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Journal of Zhejiang University. Science. B logoLink to Journal of Zhejiang University. Science. B
. 2016 May;17(5):367–374. doi: 10.1631/jzus.B1500228

Genetic polymorphism analyses of a novel panel of 19 X-STR loci in the Chinese Uygur ethnic minority* #

Yu-xin Guo 1,2,3, Jian-gang Chen 4, Yan Wang 5, Jiang-wei Yan 6, Jing Chen 6, Tian-hua Yao 7, Li-ping Zhang 4, Guang Yang 8, Hao-tian Meng 1,2,3, Yu-dang Zhang 1,2,3, Ting Mei 4, Yao-shun Liu 4, Qian Dong 1,2,3, Bo-feng Zhu 1,2,3,†,‡
PMCID: PMC4868827  PMID: 27143264

Abstract

The population genetic data and forensic parameters of 19 X-chromosome short tandem repeat (X-STR) loci in Chinese Uygur ethnic minority are presented. These loci were detected in a sample of 233 (94 males and 139 females) unrelated healthy individuals. We observed 238 alleles at the 19 X-STR loci, with the corresponding gene frequencies spanning the range from 0.0021 to 0.5644. After Bonferroni correction (P>0.0026), there were no significant deviations from Hardy-Weinberg equilibrium. The cumulative power of discrimination in females and males, and the probability of exclusion of the 19 X-STR loci were 0.999 999 999 999 999 999 998 091, 0.999 999 999 999 966, and 0.999 999 986 35, respectively. The cumulative mean exclusion chance was 0.999 999 992 849 in deficiency cases, 0.999 999 999 999 628 in normal trios, and 0.999 999 998 722 in duo cases. The high value of the forensic parameters mentioned above revealed that the novel panel of 19 loci had important values for forensic applications in the Uygur group.

Keywords: X-chromosome, Short tandem repeat (STR), Uygur, Genetic polymorphism, Forensic

1. Introduction

At present, short tandem repeat (STR) loci are applied broadly in paternity testing and individual identification of forensic cases in forensic DNA laboratories all over the world (Rosenberg et al., 2002; Deng et al., 2013; Wang et al., 2013; Zhu et al., 2013; 2014). X-chromosome STRs (X-STRs), which contain the characteristics of both autosomal and uniparental genetic markers, are verified to be of high-efficiency in cases such as the tests of mother-son kinship, half-sisters having a common biological father without the father’s DNA, or grandmother-granddaughter relationships (Liu et al., 2008; Nadeem et al., 2009; Luo et al., 2011). Although a few panels of X-STRs have been used, these X-STR kits were not enough for forensic applications, because of insufficient X-STR loci. Thus, 19 X-STRs (DXS8378, DXS7423, DXS10148, DXS10159, DXS10134, DXS7424, DXS10164, DXS10162, DXS7132, DXS10079, DXS6789, DXS101, DXS10103, DXS10101, HPRTB, DXS6809, DXS10075, DXS10074, and DXS10135) were selected to build up a novel X-STR panel.

Uygur is one of the important ethnic minorities in the People’s Republic of China and a large proportion of Uygurs live in the Xinjiang Uygur Autonomous Region, China (Xu, 2003; Jin and Chu, 2006). It is significant to obtain the information of various genetic markers in Uygur for forensic identification and population genetics. As in the previous reports, we investigated the genetic polymorphisms of 24 Y-chromosomal STR haplotypes (Zhu et al., 2014), killer cell immunoglobulin-like receptor genes (Wang et al., 2012), 21 autosomal STR loci (Deng et al., 2013), and HLA-A, -B, and -DRB1 loci with sequence-based typing (Shen et al., 2010) in the Chinese Uygur ethnic group, but the genetic polymorphism analyses of the novel panel of 19 X-STRs mentioned above have not yet been reported until now. In the present study, we used the panel to estimate the allelic frequencies of the 19 X-STR loci, calculate the important forensically statistical parameters for each locus in a sample of 233 unrelated individuals, and evaluate the allelic frequency differentiations of these loci between the Uygur group and other groups, in order to gain a better understanding of the Uygur overall genetic background.

2. Materials and methods

2.1. Sample preparation and DNA extraction

Informed consent was obtained from all the eligible individuals, and bloodstain samples were collected from 233 unrelated healthy Uygur individuals (139 females and 94 males) living in Ili of the Xinjiang Uygur Autonomous Region, China. The criteria of sample selection were: the ancestors should be unrelated within at least three generations, come from the Uygur ethnic group, and have no family migration. The study was conducted according to the human and ethical research principles of the Stomatological Hospital, Xi’an Jiaotong University, China. After sample collection, the Chelex-100 method was used to extract genomic DNA from the bloodstain samples as described by Walsh et al. (2013).

2.2. PCR amplification and X-STR genotyping

Multiplex polymerase chain reaction (PCR) was performed by the AGCU X19 STR fluorescence amplification reagents (AGCU ScienTech Inc., Wuxi, Jiangsu, China) in a single PCR system in accordance with the manufacturer’s instructions. PCR was performed on a GeneAmp PCR System 9700 Thermal Cycler (Applied Biosystems, Foster City, CA, USA) in a 25-μl reaction volume containing reaction mix, X19 primers, C-Taq, and sterile distilled H2O (sdH2O). Capillary electrophoresis was carried out on the ABI Genetic Analyzer 3500 (Applied Biosystems, Foster City, CA, USA) following the manufacturer’s instructions. Alleles of 19 X-STR loci were genotyped using the GeneMapper ID software V3.2 (Applied Biosystems, Foster City, CA, USA), based on peak heights reaching a set threshold value of 50 relative fluorescence units.

2.3. Statistical analyses

The allelic frequencies of 19 X-STR loci and Hardy-Weinberg equilibrium (HWE) were analyzed by the modified Powerstate V1.2 spreadsheet (Promega, Madison, WI, USA) (Tereba, 1999). The P-value of HWE tests was adjusted using the Bonferroni correction (P=0.05/19=0.0026). HWE was only calculated in the female samples. Forensic statistical parameters including polymorphism information content (PIC), heterozygosity (HET), the power of discrimination in females (PDF) and males (PDM), and mean exclusion chances (MEC) were performed with ChrX-STR.org 2.0 (http://www.chrx-str.org) based on allelic frequencies. Pairwise linkage disequilibrium (LD) analysis was estimated by the Genepop Version 4.0.10 (http://genepop.curtin.edu.au). In order to measure the differences of allele frequencies among different populations, the locus-by-locus Fst and P-values were calculated based on 19 X-STR allele frequencies using the analysis of molecular variance (AMOVA) method by ARLEQUIN Version 3.0 software (Excoffier et al., 2007).

3. Results and discussion

3.1. Forensic parameter analysis

HWE was tested in female samples and no significant deviations were observed after Bonferroni correction (P>0.0026). There were no significant differences for the allelic frequencies of 19 X-STRs between male and female subgroups according to exact tests, except DXS10134, DXS7424, DXS101 and DXS10074 loci. Therefore, allelic frequencies of male and female samples in these 4 loci are shown separately, while the remaining loci are shown together. The allele frequency distributions are shown in Tables 1 and 2. Forensic statistical parameters of the 19 X-STR loci including HET, PDF, PDM, probability of exclusion (PE), paternity index (PI), PIC, and MEC are shown in Table 3. The allelic frequencies of 19 X-STR loci ranged from 0.0021 to 0.5644. The HET ranged from 0.5493 at the DXS 10164 locus to 0.9258 at the DXS10135 locus. The highest and the lowest values of PE were observed at the DXS10135 locus (PE=0.8572) and the DXS10164 locus (PE=0.2928), respectively. The PDF ranged from 0.7889 at the DXS10164 locus to 0.9908 at the DXS10135 locus, and the PDM ranged from 0.6016 at the DXS10164 locus to 0.9301 at the DXS10135 locus. The cumulative PDF, PDM, and PE of the 19 X-STR loci were 0.999 999 999 999 999 999 998 091, 0.999 999 999 999 966, and 0.999 999 986 35, respectively. In the 19 X-STRs, the highest and the lowest values of PIC were surveyed at the DXS10164 locus (PIC=0.54923) and the DXS10135 locus (PIC=0.9258), respectively. The highest value of MEC in deficiency cases, normal trios and duo cases were observed at the DXS10135 locus (MEC=0.8585, 0.9256, and 0.8663, respectively). The lowest values were found at the DXS10164 locus (MEC=0.3595, 0.5493, and 0.4021, respectively). The cumulative MEC in deficiency cases, normal trios and duo cases were 0.999 999 992 849, 0.999 999 999 999 628 and 0.999 999 998 722, respectively. The parameters mentioned above revealed that the panel of 19 loci had great potential for forensic personal identification and forensic paternity testing.

Table 1.

Allele frequency distributions in Chinese Uygur group at 15 X-STR loci with no difference between male and female samples

Allele DXS 8378 DXS 7423 DXS 10148 DXS 10159 DXS 10164 DXS 10162 DXS 7132 DXS 10079 DXS 6789 DXS 10103 DXS 10101 HPRTB DXS 6809 DXS 10075 DXS 10135
 8 0.0043 0.0193
 9 0.0408 0.0300 0.0021
 10 0.3970 0.5644 0.0043
 11 0.3283 0.2639 0.0129 0.0708
 12 0.2017 0.0021 0.0880 0.0923 0.2940
 12.1 0.0021
 13 0.0129 0.0429 0.0343 0.2983 0.3498 0.0365
 14 0.0150 0.3476 0.3391 0.0064 0.0064 0.1845
 14.2 0.0064
 15 0.4893 0.0064 0.2146 0.0215 0.1116 0.0494 0.0858 0.0064 0.0021
 15.2 0.0021
 16 0.1159 0.0021 0.0494 0.0322 0.0451 0.1373 0.2275 0.0064 0.2103 0.0043
 16.1
 16.2 0.0021 0.0129
 17 0.0021 0.1824 0.0107 0.0773 0.0043 0.0837 0.0021 0.4099 0.0107
 17.2 0.0043 0.0021
 17.3
 18 0.1073 0.3734 0.1116 0.0021 0.1524 0.2833 0.0322
 18.1 0.0021
 18.2 0.0021
 18.3 0.0021
 19 0.0730 0.2532 0.2103 0.0515 0.3605 0.0279 0.0451
 19.1 0.0021
 20 0.0258 0.0021 0.1116 0.3219 0.2639 0.1094 0.0923
 20.1 0.0021 0.0086
 20.2 0.0021
 21 0.0043 0.0021 0.0193 0.1330 0.2489 0.0043 0.0923
 21.1 0.0021 0.0150
 22 0.0064 0.0150 0.0579 0.1352 0.1159
 22.1 0.0579 0.0021
 23 0.0043 0.0815 0.0215 0.0386 0.0794
 23.1 0.0665 0.0086
 23.2 0.0021
 24 0.0107 0.2811 0.1137
 24.1 0.1288 0.0043
 24.2 0.0021
 25 0.0021 0.2511 0.0043 0.0644
 25.1 0.1416
 26 0.1781 0.0043 0.0536
 26.1 0.1373
 26.2 0.0043
 27 0.1180 0.0193 0.0021 0.0451
 27.1 0.0901
 27.2 0.0021 0.0343
 28 0.0665 0.0236 0.0064 0.0536
 28.1 0.0665
 28.2 0.0644
 29 0.0150 0.0258 0.0451
 29.1 0.0365
 29.2 0.0880
 30 0.0794 0.0172 0.0408
 30.1 0.0193
 30.2 0.1180
 31 0.1159 0.1266 0.0172
 31.1 0.0043
 31.2 0.1009
 32 0.1395 0.2339 0.0215
 32.1 0.0043
 32.2 0.0451
 33 0.0901 0.2554 0.0064
 33.2 0.0043
 34 0.0408 0.2082 0.0107
 34.2 0.0043
 34.3 0.0064 0.0021
 35 0.0021 0.0923 0.0064
 36 0.0279
 37 0.0021
 38 0.0021
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Table 2.

Allele frequency distribution in Chinese Uygur group at 4 X-STR loci with difference between male and female samples

Allele DXS10134
 DXS7424
 DXS101
 DXS10074
Female Male Female Male Female Male Female Male
 7 0.0471
 8 0.0290
 10 0.0036
 11 0.0362
 12 0.0326
 13 0.0109 0.1158
 14 0.1449 0.0526 0.0145
 15 0.3696 0.2474 0.0181 0.0316 0.0652 0.0316
 16 0.2681 0.4000 0.2065 0.2737
 17 0.1051 0.1526 0.2609 0.0895
 17.3 0.0036
 18 0.0254 0.0211 0.0145 0.0632 0.2391 0.1579
 19 0.0072 0.0105 0.0254 0.1159 0.3421
 20 0.0072 0.0105 0.0145 0.1053
 21 0.0181 0.0316
 22 0.0254 0.0211
 23 0.1051 0.1053
 24 0.2500 0.2211
 25 0.1558 0.2263
 26 0.1449 0.1368
 27 0.1232 0.1053
 28 0.0616 0.0211
 29 0.0362 0.0158
 30 0.0145
 31 0.0108 0.0105
 32 0.0288 0.0213
 33 0.0612 0.0851
 34 0.0971 0.0851
 35 0.1511 0.1064
 35.3 0.0036
 36 0.2086 0.2553
 36.1 0.0036
 36.3 0.0036
 37 0.1655 0.1915
 37.2 0.0036
 37.3 0.0216 0.0106
 38 0.1439 0.0638
 38.2 0.0036 0.0106
 38.3 0.0072 0.0106
 39 0.0468 0.0532
 39.3 0.0108 0.0319
 40 0.0036
 40.3 0.0108 0.0106
 41 0.0036
 41.3 0.0036 0.0213
 42.3 0.0036 0.0213
 43.3 0.0036 0.0213
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Table 3.

Forensic efficiency parameters of 19 X-STR loci in Chinese Uygur group

Allele PIC HET PE PI PDF PDM MEC1 MEC2 MEC3
 DXS8378 0.6350 0.6948 0.4158 0.1541 0.8482 0.6919 0.4324 0.6350 0.4899
 DXS7423 0.5556 0.6272 0.3213 0.1878 0.7901 0.6245 0.3536 0.5556 0.4097
 DXS10148 0.8969 0.9086 0.8051 0.0476 0.9832 0.9047 0.8069 0.8966 0.8202
 DXS10159 0.7729 0.8044 0.6009 0.0995 0.9323 0.8010 0.6102 0.7725 0.6481
 DXS10134 0.8563 0.8079 0.7330 0.0654 0.9700 0.8692 0.7407 0.8559 0.7606
 DXS7424 0.7281 0.7661 0.5319 0.1186 0.9090 0.7628 0.5545 0.7281 0.5950
 DXS10164 0.5493 0.6042 0.2928 0.1992 0.7889 0.6016 0.3596 0.5493 0.4021
 DXS10162 0.7091 0.7511 0.5061 0.1261 0.8977 0.7479 0.5260 0.7091 0.5716
 DXS7132 0.6960 0.7434 0.4932 0.1299 0.8883 0.7402 0.5058 0.6960 0.5566
 DXS10079 0.7867 0.8132 0.6172 0.0951 0.9408 0.8097 0.6358 0.7867 0.6666
 DXS6789 0.7897 0.8181 0.6264 0.0927 0.9408 0.8146 0.6354 0.7897 0.6696
 DXS101 0.8437 0.8623 0.7119 0.0707 0.9651 0.8586 0.7206 0.8437 0.7428
 DXS10103 0.7426 0.7769 0.5509 0.1132 0.9178 0.7736 0.5725 0.7425 0.6113
 DXS10101 0.9036 0.9145 0.8170 0.0447 0.9850 0.9105 0.8187 0.9036 0.8304
 HPRTB 0.7032 0.7479 0.5008 0.1276 0.8933 0.7447 0.5168 0.7032 0.5649
 DXS6809 0.7839 0.8139 0.6184 0.0948 0.9375 0.8104 0.6260 0.7839 0.6621
 DXS10075 0.6548 0.7082 0.4362 0.1474 0.8627 0.7051 0.4584 0.6547 0.5112
 DXS10074 0.7821 0.8120 0.6150 0.0957 0.9369 0.8085 0.6250 0.7821 0.6604
 DXS10135 0.9258 0.9341 0.8572 0.0350 0.9908 0.9301 0.8585 0.9256 0.8663
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PIC, polymorphism information content; HET, heterozygosity; PE, probability of exclusion; PI, paternity index; PDF, power of discrimination in female; PDM, power of discrimination in male; MEC1, mean exclusion chances (MEC) in deficiency cases, mean exclusion chance for deficiency cases; MEC2, MEC in normal trios, mean exclusion chance for normal trios; MEC3, MEC in duo cases, mean exclusion chance for duo cases

3.2. Linkage disequilibrium analyses

It is necessary to estimate the value of LD before these STR loci are used for forensic application and population genetics. In this study, among the 171 pairwise loci of 19 X-STRs, P-values of 8 pairwise loci were found to be <0.05 in the Chinese Uygur ethnic minority. However, only one (between DXS10075 and DXS10074, P<0.0001) remained significant after Bonferroni correction (P=0.05/171=0.0003). The value of LD is affected by various factors, for example, genetic linkage, natural selection, and demographic structure. The distance between the two markers (DXS10075 and DXS10074) is 0.021 Mbp (http://chrx-str.org), and therefore genetic linkage is likely to be a major cause of the observed LD.

3.3. Haplotype diversities

According to previously reports, there were seven linkage groups observed in the 19 X-STRs. These clusters were listed as follows: DXS10135-DXS8378-DXS10148, DXS7132-DXS10074-DXS 10075-DXS10079, DXS10103-DXS10101-HPRTB, DXS10134-DXS7423, DXS10159-DXS10162-DXS 10164, DXS6809-DXS6789, and DXS7424-DXS101. The first four clusters were obtained from a database (http://xdb.qualitype.de/xdb/linkageTable.jsf), and the remaining clusters from previous studies (Edelmann et al., 2002; 2010; Szibor et al., 2005). Haplotype frequencies for the seven clusters in 94 male samples are displayed in the Table S1. The most common haplotypes in the Uygur ethnic minority were observed at DXS10134-DXS7423 (H36-15) and DXS7424-DXS101 (H16-24) with a frequency of 0.1064, followed by DXS10134-DXS7423 (H36-14, H37-15) and DXS6809-DXS6789 (H32-21) at 0.0957. Haplotype diversities for the seven cluster groups were 0.9954, 0.9977, 0.9920, 0.9556, 0.9792, 0.9669 and 0.9634, respectively.

3.4. Interpopulation differentiation

Population differentiation between the Uygur and 11 other previously published groups was analyzed by the means of AMOVA based on the allelic frequencies of 9 overlapping STR loci. The Fst and P-values of these loci are shown in the Table S2. The results showed that statistically significant differences (P<0.05) were observed between the Uygur and Greenlander (Tomas et al., 2012) and Somali (Tomas et al., 2012) at 8 loci; East Timor (Moreira et al., 2015), Japanese (Uchigasaki et al., 2013), Shenyang Han population (Uchigasaki et al., 2013) and Dane (Tomas et al., 2012) at 6 loci; Shanghai Han population (Zhang et al., 2012) at 5 loci; Bhil tribal population (Shrivastava et al., 2015) and Taiwanese (Chen et al., 2014) at 4 loci; Malay (Samejima et al., 2012) and Guangdong Han population (Zeng et al., 2011) at 3 loci. The results of AMOVA demonstrated that the allelic frequency in most of these loci distributed differently among different ethnic groups. Therefore, more studies on STR loci in different ethnic groups should improve understanding of the genetic relationships between the different ethnic groups and their genetic backgrounds.

4. Conclusions

In summary, the 19 X-STR loci were used to investigate the genetic polymorphisms of the Uygur ethnic minority and the population differentiations between the Uygur group and other populations. The value of cumulative PDF, PDM, and PE showed that these 19 X-STR loci could be used as complement for the application of autosomal STR. Moreover, these results provided basic data for population genetics and forensic science research.

List of electronic supplementary materials

Table S1 Haplotype diversities of seven clusters in Uygur male individuals (n=94)

JZUSB17-0367-TS1.pdf (68KB, pdf)

Table S2 FSt and P-values for allele frequency distribution between Uygur ethnic group and the other groups previously published

JZUSB17-0367-TS2.pdf (42.6KB, pdf)

Footnotes

*

Project supported by the Scientific Research Program of the Higher Education Institution of the Xinjiang Uygur Autonomous Region (No. XJEDU2011i33), China, the National Natural Science Foundation of China (No. 81373248), and the National Science Foundation for Distinguished Young Scholars of China (No. 81525015)

#

Electronic supplementary materials: The online version of this article (http://dx.doi.org/10.1631/jzus.B1500228) contains supplementary materials, which are available to authorized users

Compliance with ethics guidelines: Yu-xin GUO, Jian-gang CHEN, Yan WANG, Jiang-wei YAN, Jing CHEN, Tian-hua YAO, Li-ping ZHANG, Guang YANG, Hao-tian MENG, Yu-dang ZHANG, Ting MEI, Yao-shun LIU, Qian DONG, and Bo-feng ZHU declare that they have no conflict of interest.

All procedures followed were in accordance with the ethical standards of the responsible committee on human experimentation (institutional and national) and with the Helsinki Declaration of 1975, as revised in 2008 (5). Informed consent was obtained from all volunteers for being included in the study.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Table S1 Haplotype diversities of seven clusters in Uygur male individuals (n=94)

JZUSB17-0367-TS1.pdf (68KB, pdf)

Table S2 FSt and P-values for allele frequency distribution between Uygur ethnic group and the other groups previously published

JZUSB17-0367-TS2.pdf (42.6KB, pdf)

Articles from Journal of Zhejiang University. Science. B are provided here courtesy of Zhejiang University Press

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