|Year : 2022 | Volume
| Issue : 3 | Page : 123-130
Genetic polymorphism investigation of 19 X-STR loci in the Han population in Northern China
Shicheng Hao, Yan Liu, Yan Xu, Dong Zhao, Gexin Liu, Jinpei Zhang, Li Yuan
Key Laboratory of Evidence Science, China University of Political Science and Law, Ministry of Education, Beijing, China
|Date of Submission||03-Sep-2021|
|Date of Decision||11-Jul-2022|
|Date of Acceptance||12-Jul-2022|
|Date of Web Publication||02-Sep-2022|
China University of Political Science and Law, Beijing 100088
Source of Support: None, Conflict of Interest: None
To investigate the genetic polymorphisms of 19 X-STR loci in the Han population in Northern China, samples from 628 unrelated individuals (314 males and 314 females) were collected and 19 X-STR loci were amplified by AGCU X19 STR System. A total of 270 different alleles were detected in 19 X-STR loci. All loci were in Hardy − Weinberg equilibrium and there was only one pair of linkage loci (DXS10103-DXS10101). There was no significant difference in allele frequency between male and female populations. The combined power of discrimination in males was 1–1.8667 × 10−13, while the combined power of discrimination in females was 1–3.6532 × 10−22. The combined mean paternity exclusion chance (CMEC) for X-chromosomal markers in father/daughter or mother/son duos Mean paternity exclusion chance (MECDesmarais Duo) was 1–5.1109 × 10−9. Moreover, the CMEC for X-chromosomal markers in trios involving daughters (MECDesmarais) was 1–2.0292 × 10−12. The compound amplification system composed of 19 X-STR in this study showed high polymorphism in the Han population of Northern China, which had a high application value in difficult genetic relationship identification.
Keywords: Forensic genetics, genetic polymorphisms, northern Han, X chromosome STR
|How to cite this article:|
Hao S, Liu Y, Xu Y, Zhao D, Liu G, Zhang J, Yuan L. Genetic polymorphism investigation of 19 X-STR loci in the Han population in Northern China. J Forensic Sci Med 2022;8:123-30
|How to cite this URL:|
Hao S, Liu Y, Xu Y, Zhao D, Liu G, Zhang J, Yuan L. Genetic polymorphism investigation of 19 X-STR loci in the Han population in Northern China. J Forensic Sci Med [serial online] 2022 [cited 2022 Sep 30];8:123-30. Available from: https://www.jfsmonline.com/text.asp?2022/8/3/123/355567
| Introduction|| |
In consequence of X-STR's special inheritance pattern, it can exert its unique value in identifying half-parent, grandmother-granddaughter, and father-daughter relationships by excluding kinship. With the in-depth study on X-STR, the forensic application value of X-STR has become more and more prominent in practical cases, making X-STR is one of the commonly used genetic markers in forensic science.
Up to now, the database of X-STR loci (http://www.chrx-str.org/) established by professors Reinhard Szibor, Jeanett Edelmann, and Sandra Hering in 2007 has included the characteristic information of 55 X-STR loci, primers, alleles, and their sequences, the results of population genetic investigation. The X chromosome has been divided into four linkage groups at four locations. The distance between the linkage groups is <0.5cM. The recombination rate is <0.5%. In the field of forensic science, the current research work on X-STR is mainly focused on genetic polymorphism, and many scholars use X-STR to carry out human population genetic investigations such as genetic distance, population origin, and so on. The study of genetic polymorphism focuses on the construction of multiple amplification system and the investigation of population genetic data in different regions and races.,,,,,,,,, At the same time, some studies, focus on finding more X-STR loci to enrich the loci that can be used to detect complex genetic relationships. It is of great importance to investigate the genetic polymorphisms in specific populations to establish a complete forensic reference database. However, China is a country with a wide range of regions and ethnic groups. Moreover, there are still some problems in the study of X-STR genetic polymorphism, such as a small number of loci, few types of population, and so on, and there is still a big gap in the data of population genetics. Based on the above background, 19 X-STR loci were amplified by AGCU X19 STR System to study the genetic polymorphism of 628 unrelated individual samples of Han population in Northern China and were evaluated its forensic efficacy.
| Materials and Methods|| |
In this study, the sample consisted of 628 unrelated individuals (314 males and 314 females) from the Han population in Northern China, mainly from Beijing, Hebei, Henan, and Shandong. All volunteers who provided samples signed an informed consent form. This study has been approved by Ethical Committee, Institute of Evidence Law and Forensic Science, China University of Political Science and Law (Item Number: 202003, Date: November 3, 2020).
We took 6 mm2 blood card or oral swab for each sample and extract DNA by chelex method. All of the samples were amplified using the AGCU X19 STR System (AGCU ScienTech Incorporation) in the GeneAmp polymerase chain reaction (PCR) 9700 thermal cycler (Applied Biosystems, Foster City, CA, USA), containing 19 X-STRs (DXS8378, DXS7423, DXS10148, DXS10159, DXS10134, DXS7424, DXS10164, DXS10162, DXS7132, DXS10079, DXS6789, DXS101, DXS10103, DXS10101, HPRTB, DXS6809, DXS10075, DXS10074, and DXS10135). PCR amplification procedures were performed according to the reagent instructions, and each reaction system consisted of 4 μl of the reaction mixture, 2 μl of primers, 0.2 μl of A-Taq DNA polymerase, and 3.8 μl of sdH2O. Moreover, each batch of experiments contained a negative control and a positive control.
The amplified PCR products were detected by capillary electrophoresis in the ABI 3130XL Genetic Analyzer (Applied Biosystems, Foster City, CA, USA). The results of electrophoresis were analyzed in accordance with allelic ladders by the GeneMapper ID-X v1.5 software (Applied Biosystems, Foster City, CA, USA). All experimental procedures were performed according to laboratory internal control standards.
Analysis of data
The Hardy-Weinberg equilibrium (HWE) testing and linkage disequilibrium LD testing of 19 X-STR genetic markers were performed on female samples using Arlequin v3.5 software. Moreover, the software was used to analyze the significant difference in the distribution frequency of X-STR alleles in male and female populations. Allele frequencies and the forensic parameters of 19 X-STR loci were calculated using StatsX v2.0 software: The observed heterozygosity, expected heterozygosity and gene diversity (GD) in female individuals were tested. Moreover, there are other forensic statistical parameters, such as the power of discrimination in females (PDF) and in males (PDM), polymorphism information content (PIC), mean paternity exclusion chance (MECKrüger, MECKishida, MECDesmarais, MECDesmarais Duo), the combined PDF, and the combined PDM as well as the combined mean paternity exclusion chance (CMEC).
| Results and Discussions|| |
After HWE testing on a sample of 314 women, the P values of the 19 loci except for DXS6789 were all >0.05, which were consistent with HWE. After applying the Bonferroni correction (i.e., P > 0.05/19 = 0.002631579), DXS6789 was also consistent with HWE. This indicated that the population consisting of 628 unrelated Han Chinese individuals from Northern China investigated in this study was consistent with HWE and could reflect the population level. Therefore, the data from this population survey had a certain degree of credibility.
Among the 171 paired loci composed of 19 X-STR locus pairs, a total of eight pairs of loci showed LD (P < 0.05). After applying the Bonferroni correction (i.e., P < 0.05/171 = 0.000292398), there was only one pair of linkage loci (DXS10103-DXS10101). Since all X-STR loci are on the same X chromosome, LD is more likely to occur. In the process of gene transmission, if the loci are in LD, the corresponding alleles tend to be coinherited. In this case, if the production method is still used to calculate genotype frequency, the results will be inaccurate. There were 69 DXS10103-DXS10101 haplotypes with haplotype frequencies ranging from 0.0032 to 0.0924. Among them, haplotypes 16–31 had the highest frequency of 0.0924 with 29 occurrences. HD and PIC of DXS10103-DXS10101 haplotypes were >0.9, showing good polymorphism. PD and MEC were both >0.9, showing a relatively high value for forensic applications. [Table 1] shows DXS10103-DXS10101 haplotype frequencies in the Han population in Northern China.
|Table 1: DXS10103-DXS10101 haplotype frequencies in the Han population in Northern China|
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A total of 270 different alleles were detected at 19 X-STR loci in 628 unrelated individuals. Significant differences in allele distribution frequencies between the male and female populations were analyzed using Arlequin v3.5 software. The P values for all 19 loci were >0.05, indicating that the allele distribution frequencies of the 19 X-STR loci were not significantly different between the male and female populations. Meanwhile, the female population was consistent with HWE, so the pooled allele frequencies could be calculated. [Table 2] shows the pooled allele frequencies of 19 X-STR loci in the Han Chinese in Northern China. Each of the loci contained 5 (DXS8378, DXS7423) to 32 (DXS10135) alleles, with the corresponding allele frequencies ranging from 0.0011 to 0.6348.
|Table 2: The allele frequencies of 19 X-STR loci in the Han population in Northern China|
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[Table 3] shows the forensic parameters based on the pooled allele frequencies. GD ranging from 0.5067 (DXS7423) to 0.9215 (DXS10135). PIC also followed the above trend, ranged from 0.4322 (DXS7423) to 0.9150 (DXS10135), with DXS10135 being the loci with the highest polymorphic information. DPM male probability of discrimination ranged from 0.5061 (DXS7423) to 0.9205 (DXS10135), while the range for DPF female probability of discrimination was 0.6821 (DXS7423) to 0.9882 (DXS10135). The ranges for MECKruger, MECKishida, MECDesmarais, and MECDesmarais duo were 0.2475 (DXS7423) to 0.8397 (DXS10135), 0.4321 (DXS7423) to 0.9153 (DXS10135), 0.4322 (DXS7423) to 0.9150 (DXS10135), and 0.2940 (DXS7423) to 0.8487 (DXS10135), respectively.
It has been shown that a PIC >0.5 indicates that the loci are highly polymorphic and have great application in forensic medicine. 19 X-STR loci all had PIC values >0.5, showing high polymorphism. Observation of the data reveals that a low number of alleles or an uneven distribution of allele frequencies tends to characterize poorly polymorphic loci.
After calculation, the CDPM male cumulative probability of discrimination was 1–1.8867 × 10−13 while CDPF female cumulative probability of discrimination was 1-3.6532 × 10−22.The values of CMECKruger, CMECKishida, CMECDesmarais, and CMECDesmarais_duo were equal to 1–2.7759 × 10−8, 1–2.0071 × 10−12, 1–2.0292 × 10−12, and 1–5.1109 × 10−9. The overall efficiency of the multiplex amplification system could meet the requirements of forensic DNA testing. Moreover, it can provide an effective means for the identification of difficult kinship cases.
Comparing the differences between groups, we listed in [Table 4]. No differences were found between the Northern Han group and the Sichuan Han group, significant differences were found with the German group, and some degree of differences were found with the Guangdong Han group, Guangxi Zhuang group, Sichuan Tibetan group, and Japanese group. The greater the ethnic differences and the wider the geographic distribution, the greater the differences between groups. This may stem from the fact that the closer the geographic distance, the stronger the genetic homogeneity of the populations. Therefore, it is crucial to select relative populations when applying X-STR in practice.
|Table 4: Difference test results of allele frequency distribution of X-STR loci between northern Han population and other six populations|
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| Conclusions|| |
In this study, allele frequencies and forensic parameters of 19 X-STR loci were obtained by X-STR testing of 628 unrelated individuals from the Han population in Northern China. The female population was consistent with HWE and there was no difference in allele frequency between male and female population. The results of this study can reflect the polymorphic profile of the entire population, and the genetic data obtained provide a high application for the forensic practice of X-STR. In addition, the multiplex amplification system consisting of 19 X-STRs in this study has a high polymorphism in the Han Chinese population in Northern China, which is of high application in the identification of difficult genetic relationships.
Financial support and sponsorship
Conflicts of interest
There are no conflicts of interest.
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[Table 1], [Table 2], [Table 3], [Table 4]