Genetic polymorphism of 17 STR loci in Chinese population from Hunan province in Central south China

Genetic polymorphism of 17 STR loci in Chinese population from Hunan province in Central south China

Forensic Science International: Genetics 6 (2012) e151–e153 Contents lists available at SciVerse ScienceDirect Forensic Science International: Genet...

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Forensic Science International: Genetics 6 (2012) e151–e153

Contents lists available at SciVerse ScienceDirect

Forensic Science International: Genetics journal homepage: www.elsevier.com/locate/fsig

Forensic Population Genetics – Letter to the Editor Genetic polymorphism of 17 STR loci in Chinese population from Hunan province in Central south China

Dear Editor, We selected 586 unrelated healthy individuals (338 males and 248 females) whose ancestors lived in Hunan Province for at least three generations. After informed consent in compliance with the ethical norms set by Chinese legislation was acquired, we obtained bloodstains from each of the subjects. The study was approved by the ethics committee of the Third Xiangya Hospital of Central South University, and was carried out following the guidelines for publication of population data required by the journal [1] and according to the International Society of Forensic Genetics (ISFG) recommendations [2]. The laboratory has passed through proficiency testing in the field of forensic science by the Institute of Forensic Science of Chinese Ministry of Justice. Genomic DNA was extracted from the bloodstains using the Chelex-100 and proteinase K protocol [3]. The quantity of the extracted DNA was determined spectrophotometrically. The 17 short tandem repeat (STR) loci included in the AmpFlSTR Identifiler PCR Amplification Kit (Applied Biosystems, USA) and the PowerPlex 16 Monoplex System Kit (Promega, USA) were respectively co-amplified according to the manufacturer’s instruction [4]. Amplification reactions were carried out using a GeneAmp PCR system 9700 (Applied Biosystems). Laboratory internal control standards and kit controls (negative control and 9947A) were used for quality control. The amplified products were separated by capillary electrophoresis on ABI PRISM 3130 Genetic Analyzers (Applied

Biosystems, CA, USA) according to the manufacturer’s recommended protocols. The run data were analyzed together with an allelic ladder and positive and negative controls using GeneMapper ID software, version 3.2. Allele designation was established following the recommendations of the DNA commission of the ISFG [5]. Allelic frequencies, the power of discrimination (PD), the probability of paternity exclusion (PE), the polymorphic information content (PIC), and the observed heterozygosis (Ho) were calculated using the PowerStats 1.2 software. The exact test of Hardy–Weinberg equilibrium was performed using Arlequin version 3.1 [6]. A Bonferroni correction, assumes that a 0.05 significance level obtained for 15 tests (one per locus) yields an actual significance threshold of 0.0033 was used for the Hardy–Weinberg equilibrium test [7]. To compare the studied population with previously published data for an ethnic Han population data in China, pairwise comparison tests (Fst) and exact population differentiation tests (exact tests) were performed using Arlequin version 3.1. All the loci were in accordance with Hardy–Weinberg equilibrium (P > 0.0033 after Bonferroni correction). The observed heterozygosis (Ho) ranged from 0.606 (TPOX) to 0.91 (Penta E). The power of discrimination (PD) ranged from 0.783 (TPOX) to 0.986 (Penta E), and the combined power of discrimination for the 17 STR loci was 0.999999999999999987. The probability of excluding paternity (PE) ranged from 0.298 (TPOX) to 0.815 (Penta E), and the combined probability of excluding paternity for the 17 loci was 0.999997518. The polymorphic information content (PIC) ranged from 0.54 (TPOX) to 0.91 (Penta E), The 17 STR loci that were studied were highly polymorphic (PIC > 0.5). Details of the allele frequencies distribution and other relevant parameter see are shown in Table 1.

Table 1 The allele frequencies and relevant parameter. Allele THO1 5 6 7 8 9 9.3 10 11 12 12.2 13 13.2 14 14.2 15 15.2 16 16.2 17

0.001 0.112 0.27 0.055 0.483 0.036 0.041 0.002

D7S820 D8S1179 VWA

PentaD D5S818 D3S1358 D18S51

TPOX

D13S317 CSFIPO Penta E D2S1338 D16S539 FGA

D21S11 D19S433

0.0538

0.001

0.0043 0.0102 0.0299 0.0486 0.0009 0.3532 0.0691

0.0017 0.0034 0.5384 0.3063 0.0017 0.1160 0.1459

0.0034 0.0017 0.0444

0.0009 0.0068 0.0111

0.0077 0.2722

0.16 0.357 0.24

0.133 0.102 0.135

0.1348 0.2287 0.1288 0.3191 0.0009 0.1630 0.2082

0.0009 0.0222 0.1365 0.0077 0.2986 0.2329 0.0486 0.0205 0.1348

0.2235 0.2381 0.3814

0.0623 0.1561 0.1280

0.1186 0.2739 0.2244

0.041

0.193

0.0009 0.1109 0.1314

0.0026

0.1775 0.0026 0.0324

0.1007

0.0657 0.0009

0.0828

0.005

0.19

0.2543 0.0350 0.0085

0.0324

0.2022

0.0060

0.0802

0.0196

0.157

0.0247 0.0085 0.0043

0.3217

0.1587

0.0009

0.0836 0.0009

0.0009

0.074

0.1715 0.0026

0.3413

0.1416

0.0683 0.0239

0.014

0.2551

0.2355

0.0802

0.0657 0.0648

0.003 0.143 0.051

0.0077

1872-4973/$ – see front matter . Crown Copyright ß 2012 Published by Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.fsigen.2012.02.011

0.0009

0.0017 0.0384 0.0034 0.2901 0.0469 0.2287 0.1305 0.0734 0.1459 0.0034 0.0333

Forensic Population Genetics – Letter to the Editor / Forensic Science International: Genetics 6 (2012) e151–e153

e152 Table 1 (Continued ) Allele THO1 18 19 20 20.2 21 21.1 22 22.2 23 23.2 24 24.2 25 25.2 26 27 28 28.2 29 29.2 30 30.2 31 31.2 32 32.2 33 33.2 34.2 35 35.2 P PD PIC PE Ho

D7S820 D8S1179 VWA 0.002

PentaD D5S818 D3S1358 D18S51

0.1869 0.0802 0.0213

0.0631 0.0034

TPOX

D13S317 CSFIPO Penta E D2S1338 D16S539 FGA

0.0580 0.0341 0.0290

0.0717 0.0845 0.0495 0.1980 0.0418 0.1032

0.0026

0.0247

0.0213 0.0367

0.0017

0.0154

0.0230 0.0580

0.0111

0.0085 0.1860

0.0068

0.0017 0.1638

0.0017

0.0708 0.0068 0.0017

0.5059 0.85 0.63 0.397 0.679

0.7653 0.909 0.73 0.511 0.751

0.8508 0.959 0.83 0.655 0.829

0.1379 0.931 0.77 0.52 0.244

0.7427 0.934 0.77 0.622 0.812

0.705 0.921 0.75 0.514 0.753

0.1188 0.873 0.67 0.402 0.683

0.0044 0.968 0.85 0.668 836

0.799 0.783 0.54 0.298 0.606

0.7615 0.927 0.76 0.568 0.783

0.5839 0.5329 0.884 0.986 0.69 0.91 0.497 0.915 0.742 91

0.0383 0.966 0.85 0.718 0.862

0.1498 0.916 0.74 0.55 0.773

D21S11 D19S433

0.0247 0.0512 0.0589 0.0009 0.1195 0.0034 0.1860 0.0094 0.2082 0.0085 0.1818 0.0068 0.0828 0.0034 0.0401 0.0111 0.0026 0.0461 0.0085 0.2560 0.0026 0.2543 0.0171 0.1049 0.0776 0.0367 0.1391 0.0034 0.0503 0.0017 0.0009 0.0009 0.2043 0.3733 0.964 0.948 0.84 0.81 0.695 0.648 0.85 0.826

0.0026 0.0009

0.0009

0.4909 0.94 0.79 0.648 0.826

P value of H–W equilibrium test (P), observed heterozygosity (Ho), power of discrimination (PD), paternity exclusion (PE), the polymorphic information content (PIC).

We compared our results with the published data from eight other ethnic Han populations in China. Statistically significant differences (P < 0.05) were found between the present population and the Jilin [8], Shanghai [9], Yunnan [10], Peking [11], and Sichuan [12] populations. No statistically significant differences were seen between the current population and the Minnan [13], Hang Kong [14], and Zhejiang [15] populations (Table 2). With the coastal economic development of China, a lot of migrant workers have migrated to the newly developed coastal cities from inland regions. China’s population structure has undergone major

changes in the last one hundred years and this flow of population to the coast may be one of the main causes for these changes. STRs are widely used in forensic science to investigate biological stains from crime scene samples, to identify unknown corpses in natural disasters, and to investigate family relationships. This study of allele frequencies will serve as a reference database for individual and paternal identification in people from the Hunan Province of China. This database will also be of value for comparative studies on the genetics and diversity of other population.

Table 2 The Comparisons with other 8 Han ethnic population in China. Allele

Shanghai

Yunnan

Peking

Minnan

Jilin

Sichuan

Hongkong

Zhejiang

1. THO1 2. D7S820 3. D8S1179 4. FGA 5. D3S1358 6. VWA 7. D18S51 8. D5S818 9. PentaD 10. TPOX 11. D13S317 12. D21S11 13. CSF1PO 14. D2S1338 15. D16S539 16. D19S433 17. Penta E

0.0000 0.0020 0.0088 0.6833 0.1173 0.5396 0.3900 0.0166 0.0000 0.4858 0.2972 0.5005 0.1515 0.0000 0.3177 0.0020 0.0000

0.6471 0.8387 0.8915 0.8397 0.4233 0.6540 0.0000 0.1173 – 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 –

0.7090 0.2818 0.0636 0.8545 0.0371 0.6090 0.5454 0.7545 0.0508 0.4909 0.5909 0.0363 0.0599 – 0.1363 – 0.8909

0.6181 0.5818 0.5545 0.4545 0.2454 0.4181 0.2502 0.6272 – 0.6000 0.1545 0.6364 0.2090 0.5455 0.6545 0.9909 –

0.0381 0.5636 0.0727 0.8909 0.1818 0.8543 0.9181 0.4363 – 0.8866 0.0272 0.7859 0.7545 0.3636 0.7272 0.9909 –

0.1876 0.1909 0.8514 0.0000 0.8025 0.4909 0.7181 0.7636 0.7096 0.4676 0.9765 0.8817 0.4090 – 0.8909 – 0.9472

0.2909 0.7909 0.5363 0.9636 0.9272 0.7636 0.6412 0.4181 – 0.6363 0.5636 0.7272 0.7341 0.9227 0.9090 0.4454 –

0.5545 0.7272 0.8000 0.6727 0.4000 0.6181 0.9272 0.5636 – 0.5181 0.5727 0.9636 0.8000 0.4090 0.2363 0.4818 –

Jilin [8], Shanghai [9], Yunnan [10], Peking [11], Sichuan [12], Minnan [13], Hong Kong [14], Zhejiang [15]. The bold values is to show the significant difference between this population and the compared populations.

Forensic Population Genetics – Letter to the Editor / Forensic Science International: Genetics 6 (2012) e151–e153

References

e153

Ji-fang Wena,b,* Department of Forensic Medicine, School of Basic Medicine Sciences, Central South University, Tongzipo Road 172, Changsha 410013, PR China b Department of Pathology, School of Basic Medicine Sciences, Central South University, Tongzipo Road 172, Changsha 410013, PR China a

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Yun-feng Chang Department of Forensic Medicine, School of Basic Medicine Sciences, Central South University, Tongzipo Road 172, Changsha 410013, PR China

Li Yang Ji-feng Cai Department of Forensic Medicine, School of Basic Medicine Sciences, Central South University, Tongzipo Road 172, Changsha 410013, PR China Sanaa Mohamed Aly Forensic Medicine department, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt Qin-lai Liu Ya-dong Guo Yan Gu Department of Forensic Medicine, School of Basic Medicine Sciences, Central South University, Tongzipo Road 172, Changsha 410013, PR China *Corresponding author at: Department of Forensic Medicine, School of Basic Medicine Sciences, Central South University, Tongzipo Road 172, Changsha 410013, PR China. Tel.: +86 0731 82355414; fax: +86 0731 82355414 E-mail address: [email protected] (J.-f. Wen) 6 July 2011