5S818 (Lanes 1, 2, 3, 4, 5 and 6: Genotypes 10–10, 10–11, 11–11, 11–12, 11–13 and 13–13, respectively).

Figure 2

Measured spectra for the 57 samples of the genotype 10–10.

Figure 3

Optimum PDV discriminant model between the genotypes 10–10 and 10–11. (“▴” the calibration sample and “△” the prediction sample for the 10–10 genotype; “•” the calibration sample and “○” the prediction sample for the 10–11 genotype).

Figure 4

Built genotyping-tree structure of the six studied genotypes based on the difference of homozygote and heterozygote.

Figure 5

Optimum PDV discriminant model between the class of 10–10, 11–11 and 13–13 and the one of 10–11, 11–12 and 11–13. (“▴” the calibration sample and “△” the prediction sample for the genotypes 10–10; 11–11 and 13–13; “•” the calibration sample and “○” the prediction sample for the ones 10–11, 11–12 and 11–13).

Figure 6

Built genotyping-tree structure of the six studied genotypes based on the different total numbers of the core repeat units of the genotypes.

Figure 7

Optimum PDV discriminant model between the class of 10–10, 10–11, 11–11, 11–12 and the one of 11–13, 13–13. (“▴” the calibration sample and “△” the prediction sample for the genotypes 10–10, 10–11, 11–11 and 11–12; “•” the calibration sample and “○” the prediction sample for the ones 11–13 and 13–13).

Figure 8

Optimum PDV discriminant model between the class of 10–10, 10–11 and the one of 11–11, 11–12. (“▴” the calibration sample and “△” the prediction sample for the genotypes 10–10 and 10–11; “•” the calibration sample and “○” the prediction sample for the ones 11–11 and 11–12).

Figure 9

Optimum PDV discriminant model between the genotypes 11–13 and 13–13. (“▴” the calibration sample and “△” the prediction sample for the 11–13 genotype; “•” the calibration sample and “○” the prediction sample for the 13–13 genotype).

Figure 10

Optimum PDV discriminant model between the genotypes 11–11 and 11–12. (“▴” the calibration sample and “△” the prediction sample for the 11–11 genotype; “•” the calibration sample and “○” the prediction sample for the 11–12 genotype).