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

Genetic polymorphism analyses of a novel panel of 19 X-STR loci in the Chinese Uygur ethnic minority # # 新疆维吾尔族人群19个X-STR新组合基因座 遗传多态性研究 1 2 3 first-author 4 5 6 6 7 4 8 1 2 3 1 2 3 4 4 1 2 3 1 2 3 corresp ‡Corresponding Author ‡Corresponding Author †E-mail:zhubofeng7372@126.com †E-mail:zhubofeng7372@126.com zhubofeng7372@126.com Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China Research Center of Stomatology, Stomatological Hospital, Xi'an Jiaotong University, Xi’an 710004, China Research Center of Stomatology, Stomatological Hospital, Xi'an Jiaotong University, Xi’an 710004, China Department of Biochemistry, Preclinical Medicine College, Xinjiang Medical University, Urumqi 830011, China Department of Biochemistry, Preclinical Medicine College, Xinjiang Medical University, Urumqi 830011, China Criminal Police Detachment of Yili Public Security Bureau, Yili 835000, China Criminal Police Detachment of Yili Public Security Bureau, Yili 835000, China Key Laboratory of Genome Sciences, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China Key Laboratory of Genome Sciences, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China Department of General Dentistry, Stomatological Hospital, Xi'an Jiaotong University, Xi’an 710004, China Department of General Dentistry, Stomatological Hospital, Xi'an Jiaotong University, Xi’an 710004, China Department of Pathology and Laboratory Medicine, Loma Linda University Medical Center, California 92354, USA Department of Pathology and Laboratory Medicine, Loma Linda University Medical Center, California 92354, USA 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. 目的 2 研究新疆维吾尔族人群19个X染色体短串联重复序列（X-STR）基因座和他们组成的7组连锁基因座的单倍型多样性，评价19个X-STR新组合位点的多态信息量和累积个体识别力。为群体遗传学和法医学的应用基础研究提供数据支持；并比较维吾尔族和11个民族在共有的X-STR基因座的遗传学差异。 创新点 2 首次应用一个新的复合扩增检测体系，研究19个X-STR基因座新的组合（DXS8378、DXS7423、DXS10148、DXS10159、DXS10134、DXS7424、DXS10164、DXS10162、DXS7132、DXS10079、DXS6789、DXS101、DXS10103、DXS10101、HPRTB、DXS6809、DXS10075、DXS10074和DXS10135）在新疆维吾尔族的遗传多态性。 方法 2 从233个新疆维吾尔族无关、健康个体的血痕中提取基因组DNA。应用一个新的复合扩增体系，同时对19个X-STR基因座进行扩增，用毛细管电泳进行基因扫描和分型。系统分析和评价这些X-STR基因座常用的各种法医学参数及应用价值；并对7组连锁的基因座组成的单倍型进行分析。基于分子方差分析的方法对新疆维吾尔族和其他11个民族共有的X-STR基因座进行比较研究，探寻这些群体在等位基因频率分布上的差异。 结论 2 研究19个X-STR基因座共发现238个等位基因，相应的基因频率分布在0.0021~0.5644；女性累积个体识别力为0.999 999 999 999 999 999 998 091，男性为0.999 999 999 999 966，累积非父排除率为0.999 999 986 35。分子方差分析的结果显示新疆维吾尔族人群与格陵兰和索马里人群差异最大，有8个基因座存在差异；与马来西亚和关中汉族人群差异最小，仅3个基因座存在差异。结果表明：这19个X-STR基因座多态性高、且具有较高的累积个体识别力，可很好地应用于法医学及群体遗传学研究，也为新疆维吾尔族人群的遗传背景的研究提供基础资料。 X-chromosome Short tandem repeat (STR) Uygur Genetic polymorphism Forensic X染色体 短串联重复序列（STR） 维吾尔族 基因多态性 法医学 Introduction 1 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 2002 ; Deng et al., 2013 2013 ; Wang et al., 2013 2013 ; Zhu et al., 2013 2013 ; 2014 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 2008 ; Nadeem et al., 2009 2009 ; Luo et al., 2011 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 2003 ; Jin and Chu, 2006 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 2014 ), killer cell immunoglobulin-like receptor genes (Wang et al., 2012 2012 ), 21 autosomal STR loci (Deng et al., 2013 2013 ), and HLA-A, -B, and -DRB1 loci with sequence-based typing (Shen et al., 2010 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. Materials and methods 1 Sample preparation and DNA extraction 2 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 2013 ). PCR amplification and X-STR genotyping 2 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 H 2 O (sdH 2 O). 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. Statistical analyses 2 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 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 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 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 2007 ). Results and discussion 1 Forensic parameter analysis 2 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 1 and 2 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 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. 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 2 Allele 2 DXS10134 2 DXS7424 2 DXS101 2 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 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 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 Linkage disequilibrium analyses 2 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 http://chrx-str.org ), and therefore genetic linkage is likely to be a major cause of the observed LD. Haplotype diversities 2 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 http://xdb.qualitype.de/xdb/linkageTable.jsf ), and the remaining clusters from previous studies (Edelmann et al., 2002 2002 ; 2010 2010 ; Szibor et al., 2005 2005 ). Haplotype frequencies for the seven clusters in 94 male samples are displayed in the Table S1 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. Interpopulation differentiation 2 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 S2 . The results showed that statistically significant differences ( P < 0.05) were observed between the Uygur and Greenlander (Tomas et al., 2012 2012 ) and Somali (Tomas et al., 2012 2012 ) at 8 loci; East Timor (Moreira et al., 2015 2015 ), Japanese (Uchigasaki et al., 2013 2013 ), Shenyang Han population (Uchigasaki et al., 2013 2013 ) and Dane (Tomas et al., 2012 2012 ) at 6 loci; Shanghai Han population (Zhang et al., 2012 2012 ) at 5 loci; Bhil tribal population (Shrivastava et al., 2015 2015 ) and Taiwanese (Chen et al., 2014 2014 ) at 4 loci; Malay (Samejima et al., 2012 2012 ) and Guangdong Han population (Zeng et al., 2011 2011 ) at 3 loci. The results of AMOVA demonstrated that the allelic frequency in most of these loci distributed differently among different ethnic groups. 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Informed consent was obtained from all volunteers for being included in the study. 10.1631/jzus.B1500228 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) 2015-09-22 2016-04-15 2015-12-26 2022-01-05 Copyright © Zhejiang University and Springer-Verlag Berlin Heidelberg 2016 2016 Journal of Zhejiang University-SCIENCE B (Biomedicine and Biotechnology) 05 17