- Email: [email protected]
Population genetic analysis of Xiamen Han population on 21 short tandem repeat loci
Legal Medicine 26 (2017) 41–44
Contents lists available at ScienceDirect
Legal Medicine journal homepage: www.elsevier.com/locate/legalmed
Announcement of Population Data
Population genetic analysis of Xiamen Han population on 21 short tandem repeat loci Lili Wu a,1, Bin Pei b,1, Peng Ran b, Xiuyu Song a,b,⇑ a b
The First Clinical Medical Institute, Fujian Medical University, Fuzhou City, Fujian Prov. 350108, PR China Forensic Identification of Justice of Center Blood Station in Xiamen, Xiamen City, Fujian Prov. 361004, PR China
a r t i c l e
i n f o
Article history: Received 26 September 2016 Received in revised form 19 January 2017 Accepted 1 March 2017 Available online 7 March 2017 Keywords: Forensic science Short tandem repeat GlobalFilerTM Express Xiamen Han
a b s t r a c t GlobalFilerTM Express amplification kit incorporates 21 commonly used autosomal short tandem repeat (STR) loci and three gender determination loci. In this study, we analyzed GlobalFiler STR loci on 1006 unrelated individuals sampled of the Han population from Xiamen city, Fujian province, China. No deviations from Hardy–Weinberg equilibrium were observed. The combined probability of exclusion (CPE) for all 21 STR loci were >0.99999999771. A comparison of the allele frequencies in the population under study has been performed with other published from East Asian population for the same loci. Multiple STR loci showed significant differences between Han population from Xiamen and Korea, as well as Japan. Ó 2017 Elsevier B.V. All rights reserved.
1. Introduction
2. Materials and methods
A set of highly polymorphic short tandem repeat (STR) loci for human individual identification (HID) has proven to be successful in forensic investigations [1] . A total of 24 autosomal STR loci were commonly used in forensics [2], which were embedded in several multiplex amplification kits. Recently, the six-dye GlobalFilerTM Express Amplification kit were developed by Thermo Fisher Scientific company [3], which includes 21 autosomal STRs of above 24 markers and three gender determination loci (Amelogenin, Yindel, and DYS391). The autosomal STR loci in GlobalFiler kit are D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, VWA, TPOX, D18S51, D5S818, FGA, D12S391, D1S1656, D2S441, D10S1248, D22S1045, and SE33. Xiamen city, In China’s southeast coast, south of Fujian province, among the new commercial Human Identification (HID) kits, population studies based on the GlobalFiler kit (Thermo Scientific) have not been reported. In this study, to estimate the allele frequencies and forensic statistical parameters of 21 GlobalFiler STR loci on Han population from Xiamen, we typed a total of 1006 samples.
2.1. Samples and experiments
⇑ Corresponding author at: Forensic Identification of Justice of Center Blood Station in Xiamen, No. 121, Hubinnan Road, Siming District, Xiamen City, Fujian Prov. 361004, PR China. E-mail addresses: [email protected] (L. Wu), [email protected] (B. Pei), [email protected] (P. Ran), [email protected] (X. Song). 1 These authors contributed equally to the article. http://dx.doi.org/10.1016/j.legalmed.2017.03.002 1344-6223/Ó 2017 Elsevier B.V. All rights reserved.
A total of 1006 unrelated Han blood donors were sampled from Xiamen after acquiring their informed consent. All DNA samples were amplified using GlobalFilerTM STR kit (Thermo Fisher Scientific Company, Carlsbad, USA) in the GeneAmp PCR System 9700 (Thermo Fisher Scientific Company) according to manufacturer’s recommendation. A total of 24 loci were amplified, including 21 autosomal STR loci and three gender determination loci. The PCR products were separated by capillary electrophoresis in an ABI PRISM 3730xL Genetic Analyzer (Thermo Fisher Scientific Company), and the GeneMapperÒ ID-X Software v1.4 (Thermo Fisher Scientific Company) was used for genotype assignment. DNA typing and assignment of nomenclature were based on the ISFG recommendations [4,5].
2.2. Statistical analyses The allele frequencies were estimated from corresponding genotype counts. The exact tests of Hardy-Weinberg equilibrium (HWE) and linkage disequilibrium (LD) were performed using Arlequin v3.5 [6], and the observed heterozygosity (Ho) were also estimated. Match probability (MP), power of discrimination (PD), and power of exclusion (PE) were estimated using ModifiedPowerstates [7]. The exact test of population differentiation was
42
L. Wu et al. / Legal Medicine 26 (2017) 41–44
Table 1 Allele frequencies of 21 autosomal STR obtained for a population of 1006 Han individuals from Xiamen, China. Allele 3 5 6 6.3 7 7.3 8 8.1 8.3 9 9.1 9.2 10 10.1 10.3 11 11.3 12 12.1 12.2 12.3 13 13.2 13.3 14 14.2 15 15.2 16 16.2 17 17.2 18 Ob.H PD PE MP PIC P Allele 9 10 11 12 13 14 14.2 15 15.3 16 16.1 16.3 17 17.3 18 18.1 18.3 19 19.1 19.2 19.3 20 20.1 20.2 20.3 21 21.2 22 22.2 23 23.2 24 24.1
D13S179
D16S539
D5S818
TH01
D8S1179
CSF1PO
D10S1248
TPOX
D2S441
D7S820
0.0005
0.0005
0.0010
0.5290
0.0010 0.0005
0.1320 0.0010
D19S441
0.0005 0.0005
0.0020
0.0005
0.0309
0.2750
0.0080
0.0030
0.0005 0.0970 0.0005 0.2450 0.0005 0.0523
0.1405
0.2910
0.0749
0.0060 0.5053
0.0020 0.0005
0.0005
0.0005
0.0480
0.1150
0.0335
0.2130 0.0025
0.0010
0.2930
0.0730
0.0270
0.3235 0.0730 0.2070
0.0665 0.0040 0.0010 0.1640 0.0020 0.0010 0.3490 0.0005 0.2460
0.0160
0.0005 0.0300
0.1190
0.0010
0.0005
0.0110
0.0005
0.0330 0.1510
0.1200
0.1900
0.0547
0.1240
0.2580
0.2340
0.2610
0.3248
0.0020
0.1280
0.2400
0.1600
0.2100 0.0010
0.2329
0.1303
0.3635 0.0010
0.0005
0.0070
0.0126 0.0019 0.0440 0.0050
0.0330
0.0910
0.1320
0.1942
0.0730
0.3680
0.0040
0.0005 0.0160
0.0100
0.1880
0.0110
0.2380
0.0010
0.0010
0.1550
0.0030
0.2003
0.8140 0.9290 0.6250 0.0710 0.7700 0.2976
0.7620 0.9170 0.5300 0.0830 0.7500 0.1572
D22S1045
D3S1358
0.0630
0.1002
0.0140
0.0180
0.0015
0.7660 0.9190 0.5380 0.0810 0.7500 0.2797
0.6840 0.8440 0.4040 0.1560 0.6300 0.2969
0.0030 0.8340 0.9590 0.6640 0.0410 0.8300 0.1451
0.7400 0.8820 0.4920 0.1180 0.6900 0.8593
0.0010 0.7510 0.9000 0.5120 0.1000 0.7100 0.9289
0.5980 0.7930 0.2890 0.2070 0.5600 0.1723
0.7830 0.9230 0.5680 0.0770 0.7600 0.7806
0.7470 0.9120 0.5040 0.0880 0.7300 0.1002
vWA
D1S1656
D2S1338
SE33
D18S51
D21S11
D12S391
FGA
0.0005 0.0005 0.2080 0.0005 0.0040 0.0240
0.0010 0.0570 0.0580 0.1150 0.0670
0.0010 0.0020 0.0490
0.0030 0.2550
0.2740
0.3280
0.0337
0.2640
0.2980
0.1560
0.1970
0.2370
0.2593
0.0230
0.0750
0.1953
0.0080 0.0826 0.0730 0.0153
0.0010
0.0090
0.0837
0.0201 0.0010
0.2850 0.0010 0.2150
0.0005 0.0030 0.0010 0.0088
0.0010 0.0050 0.0410 0.1713 0.2044 0.1890
0.0120
0.0190
0.0160 0.0010
0.1263
0.0080
0.0680
0.0470
0.0900
0.0800
0.0005
0.1080
0.0730
0.0560
0.2330 0.0010
0.0220
0.1980
0.0740
0.0370
0.2015 0.0010
0.0540
0.0250
0.1740
0.0213
0.0005 0.1160
0.0230
0.0870
0.0018 0.0010 0.0010
0.0010
0.0130
0.1260
0.0650
0.0005 0.0540 0.0005
0.0020 0.0015
0.0005
0.0340 0.0370
0.0015
0.1860 0.1390
0.0320 0.0200 0.0110 0.0440 0.0030 0.0370 0.0005
0.0045
0.0534 0.0010
0.0022
0.0176
0.1060 0.0050 0.1680 0.0070 0.2110 0.0070 0.1870 0.0005
0.2810 0.0380 0.2470 0.1180 0.0690 0.1340 0.0080 0.0300 0.0010 0.0030 0.8000 0.9430 0.5990 0.0570 0.8000 0.1192
43
L. Wu et al. / Legal Medicine 26 (2017) 41–44 Table 1 (continued) Allele
D22S1045
D3S1358
vWA
D1S1656
24.2 25 25.2 26 26.2 27 Allele .27.2 28 28.1 28.2 29 29.2 30 30.2 30.3 31 31.2 32 32.2 32.3 33 33.2 34 34.2 35.2 36.2 Ob.H PD PE MP PIC P
D2S1338
SE33
0.0700
0.0770 0.0009 0.0700
0.0120
D18S51
D21S11
D12S391
0.0020
0.0025
D21S
D12
FGA
0.0710
0.0010
0.0017 0.0040
0.0010
0.0100
0.0020
0.0015
0.0830 0.0030 D22S1045
D3S1358
vWA
D1S1656
D2S1338
SE33
D18S51
0.0790 0.0005 0.0010 0.0800
FGA 0.0040 0.1000 0.0032 0.0460 0.0058 0.0113
0.0010 0.2400
0.0010
0.0660 0.2680 0.0090 0.0070 0.0950 0.0810 0.0330 0.1440 0.0010 0.0040 0.0380 0.0005 0.0040 0.0005
0.0530 0.0005 0.0280 0.0090
0.0080 0.0030
0.7680 0.9090 0.5420 0.0910 0.7300 0.7445
0.7480 0.8860 0.5060 0.1140 0.7000 0.5849
0.8070 0.9260 0.6120 0.0740 0.7700 0.4419
0.8130 0.9540 0.6240 0.0460 0.8200 0.0523
0.8670 0.9670 0.7280 0.0330 0.8500 0.9685
0.0005 0.9350 0.9920 0.8680 0.0080 0.9400 0.5403
0.8730 0.9640 0.7400 0.0360 0.8500 0.3103
0.8320 0.9480 0.6600 0.0520 0.8100 0.6756
0.8510 0.9550 0.6970 0.0450 0.8300 0.5717
0.8570 0.9660 0.7080 0.0340 0.8500 0.6028
Ob. H: observed heterozygosity. PD, discrimination power. PE, exclusion power. MP, matching probability. PIC, polymorphism information content. P, probability value of exact test for Hardy–Weinberg equilibrium using Markov chain.
Table 2 Comparative analysis between Han population from Xiamen and other neighboring populations: Korea; Japan; Han population from Fujian Province. In bold significant p values after Bonferroni correction (p < 0.05/7 = 0.0083). Locus
Xiamen VS Korea
Xiamen VS Japan
Xiamen VS Fujian
Korea VS Japan
Korea VS Fujian
Japan VS Fujian
D13S317 D3S1358 D16S539 vWA D5S818 TH01 D22S1045 CSF1PO D1S1656 D10S1248 D2S1338 TPOX D2S441 D8S1179 SE33 D18S51 D21S11 D12S391 D19S433 FGA D7S820
0.9910 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0811 0.0000 0.0000 0.0000 0.0000 0.0000
0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.7297 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.7207 0.0000 0.0000 0.9730 0.0000 0.6577 0.0000 0.0000 0.0000 0.0000 0.0000
0.0000 0.3874 0.0000 0.0000 0.2072 0.0000 0.2252 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.3153 0.0000 0.1622 0.0000 0.0000 0.0000 0.0000 0.0000
0.0000 0.0000 0.0000 0.0000 0.1892 0.0000 0.0991 0.0000 0.0000 0.0000 0.0000 0.7928 0.0000 0.0000 0.0000 0.5946 0.0000 0.0000 0.0451 0.0000 0.0000
0.0090 0.0000 0.0000 0.0000 0.0811 0.0000 0.5676 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0270 0.0000 0.0000 0.0000 0.0000 0.0000
44
L. Wu et al. / Legal Medicine 26 (2017) 41–44
performed between Han population from Xiamen of the present study and the other East Asian populations using Arlequin v3.5 [6]. 3. Results Allele frequencies and population statistical and forensic parameters for the 21 autosomal loci are presented in Table 1. The allele frequency of the 21 loci in Xiamen Han population was 0.0005–0.5290. Allele 8 of TPOX was found to exhibit the highest allele frequency with 0.5290 in the total samples analysed for the population. The heterozygosity (Ho) of the 21 autosomal STR loci ranged from 0.5980 (TPOX) to 0.9350 (SE33). The SE33 locus showed the largest number of different alleles (35 alleles) and TPOX loci showed the smallest number of different alleles (8 alleles). The power of discrimination values (PD) for all tested loci was above 0.7900; the highest observed at SE33 with 0.9920 and the least at TPOX with 0.7930. The combined probability of exclusion (CPE) for all 21 STR loci were >0.99999999771, combined power of discrimination (CPD) >0.9999999999999999, combined matching probability (CMP) >7.690 10 26. 4. Other remarks No deviations from Hardy–Weinberg equilibrium were observed (see Table 1). Linkage disequilibrium has been tested using shuffling test for all possible combinations between loci obtaining an exact probability higher than 0.05 indicating independence of loci in all cases (data not shown). Locus by locus comparisons with available published data on other East Asian populations: Korea [8], Japan [9], Han population from Fujian Province [10]are presented in Table 2. Significant differences were found between Han population from Xiamen and Korean at 19 loci; Japanese at 20 loci. It is important to note that population in Xiamen and Fujian also, at 18 loci, which can be interpreted as the population migration. In addition, important differences between Korean versus Japanese and Japanese versus Han population from Fujian Province comparisons were observed, Table 2. 5. Conclusions In conclusion, we report the allele frequencies and forensic statistical parameters of the GlobalFiler STR loci in Han population from Xiamen. The results may serve as a forensic database reference of Chinese populations. In this study, GlobalFilerÒ showed large paternity index values for Han population from Xiamen indicating that the kit is a valuable asset in paternity testing.
Conflict of interest The authors declare that they have no conflict of interest. This study follows the new guidelines for publication of population data requested by the journal [11,12]. Acknowledgments This study was supported by grants from the Nation Science Foundation of Fujian Province (2013D002, D2014D004). References [1] H.A. Hammond, L. Jin, Y. Zhong, C.T. Caskey, R. Chakraborty, Evaluation of 13 short tandem repeat loci for use in personal identification applications, Am. J. Hum. Genet. 55 (1) (1994) 175–189. [2] K.B. Gettings, R.A. Aponte, P.M. Vallone, J.M. Butler, STR allele sequence variation: current knowledge and future issues, Forensic Sci. Int. Genet. 18 (2015) 118–130, http://dx.doi.org/10.1016/j.fsigen. 2015.06.005. [3] D.Y. Wang, S. Gopinath, R.E. Lagacé, W. Norona, L.K. Hennessy, M.L. Short, J.J. Mulero, Developmental validation of the GlobalFilerÒ Express PCR Amplification Kit: a 6-dye multiplex assay for the direct amplification of reference samples, Forensic Sci. Int. Genet. 19 (2015) 148–155, http://dx.doi. org/10.1016/j.fsigen.2015.07.013. [4] W. Bar, B. Brinkmann, B. Budowle, A. Carracedo, P. Gill, P. Lincoln, W. Mayr, B. Olaisen, DNA recommendations—further report of the DNA Commission of the ISFH regarding the use of short tandem repeat systems, Int. J. Legal Med. 110 (4) (1997) 175–176. [5] B. Olaisen, W. Bar, B. Brinkmann, B. Budowle, A. Carracedo, P. Gill, P. Lincoln, W. R. Mayr, S. Rand, DNA recommendations 1997 of the International Society for Forensic Genetics, Vox Sang. 74 (1) (1998) 61–63. [6] L. Excoffier, H.E.L. Lischer, Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows, Mol. Ecol. Resour. 10 (3) (2010) 564–567. [7] F. Zhao, X. Wu, G. Cai, C. Xu, The application of Modified-Powerstates software in forensic biostatistics, Chin. J. Forensic Med. 18 (5) (2003) 297–298 (in Chinese). [8] S.B. Hong, S.H. Kim, K.C. Kim, M.H. Park, J.Y. Lee, J.M. Song, M.S. Han, W. Kim, Korean population genetic data and concordance for the PowerPlex ESX 17, AmpFlSTR Identifiler, and PowerPlex 16 systems, Forensic Sci. Int. Genet. 7 (3) (2013) 47–51, http://dx.doi.org/10.1016/j.fsigen.2013.01.002. [9] K. Fujii, H. Watahiki, Y. Mita, et al., Allele frequencies for 21 autosomal short tandem repeat loci obtained using GlobalFiler in a sample of 1501 individuals from the Japanese population, Leg. Med. 17 (5) (2015) 306–308, http://dx.doi. org/10.1016/j.legalmed.2015.08.007. [10] H.H. Lian, W.D. Ge, F. Lin, B. Li, Genetic polymorphisms of 21 autosomal STR loci of Fujian Han population, Fa Yi Xue Za Zhi 31 (3) (2015) 211–214 (in Chinese). [11] A. Carracedo, J.M. Butler, L. Gusmao, A. Linacre, W. Parson, L. Roewer, P.M. Schneider, New guidelines for the publication of genetic population data, Forensic Sci. Int. Genet. 7 (2) (2013) 217–220. [12] A. Carracedo, J.M. Butler, L. Gusmao, A. Linacre, W. Parson, L. Roewer, P.M. Schneider, Update of the guidelines for the publication of genetic population data, Forensic Sci. Int. Genet. 10 (2014) A1–A2.
Contents lists available at ScienceDirect
Legal Medicine journal homepage: www.elsevier.com/locate/legalmed
Announcement of Population Data
Population genetic analysis of Xiamen Han population on 21 short tandem repeat loci Lili Wu a,1, Bin Pei b,1, Peng Ran b, Xiuyu Song a,b,⇑ a b
The First Clinical Medical Institute, Fujian Medical University, Fuzhou City, Fujian Prov. 350108, PR China Forensic Identification of Justice of Center Blood Station in Xiamen, Xiamen City, Fujian Prov. 361004, PR China
a r t i c l e
i n f o
Article history: Received 26 September 2016 Received in revised form 19 January 2017 Accepted 1 March 2017 Available online 7 March 2017 Keywords: Forensic science Short tandem repeat GlobalFilerTM Express Xiamen Han
a b s t r a c t GlobalFilerTM Express amplification kit incorporates 21 commonly used autosomal short tandem repeat (STR) loci and three gender determination loci. In this study, we analyzed GlobalFiler STR loci on 1006 unrelated individuals sampled of the Han population from Xiamen city, Fujian province, China. No deviations from Hardy–Weinberg equilibrium were observed. The combined probability of exclusion (CPE) for all 21 STR loci were >0.99999999771. A comparison of the allele frequencies in the population under study has been performed with other published from East Asian population for the same loci. Multiple STR loci showed significant differences between Han population from Xiamen and Korea, as well as Japan. Ó 2017 Elsevier B.V. All rights reserved.
1. Introduction
2. Materials and methods
A set of highly polymorphic short tandem repeat (STR) loci for human individual identification (HID) has proven to be successful in forensic investigations [1] . A total of 24 autosomal STR loci were commonly used in forensics [2], which were embedded in several multiplex amplification kits. Recently, the six-dye GlobalFilerTM Express Amplification kit were developed by Thermo Fisher Scientific company [3], which includes 21 autosomal STRs of above 24 markers and three gender determination loci (Amelogenin, Yindel, and DYS391). The autosomal STR loci in GlobalFiler kit are D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, VWA, TPOX, D18S51, D5S818, FGA, D12S391, D1S1656, D2S441, D10S1248, D22S1045, and SE33. Xiamen city, In China’s southeast coast, south of Fujian province, among the new commercial Human Identification (HID) kits, population studies based on the GlobalFiler kit (Thermo Scientific) have not been reported. In this study, to estimate the allele frequencies and forensic statistical parameters of 21 GlobalFiler STR loci on Han population from Xiamen, we typed a total of 1006 samples.
2.1. Samples and experiments
⇑ Corresponding author at: Forensic Identification of Justice of Center Blood Station in Xiamen, No. 121, Hubinnan Road, Siming District, Xiamen City, Fujian Prov. 361004, PR China. E-mail addresses: [email protected] (L. Wu), [email protected] (B. Pei), [email protected] (P. Ran), [email protected] (X. Song). 1 These authors contributed equally to the article. http://dx.doi.org/10.1016/j.legalmed.2017.03.002 1344-6223/Ó 2017 Elsevier B.V. All rights reserved.
A total of 1006 unrelated Han blood donors were sampled from Xiamen after acquiring their informed consent. All DNA samples were amplified using GlobalFilerTM STR kit (Thermo Fisher Scientific Company, Carlsbad, USA) in the GeneAmp PCR System 9700 (Thermo Fisher Scientific Company) according to manufacturer’s recommendation. A total of 24 loci were amplified, including 21 autosomal STR loci and three gender determination loci. The PCR products were separated by capillary electrophoresis in an ABI PRISM 3730xL Genetic Analyzer (Thermo Fisher Scientific Company), and the GeneMapperÒ ID-X Software v1.4 (Thermo Fisher Scientific Company) was used for genotype assignment. DNA typing and assignment of nomenclature were based on the ISFG recommendations [4,5].
2.2. Statistical analyses The allele frequencies were estimated from corresponding genotype counts. The exact tests of Hardy-Weinberg equilibrium (HWE) and linkage disequilibrium (LD) were performed using Arlequin v3.5 [6], and the observed heterozygosity (Ho) were also estimated. Match probability (MP), power of discrimination (PD), and power of exclusion (PE) were estimated using ModifiedPowerstates [7]. The exact test of population differentiation was
42
L. Wu et al. / Legal Medicine 26 (2017) 41–44
Table 1 Allele frequencies of 21 autosomal STR obtained for a population of 1006 Han individuals from Xiamen, China. Allele 3 5 6 6.3 7 7.3 8 8.1 8.3 9 9.1 9.2 10 10.1 10.3 11 11.3 12 12.1 12.2 12.3 13 13.2 13.3 14 14.2 15 15.2 16 16.2 17 17.2 18 Ob.H PD PE MP PIC P Allele 9 10 11 12 13 14 14.2 15 15.3 16 16.1 16.3 17 17.3 18 18.1 18.3 19 19.1 19.2 19.3 20 20.1 20.2 20.3 21 21.2 22 22.2 23 23.2 24 24.1
D13S179
D16S539
D5S818
TH01
D8S1179
CSF1PO
D10S1248
TPOX
D2S441
D7S820
0.0005
0.0005
0.0010
0.5290
0.0010 0.0005
0.1320 0.0010
D19S441
0.0005 0.0005
0.0020
0.0005
0.0309
0.2750
0.0080
0.0030
0.0005 0.0970 0.0005 0.2450 0.0005 0.0523
0.1405
0.2910
0.0749
0.0060 0.5053
0.0020 0.0005
0.0005
0.0005
0.0480
0.1150
0.0335
0.2130 0.0025
0.0010
0.2930
0.0730
0.0270
0.3235 0.0730 0.2070
0.0665 0.0040 0.0010 0.1640 0.0020 0.0010 0.3490 0.0005 0.2460
0.0160
0.0005 0.0300
0.1190
0.0010
0.0005
0.0110
0.0005
0.0330 0.1510
0.1200
0.1900
0.0547
0.1240
0.2580
0.2340
0.2610
0.3248
0.0020
0.1280
0.2400
0.1600
0.2100 0.0010
0.2329
0.1303
0.3635 0.0010
0.0005
0.0070
0.0126 0.0019 0.0440 0.0050
0.0330
0.0910
0.1320
0.1942
0.0730
0.3680
0.0040
0.0005 0.0160
0.0100
0.1880
0.0110
0.2380
0.0010
0.0010
0.1550
0.0030
0.2003
0.8140 0.9290 0.6250 0.0710 0.7700 0.2976
0.7620 0.9170 0.5300 0.0830 0.7500 0.1572
D22S1045
D3S1358
0.0630
0.1002
0.0140
0.0180
0.0015
0.7660 0.9190 0.5380 0.0810 0.7500 0.2797
0.6840 0.8440 0.4040 0.1560 0.6300 0.2969
0.0030 0.8340 0.9590 0.6640 0.0410 0.8300 0.1451
0.7400 0.8820 0.4920 0.1180 0.6900 0.8593
0.0010 0.7510 0.9000 0.5120 0.1000 0.7100 0.9289
0.5980 0.7930 0.2890 0.2070 0.5600 0.1723
0.7830 0.9230 0.5680 0.0770 0.7600 0.7806
0.7470 0.9120 0.5040 0.0880 0.7300 0.1002
vWA
D1S1656
D2S1338
SE33
D18S51
D21S11
D12S391
FGA
0.0005 0.0005 0.2080 0.0005 0.0040 0.0240
0.0010 0.0570 0.0580 0.1150 0.0670
0.0010 0.0020 0.0490
0.0030 0.2550
0.2740
0.3280
0.0337
0.2640
0.2980
0.1560
0.1970
0.2370
0.2593
0.0230
0.0750
0.1953
0.0080 0.0826 0.0730 0.0153
0.0010
0.0090
0.0837
0.0201 0.0010
0.2850 0.0010 0.2150
0.0005 0.0030 0.0010 0.0088
0.0010 0.0050 0.0410 0.1713 0.2044 0.1890
0.0120
0.0190
0.0160 0.0010
0.1263
0.0080
0.0680
0.0470
0.0900
0.0800
0.0005
0.1080
0.0730
0.0560
0.2330 0.0010
0.0220
0.1980
0.0740
0.0370
0.2015 0.0010
0.0540
0.0250
0.1740
0.0213
0.0005 0.1160
0.0230
0.0870
0.0018 0.0010 0.0010
0.0010
0.0130
0.1260
0.0650
0.0005 0.0540 0.0005
0.0020 0.0015
0.0005
0.0340 0.0370
0.0015
0.1860 0.1390
0.0320 0.0200 0.0110 0.0440 0.0030 0.0370 0.0005
0.0045
0.0534 0.0010
0.0022
0.0176
0.1060 0.0050 0.1680 0.0070 0.2110 0.0070 0.1870 0.0005
0.2810 0.0380 0.2470 0.1180 0.0690 0.1340 0.0080 0.0300 0.0010 0.0030 0.8000 0.9430 0.5990 0.0570 0.8000 0.1192
43
L. Wu et al. / Legal Medicine 26 (2017) 41–44 Table 1 (continued) Allele
D22S1045
D3S1358
vWA
D1S1656
24.2 25 25.2 26 26.2 27 Allele .27.2 28 28.1 28.2 29 29.2 30 30.2 30.3 31 31.2 32 32.2 32.3 33 33.2 34 34.2 35.2 36.2 Ob.H PD PE MP PIC P
D2S1338
SE33
0.0700
0.0770 0.0009 0.0700
0.0120
D18S51
D21S11
D12S391
0.0020
0.0025
D21S
D12
FGA
0.0710
0.0010
0.0017 0.0040
0.0010
0.0100
0.0020
0.0015
0.0830 0.0030 D22S1045
D3S1358
vWA
D1S1656
D2S1338
SE33
D18S51
0.0790 0.0005 0.0010 0.0800
FGA 0.0040 0.1000 0.0032 0.0460 0.0058 0.0113
0.0010 0.2400
0.0010
0.0660 0.2680 0.0090 0.0070 0.0950 0.0810 0.0330 0.1440 0.0010 0.0040 0.0380 0.0005 0.0040 0.0005
0.0530 0.0005 0.0280 0.0090
0.0080 0.0030
0.7680 0.9090 0.5420 0.0910 0.7300 0.7445
0.7480 0.8860 0.5060 0.1140 0.7000 0.5849
0.8070 0.9260 0.6120 0.0740 0.7700 0.4419
0.8130 0.9540 0.6240 0.0460 0.8200 0.0523
0.8670 0.9670 0.7280 0.0330 0.8500 0.9685
0.0005 0.9350 0.9920 0.8680 0.0080 0.9400 0.5403
0.8730 0.9640 0.7400 0.0360 0.8500 0.3103
0.8320 0.9480 0.6600 0.0520 0.8100 0.6756
0.8510 0.9550 0.6970 0.0450 0.8300 0.5717
0.8570 0.9660 0.7080 0.0340 0.8500 0.6028
Ob. H: observed heterozygosity. PD, discrimination power. PE, exclusion power. MP, matching probability. PIC, polymorphism information content. P, probability value of exact test for Hardy–Weinberg equilibrium using Markov chain.
Table 2 Comparative analysis between Han population from Xiamen and other neighboring populations: Korea; Japan; Han population from Fujian Province. In bold significant p values after Bonferroni correction (p < 0.05/7 = 0.0083). Locus
Xiamen VS Korea
Xiamen VS Japan
Xiamen VS Fujian
Korea VS Japan
Korea VS Fujian
Japan VS Fujian
D13S317 D3S1358 D16S539 vWA D5S818 TH01 D22S1045 CSF1PO D1S1656 D10S1248 D2S1338 TPOX D2S441 D8S1179 SE33 D18S51 D21S11 D12S391 D19S433 FGA D7S820
0.9910 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0811 0.0000 0.0000 0.0000 0.0000 0.0000
0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.7297 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.7207 0.0000 0.0000 0.9730 0.0000 0.6577 0.0000 0.0000 0.0000 0.0000 0.0000
0.0000 0.3874 0.0000 0.0000 0.2072 0.0000 0.2252 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.3153 0.0000 0.1622 0.0000 0.0000 0.0000 0.0000 0.0000
0.0000 0.0000 0.0000 0.0000 0.1892 0.0000 0.0991 0.0000 0.0000 0.0000 0.0000 0.7928 0.0000 0.0000 0.0000 0.5946 0.0000 0.0000 0.0451 0.0000 0.0000
0.0090 0.0000 0.0000 0.0000 0.0811 0.0000 0.5676 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0270 0.0000 0.0000 0.0000 0.0000 0.0000
44
L. Wu et al. / Legal Medicine 26 (2017) 41–44
performed between Han population from Xiamen of the present study and the other East Asian populations using Arlequin v3.5 [6]. 3. Results Allele frequencies and population statistical and forensic parameters for the 21 autosomal loci are presented in Table 1. The allele frequency of the 21 loci in Xiamen Han population was 0.0005–0.5290. Allele 8 of TPOX was found to exhibit the highest allele frequency with 0.5290 in the total samples analysed for the population. The heterozygosity (Ho) of the 21 autosomal STR loci ranged from 0.5980 (TPOX) to 0.9350 (SE33). The SE33 locus showed the largest number of different alleles (35 alleles) and TPOX loci showed the smallest number of different alleles (8 alleles). The power of discrimination values (PD) for all tested loci was above 0.7900; the highest observed at SE33 with 0.9920 and the least at TPOX with 0.7930. The combined probability of exclusion (CPE) for all 21 STR loci were >0.99999999771, combined power of discrimination (CPD) >0.9999999999999999, combined matching probability (CMP) >7.690 10 26. 4. Other remarks No deviations from Hardy–Weinberg equilibrium were observed (see Table 1). Linkage disequilibrium has been tested using shuffling test for all possible combinations between loci obtaining an exact probability higher than 0.05 indicating independence of loci in all cases (data not shown). Locus by locus comparisons with available published data on other East Asian populations: Korea [8], Japan [9], Han population from Fujian Province [10]are presented in Table 2. Significant differences were found between Han population from Xiamen and Korean at 19 loci; Japanese at 20 loci. It is important to note that population in Xiamen and Fujian also, at 18 loci, which can be interpreted as the population migration. In addition, important differences between Korean versus Japanese and Japanese versus Han population from Fujian Province comparisons were observed, Table 2. 5. Conclusions In conclusion, we report the allele frequencies and forensic statistical parameters of the GlobalFiler STR loci in Han population from Xiamen. The results may serve as a forensic database reference of Chinese populations. In this study, GlobalFilerÒ showed large paternity index values for Han population from Xiamen indicating that the kit is a valuable asset in paternity testing.
Conflict of interest The authors declare that they have no conflict of interest. This study follows the new guidelines for publication of population data requested by the journal [11,12]. Acknowledgments This study was supported by grants from the Nation Science Foundation of Fujian Province (2013D002, D2014D004). References [1] H.A. Hammond, L. Jin, Y. Zhong, C.T. Caskey, R. Chakraborty, Evaluation of 13 short tandem repeat loci for use in personal identification applications, Am. J. Hum. Genet. 55 (1) (1994) 175–189. [2] K.B. Gettings, R.A. Aponte, P.M. Vallone, J.M. Butler, STR allele sequence variation: current knowledge and future issues, Forensic Sci. Int. Genet. 18 (2015) 118–130, http://dx.doi.org/10.1016/j.fsigen. 2015.06.005. [3] D.Y. Wang, S. Gopinath, R.E. Lagacé, W. Norona, L.K. Hennessy, M.L. Short, J.J. Mulero, Developmental validation of the GlobalFilerÒ Express PCR Amplification Kit: a 6-dye multiplex assay for the direct amplification of reference samples, Forensic Sci. Int. Genet. 19 (2015) 148–155, http://dx.doi. org/10.1016/j.fsigen.2015.07.013. [4] W. Bar, B. Brinkmann, B. Budowle, A. Carracedo, P. Gill, P. Lincoln, W. Mayr, B. Olaisen, DNA recommendations—further report of the DNA Commission of the ISFH regarding the use of short tandem repeat systems, Int. J. Legal Med. 110 (4) (1997) 175–176. [5] B. Olaisen, W. Bar, B. Brinkmann, B. Budowle, A. Carracedo, P. Gill, P. Lincoln, W. R. Mayr, S. Rand, DNA recommendations 1997 of the International Society for Forensic Genetics, Vox Sang. 74 (1) (1998) 61–63. [6] L. Excoffier, H.E.L. Lischer, Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows, Mol. Ecol. Resour. 10 (3) (2010) 564–567. [7] F. Zhao, X. Wu, G. Cai, C. Xu, The application of Modified-Powerstates software in forensic biostatistics, Chin. J. Forensic Med. 18 (5) (2003) 297–298 (in Chinese). [8] S.B. Hong, S.H. Kim, K.C. Kim, M.H. Park, J.Y. Lee, J.M. Song, M.S. Han, W. Kim, Korean population genetic data and concordance for the PowerPlex ESX 17, AmpFlSTR Identifiler, and PowerPlex 16 systems, Forensic Sci. Int. Genet. 7 (3) (2013) 47–51, http://dx.doi.org/10.1016/j.fsigen.2013.01.002. [9] K. Fujii, H. Watahiki, Y. Mita, et al., Allele frequencies for 21 autosomal short tandem repeat loci obtained using GlobalFiler in a sample of 1501 individuals from the Japanese population, Leg. Med. 17 (5) (2015) 306–308, http://dx.doi. org/10.1016/j.legalmed.2015.08.007. [10] H.H. Lian, W.D. Ge, F. Lin, B. Li, Genetic polymorphisms of 21 autosomal STR loci of Fujian Han population, Fa Yi Xue Za Zhi 31 (3) (2015) 211–214 (in Chinese). [11] A. Carracedo, J.M. Butler, L. Gusmao, A. Linacre, W. Parson, L. Roewer, P.M. Schneider, New guidelines for the publication of genetic population data, Forensic Sci. Int. Genet. 7 (2) (2013) 217–220. [12] A. Carracedo, J.M. Butler, L. Gusmao, A. Linacre, W. Parson, L. Roewer, P.M. Schneider, Update of the guidelines for the publication of genetic population data, Forensic Sci. Int. Genet. 10 (2014) A1–A2.