Keywords

Allele Frequencies; Chinese Minorities Population; Non-CODIS loci Paternity Testing STR.

Introduction

Short tandem repeats (STR) are one of highly polymorphism genetic markers in the human genome [1]. The IdentifilerTM [2], Promega Fusion System [3] and DNA Typer 15plusTM [4] PCR amplification kits have high Discrimination Power and Probability of Paternity Exclusion. In most cases, using these kits would be sufficient for human individual identification and standard trio paternity testing. However, in some complex relationships cases, such as single parent/child paternity analysis, uncle–nephew, grandparents–grandchildren, more STR loci are required to determine more precisely the relationships [5-9]. In this study, 22 STR from a polymorphism systems constructed by our own laboratory were tested to evaluate their performance in both single source comparison and kinship analysis for the two minorities from Yunnan Province, China. The distributions of allelic frequencies and forensic statistical parameters of these 22 STRs loci in the two population were generated. Hardy-Weinberg Equilibrium of each locus tested. The genetic distances (i.e., Fst) among the two population and other Chinese populations were estimated.

Materials and Methods

Population samples

A total of 200 samples from healthy unrelated Wa volunteers and 98 samples from Bai volunteers were collected, with informed consent, from Yunnan province of China.

PCR amplification and electrophoresis

PCR reactions were performed in a total volume of 10μl containing one 1.0mm.blood card, 2×buffer mix, 2×primer mix (Institute of Forensic Science of China). Amplification was carried out by GeneAmp 9700 (Applied Biosystems, USA) with some modification of PCR condition. Pre-PCR denaturation was performed at 95°C for 11 min, followed by 28 cycles of denaturing at 94°C for 45s, annealing at 59°C for 2min, extension at 72°C for 1min, and a final extension at 60°C for 30 min. PCR products were analyzed by an ABI 3730xl Genetic Analyzer (Applied Biosystems, USA). Data were analyzed using Genemapper ID 3.2 software (Applied Biosystems, USA) and the alleles were determined by comparing with the allelic ladders.

Statistical analysis

We calculated the allele frequency at each locus from the numbers of alleles in the population samples. Forensic statistical parameters were calculated with the software PowerStatsV1.2 (Promega, USA) [10]. Hardy–Weinberg Equilibrium (HWE) expected Heterozygosity (He) of each locus and the genetic distance (Fst) between the two population and other Chinese populations were tested by using the Genepop Version 4.2 software package (genepop.curtin.edu.au).

Results and Discussion

The observed allele frequencies and forensic statistical parameters of the loci in the two population are shown in Table 1-4. The genotype frequency distributions in the 22 STR loci showed no deviations from the Hardy–Weinberg equilibrium by an exact test. Deviations from HWE were detected at D3S4529 (p-value = 0.0031)in Wa population and (p-value = 0.0316) in Bai population. After Bonferroni correction (i.e., p-value = 0.05/22 = 0.00227), no locus was significant.

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Table 1:

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Table 1. Allele frequencies of 22 STR in Wa population (n =200).

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Table 2:

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Table 2. Allele frequencies of 22 STR in Bai population (n =98).

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Table 3:

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Table 3. Forensic statistical parameters of 22 STR in Wa population.

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Table 4:

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Table 4. Forensic statistical parameters of 22 STR in Bai population.

Among the 22 STR loci in Wa population, 14 loci had He greater than 0.7, and 5 loci had DP greater than 0.9. The power of discrimination ranged from 0.7649 (D1GATA113) to 0.9287 (D9S2157), whereas the power of exclusion ranged from 0.2849 (D1S1677) to 0.6753 (D3S4529). The expected heterozygosity, power of discrimination and polymorphism information content of D9S2157 was the highest among the loci. The others had medium probability of exclusion and discrimination power. The cumulative discrimination power across these 22 loci in Wa population was >0.9 999 999 999 99. The combined probability of exclusion trios is 0.9999990508.

Among the 22 STR loci in Bai population, 13 loci had He greater than 0.7, and 5 loci had DP greater than 0.9. The power of discrimination ranged from 0.7722 (D1S1627) to 0.9248 (D2S441), whereas the power of exclusion ranged from 0.3455 (D1S1627) to 0.6105 (D2S441). The expected heterozygosity, power of discrimination and polymorphism information content of D2S441 was the highest among the loci. The others had medium probability of exclusion and discrimination power. The cumulative discrimination power across these 22 loci in Bai population was >0.9 999 999 999 99. The combined probability of exclusion trios is 0.9999980034.

The population data of this study were compared with previously published data from other Chinese populations [11] using the Genepop Version 4.2 software package. Table 5 shows the genetic distance (Fst) between the Wa population, Bai population and Chinese Han population. Apparently, Wa population is distant from Bai population, and both the two populations are distant from Chinese Han population, the Fst values are all more than 0.01 with the 22 loci. This observation further confirms that the Wa and Bai population are relatively isolated from the other populations in China. Generally, these statistical analysis results of this study suggest that these 22 loci had high or medium polymorphism and can be used as genetic markers in human identity testing in the Wa and Bai populations from Yunnan province, China.

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Table 5:

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Table 5. Population pair wise Fst among three populations.

Acknowledgements

This work was funded by Special fund for basic scientific research business of central public research institutes [No. 2014JB001].

References

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