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Allele frequency data of 20 STR loci in 2000 Korean individuals

Published:September 11, 2017DOI:https://doi.org/10.1016/j.fsigss.2017.09.055

      Abstract

      To increase the discrimination power of human identification in forensic and to evaluate expanded short tandem repeat (STR) loci, we examined a Korean sample population of 2000 unrelated individuals using both GlobalFiler™ PCR Amplification kit and PowerPlex® Fusion System. Allele frequencies for the 20 STR loci (D3S1358, vWA, D16S539, CSF1PO, TPOX, D8S1179, D21S11, D18S51, D2S441, D19S433, TH01, FGA, D22S1045, D5S818, D13S317, D7S820, D10S1248, D1S1656, D12S391, and D2S1338) were calculated. Allele frequencies of the 20 STR loci would be useful for personal identification and paternity testing in forensics and as a standard reference database in Korea.

      Keywords

      1. Introduction

      STRs are the major molecular markers for paternity testing and individual identification [
      • Butler J.M.
      • Hill C.R.
      Biology and genetics of new autosomal STR loci useful for forensic DNA analysis.
      ]. Recently, the Korean DNA database management committee announced an expansion of the 13 STR loci for enhancement of discrimination power, identification of missing persons and human remains, and international compatibility for data sharing [
      • Hares D.R.
      Selection and implementation of expanded CODIS core loci in the United States.
      ]. To meet these objectives of forensics and evaluate the expanded STR loci, Supreme Prosecutors’ Office (SPO) and National Forensic Service (NFS) examined a Korean sample population of 2000 unrelated individuals [
      • Park H.-C.
      • Kim K.
      • Nam Y.
      • et al.
      Population genetic study for 24 STR loci and Y indel (GlobalFilerTM PCR amplification kit and PowerPlexR fusion system) in 1000 Korean individuals.
      ]. In this study, we calculated the allele frequencies obtained from 20 autosomal STR loci and estimated population genetics parameters of the Korean sample population.

      2. Materials and methods

      2.1 Sample preparation

      A total of 2000 anonymous blood samples from unrelated Korean individuals (870 females, 1130 males) were obtained from the Korean Red Cross (KRC) and the National Biobank of Korea (NBK). This study was approved by the Institutional Review Board of KRC and the Ethics Committee and Institutional Review Board of Yonsei University in Korea.

      2.2 PCR amplification and genotyping

      The 20 autosomal STR loci were simultaneously amplified by the multiplex PCR method using two commercial human identification kits such as GlobalFiler™ PCR Amplification kit (GF) and PowerPlex® Fusion System (PPF). The PCR products were subjected to standard capillary electrophoresis by 3500×l genetic analyzer (Life Technologies).

      2.3 Analysis of data

      STR analyses were performed in accordance with recommendations of the DNA Commission of the International Society of Forensic Genetics (ISFG) [
      • Schneider P.M.
      Scientific standards for studies in forensic genetics.
      ]. The data were analyzed using the GeneMapper ID-X software v1.4 (Life Technologies). The statistical parameters of population genetics were evaluated by calculating allele frequency, probability of match (PM), power of discrimination (PD), polymorphism information content (PIC), and power of exclusion (PE) with the Excel spreadsheet PowerStats 1.2 software [
      • Tereba
      Tools for analysis of population statistics.
      ]. The observed heterozygosity (Ho), expected heterozygosity (He), linkage disequilibrium tests (No. of permutations: 10,000, p = 0.05), and Hardy-Weinberg equilibrium (HWE) exact test (No. of dememorization steps: 100,000, p = 0.05) were determined by using the Arlequin 3.5 software [
      • Guo S.W.
      • Thompson E.A.
      Performing the exact test of Hardy-Weinberg proportion for multiple alleles.
      ,
      • Excoffier L.
      • Lischer H.
      Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows.
      ].

      3. Results and discussion

      The 20 autosomal STR loci (the original CODIS core set: D3S1358, vWA, D16S539, CSF1PO, TPOX, D8S1179, D21S11, D18S51, TH01, FGA, D5S818, D13S317, D7S820; and the additional set: D2S441, D19S433, D22S1045, D10S1248, D1S1656, D12S391, D2S1338) were genotyped using samples from 2000 unrelated Korean individuals. Allele frequencies and forensic parameters for the 20 STR loci are shown in Table 1. All the examined loci showed no deviation from the HWE. The observed heterozygosities ranged from 0.6395 at TPOX to 0.9495 at D10S1248. Among expected heterozygosities, the D10S1248 was the most discriminating (0.9401), whereas the TPOX was the least discriminating (0.6282). The average PD for all the tested loci was 0.9163. The highest PD was 0.9695 at D2S1338 and the lowest PD was 0.7892 at TPOX. A pair-wise analysis of the linkage disequilibrium was performed for the loci located on the same chromosome, such as D2S441, TPOX, and D2S1338 on chromosome 2; D5S818 and CSF1PO on chromosome 5; and D12S391 and vWA on chromosome 12. No linkage disequilibrium was noted between any pair of loci. Therefore, these 20 STR loci can be regarded as statistically independent. Concordance testing was examined with the two commercial STR kits (GF and PPF) to determine if there is any allelic dropout or null alleles present in the same samples [
      • Hill C.R.
      • Duewer D.L.
      • Kline M.C.
      • Sprecher C.J.
      • McLaren R.S.
      • Rabbach D.R.
      • Krenke B.E.
      • Ensenberger M.G.
      • Fulmer P.M.
      • Storts D.R.
      • Butler J.M.
      Concordance and population studies along with stutter and peak height ratio analysis for the PowerPlex® ESX 17 and ESI 17 systems.
      ]. Eleven non-concordances were observed during this study and the concordance rate was 99.9725% (39,989 out of 40,000 genotypes) (Table 2). For all the 20 STR loci, the combined PM and PE were 2.5963 × 10−23 and 0.99999995, repectively. As a result, a 20 STR panel is efficient and enough for the analysis of paternity testing and forensic application in comparison with a 13 STR panel with the combined PM (2.8090 × 10−14) and PE (0.99995). The 20 STR loci would serve as a reference database that provides a better representation of the Korean population.
      Table 1Allele frequency data and population genetics parameters of 20 autosomal short tandem repeats (STRs) in a Korean population (n = 2000).
      AlleleD3S1358vWAD16S539CSF1POTPOXD8S1179D21S11D18S51D2S441D19S433
      70.00030.00100.00030.00030.0003
      80.00250.00050.49100.00080.0003
      90.29350.04800.10900.00150.00050.0005
      9.10.0495
      9.20.0003
      9.3
      100.14800.23100.02730.12480.00050.2085
      110.00030.26050.23700.34280.08900.00850.34750.0038
      11.20.0018
      120.00600.18650.39780.02830.15200.04950.21000.0325
      12.20.0053
      130.00130.00080.09480.07430.00150.22980.22630.05500.3143
      13.20.0303
      140.04030.20700.01400.00900.17200.20500.12100.2775
      14.20.00030.1065
      150.39650.02830.00150.15330.15750.00800.0518
      15.20.1350
      160.30630.18550.06130.11400.0083
      16.20.0270
      170.17630.27230.01400.06450.0003
      17.20.0048
      17.3
      180.06950.20130.00130.0558
      18.20.0008
      18.3
      190.00330.09130.00030.0453
      19.20.0003
      200.00050.01330.0308
      20.2
      210.00030.0195
      21.2
      220.00030.0125
      22.2
      230.0043
      23.2
      240.0033
      24.2
      250.0008
      25.2
      260.00030.0010
      26.2
      270.0015
      27.2
      280.0465
      28.20.0058
      290.2255
      29.20.0013
      300.3580
      30.20.0055
      310.0950
      31.20.0645
      320.0235
      32.20.1145
      330.0058
      33.20.0488
      340.0015
      34.20.0015
      350.0005
      360.0003
      PM0.13220.07050.08450.11870.21080.04390.06940.03600.07850.0740
      PD0.86780.92950.91550.88130.78920.95610.93060.96400.92150.9260
      PIC0.66270.76860.74570.67950.56160.82420.76540.84020.75000.7604
      PE0.43530.58430.57330.43370.33960.66360.58060.69490.55530.5788
      Hobs0.70450.79200.78650.70350.63950.83400.79000.85050.76900.7870
      Hexp0.71160.79900.78030.72450.62820.84380.78970.85590.77170.7894
      AlleleTH01FGAD22S1045D5S818D13S317D7S820D10S1248D1S1656D12S391D2S1338
      50.0003
      60.16830.0005
      70.24900.01150.00180.0050
      80.04180.00630.26250.14630.0003
      90.48280.08830.14250.0523
      9.1
      9.2
      9.30.0450
      100.01200.19000.13700.17300.00130.0003
      110.00130.18900.32930.23150.34100.00250.0490
      11.2
      120.00200.22680.18250.23730.08280.0413
      12.2
      130.00180.13780.03350.03950.35930.1213
      13.20.0003
      140.00400.00830.00830.00530.24530.07430.0010
      14.2
      150.29380.00130.00050.00030.21200.26200.0163
      15.2
      160.25250.00030.07980.25450.00700.0045
      16.2
      170.00300.23030.01650.09250.10300.0950
      17.20.0003
      17.30.0540
      180.02130.02350.00050.01280.26980.1263
      18.2
      18.30.0328
      190.05430.00300.00130.22750.1700
      19.2
      200.05800.00300.15580.1125
      20.20.0005
      210.11430.00130.11050.0185
      21.20.0025
      220.18750.05380.0493
      22.20.0035
      230.22280.03000.1803
      23.20.0073
      240.17730.01630.1378
      24.20.0038
      250.09550.00680.0828
      25.20.0015
      260.03780.00130.0168
      26.20.0003
      270.00600.00100.0048
      27.20.0005
      280.00230.0013
      28.2
      290.00050.0005
      PM0.15530.03830.09780.08280.06600.08410.10000.04810.05270.0305
      PD0.84470.96170.90220.91720.93400.91590.90000.95190.94730.9695
      PIC0.62460.83680.71890.74370.77500.73930.71340.81180.80240.8585
      PE0.36770.67820.50290.54730.56790.52880.50210.65590.63950.7397
      Hobs0.65900.84150.74600.77150.78300.76100.94950.74550.82850.8215
      Hexp0.67290.85350.76080.77730.80410.77200.94010.75260.82980.8242
      PM, probability of match; PD, power of discrimination; PIC, polymorphism information content; PE, power of exclusion; Hobs, observed heterozygosity; Hexp, expected heterozygosity.
      Table 2Genotype non-concordances between GlobalFiler™ PCR Amplification kit (GF) and PowerPlex® Fusion System (PPF) in a Korean sample population of 2000 individuals.
      Sample IDLocusGFPPF
      15KR0270D16S5399–1010Silent allele in PPF
      15KR0271D19S43313.213–13.2Silent allele in GF
      15KR0545D19S4331413–14Silent allele in GF
      15KR0606TPOX8–118Silent allele in PPF
      15KR0891D7S82010–1212Silent allele in PPF
      15KR0906D19S43314.2–1515Silent allele in PPF
      15KR0938D18S5114–2020Silent allele in PPF
      p03 c07D19S43317.214–17.2Silent allele in GF
      p05 g06D19S43315.213–15.2Silent allele in GF
      p06 e03D19S4331413–14Silent allele in GF
      p09 c06TPOX8–118Silent allele in PPF

      4. Conclusion

      The common allele frequency table was built in collaboration with Supreme Prosecutors’ Office (SPO) and National Forensic Service (NFS). Allele frequencies of the 20 STR loci would be used for forensic personal identification and paternity testing in the Korean population.

      Conflict of interest

      None.

      Acknowledgements

      This work was supported by a grant from Supreme Prosecutors’ Office of the Republic of Korea and by a grant ( NFS2016DNA03 ) from the Forensic Research Program of the National Forensic Service .

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