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Forensic Science International: Genetics xxx (2011) xxxxxx

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Forensic Science International: Genetics

journal homepage: www.elsevier.com/locate/fsig

Letter to the Editor

Allele frequencies of the new European Standard Set (ESS) loci plus SE33 locus in a population from the Republic of Macedonia Dear Editor, The highly polymorphic short tandem repeat (STR) loci in the human genome are widely used for forensic and paternity testing as well as for population genetic studies. Introducing set of STR loci as observed markers made marvels progress in this eld of forensic science [1,2]. Nowadays, in response to the ENFSI and EDNAP groups call for new STR multiplexes for Europe, Promega developed a suite of four new DNA proling kits. One of them is PowerPlex ESI 17 that we have used in this study. In our previous population studies of Macedonian human population, we have used 15 STR loci included in the AmpFlSTR1Identiler1 [3] and 17 Y-chromosomal short tandem repeats loci incorporated in the AmpFistr1YlerTM PCR Amplication Kit (data submitted to the FSI Genetics). All obtained results were included in Macedonian referent database. In order of future development of this database we have decide to analyze 6 additional new STR loci (D22S1045, D1S1656, D10S1248, D2S441, D12S391, and SE33). Some of these loci were described even 15 years ago [4,5]. This study is based on an observation of representative sample of Macedonia human population. A total of 205 unrelated individuals of which 105 males and 100 females, from different regions of Macedonia, participated in this study. All tested individuals have been voluntary donors appropriately informed about the research. Qiagen MicroTM Tissue Kit was used for DNA extraction from whole blood, Quantiler1 assay for quantication and PowerPlex ESI 171 System for amplication and detection (D18S51, D21S11, TH01, D3S1358, Amelogenin, D16S539, D2S1338, D1S1656, D10S1248, FGA, D8S1179, vWA, D22S1045, D19S433, D12S391, D2S441 and SE33). The total volume of each reaction was 12.5 ml. The PCR amplications have been carried out in ABI 9700 Thermal Cycler according to the manufacturers recommendations. Electrophoresis of the amplication products was performed on an ABI 310 PRISM. Numerical allele designations of the proles were obtained by processing with Gene Mapper1 IDv 3.2 Software. Deviation from HardyWeinberg equilibrium, observed and expected heterozygosity, power of discrimination and power of exclusion were calculated. Also, we have compared Macedonian data with data obtained from other neighboring populations with available data for observed loci. Deviation from HardyWeinberg equilibrium [6], observed and expected heterozygosity [7], exact test of population differentiation [8] and pairwise Fst [9] were calculated within Powermarker v3.25 [10], since power of discrimination and power of exclusion within Microsoft1 Excel workbook templatePowerStats [11]. Allele frequencies and all calculated forensic parameters are shown in Supplementary Table 1. All data are available on http:// www.ingeb.ba/rebida/ESI17/macedonia.html. No statistically signicant deviation (p < 0.05) from HardyWeinberg equilibrium was found except for D1S1656 and SE33 loci (Table 1). Heterozygosity excess has been detected for SE33 locus. Allele frequencies of observed six loci within Macedonian population have been compared with data obtained from geographically neighboring Southeast European populations such as Serbia and Bosnia Herzegovina (our unpublished data). After Bonferronis correction, statistical signicance was considered as

Table 1 The distribution of allele frequencies and calculated forensic parameters for the Macedonian population over 5 new ESS loci and SE33 locus (n = 205). Allele 2n 1 6.3 9 10 11 11.3 12 12.1 12.3 13 13.2 14 14.2 15 15.3 16 16.1 16.3 17 D1S1656 410 0.1146 0.1683 0.0683 0.0780 0.1244 0.0463 0.1366 0.0390 0.0341 D2S441 410 0.0024 0.1268 0.3365 0.0951 0.0415 0.0039 0.0024 0.0390 0.3073 0.0439 0.0024 D10S1248 410 0.0268 0.2341 0.3293 0.1780 0.1829 0.0439 D12S391 410 0.0049 0.0024 0.0512 0.0317 0.1000 SE33 410 0.0024 0.0024 0.0254 0.0122 0.0073 0.0098 0.0073 0.0463 0.0366 0.0024 0.0659 D22S1045 410 0.0024 0.1366 0.0122 0.0537 0.3634 0.3220 0.0951

1872-4973/$ see front matter 2011 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.fsigen.2011.07.004

Please cite this article in press as: Z. Jakovski, et al., Allele frequencies of the new European Standard Set (ESS) loci plus SE33 locus in a population from the Republic of Macedonia, Book review. Forensic Sci. Int. Genet. (2011), doi:10.1016/j.fsigen.2011.07.004

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2 Table 1 (Continued ) Allele 2n 17.2 17.3 18 19 19.2 19.3 20 20.2 20.3 21 21.2 22 22.2 23 24 24.1 24.2 25 25.2 26 27 27.2 28 28.2 29 29.2 30.2 31.2 32.2 33 33.2 34.2 35 36 37.2 PD PE P H(ex) H(ob) D1S1656 410 0.0902 0.0146 0.0024 0.0098 0.973 0.791 0.0223 0.8950 0.8976 D2S441 410 0.929 0.506 0.1076 0.7636 0.6976 D10S1248 410 0.0024 0.0024 0.902 0.599 0.2502 0.7689 0.8000 D12S391 410 0.0024 0.1732 0.1171 0.0049 0.0902 0.0024 0.1317 0.1146 0.0707 0.0463 0.0293 0.0024 0.0024 0.976 0.721 0.0582 0.8955 0.8634 SE33 410 0.0049 0.0756 0.1098 0.0049 0.0537 0.0122 0.0122 0.0122 0.0073 0.0366 0.0024 0.0024 0.0390 0.0024 0.0244 0.0024 0.0756 0.0024 0.0512 0.0024 0.0610 0.0488 0.0146 0.0220 0.0024 0.0073 0.0024 0.0073 0.0024 0.0024 0.989 0.810 0.0029 0.9473 0.9073 D22S1045 410 0.0073 0.0073 0.878 0.579 0.3163 0.7334 0.7854 Letter to the Editor / Forensic Science International: Genetics xxx (2011) xxxxxx

PD, power of discrimination; PE, power of exclusion; P, HardyWeinberg equilibrium, exact test; H(ob), observed heterozygosity; H(ex), expected heterozygosity.

p < 0.015. Statistically signicant differences of allele frequencies were noticed for D12S391 locus (p = 0.0019) between Macedonian and Serbian population, as well as between Macedonian and Bosnia Herzegovina population (p = 0.0005). Pairwise Fst, calculated according to the results observed over these 6 loci, shows no signicant genetic difference among Macedonian and Serbian population (0.14%), as well as among Macedonian and Bosnia Herzegovina population (0.15%). According to our preliminary results, no disconcordance between PowerPlex ESI 17 and Identiler or PowerPlex 16 was recorded. Detailed concordance study, which is going to include almost thousand samples from this part of Europe, is ongoing. In the course of the elaboration of this population study, we adhered to the new guidelines published in this journal, wherein we would like to point out that we accept the requirements pertaining to the publication of this type of papers [12], as well a ISFG recommendations [13]. Also we follow recommendations of the European Council resolution (9192/01) calls upon EU countries to use the European Standard Set (ESS) as a minimum to enable international comparison of DNA proles as well as the paper for the evolution of DNA databases and recommendations [14]. Acknowledgment We would like to thank to the Promega Corporation for supporting this study.

References
[1] P. Gill, C.P. Kimpton, A. Urquhart, et al., Automated short tandem repeat (STR) analysis in forensic caseworka strategy for the future, Electrophoresis 16 (1995) 15431552. [2] J.A. Thomson, V. Pilotti, P. Stevens, K.L. Ayres, P.G. Debenham, Validation of short tandem repeat analysis for the investigation of cases of disputed paternity, Forensic Sci. Int. 100 (1998) 116. [3] Z. Jakovski, K. Nikolova, I. Furac, M. Masic, B. Janeska, M. Kubat, Allele frequencies for 15 STR loci in a population from the Republic of Macedonia, Int. J. Legal Med. 120 (2006) 5355. [4] M.V. Lareu, C. Pestoni, M. Schurenkamp, S. Rand, B. Brinkmann, A. Carracedo, A highly variable STR at the D12S391 locus, Int. J. Legal Med. 109 (3) (1996) 134138. [5] M.V. Lareu, S. Barral, A. Salas, C. Pestoni, A. Carracedo, Sequence variation of a hypervariable short tandem repeat at the D1S1656 locus, Int. J. Legal Med. 111 (5) (1998) 244247. [6] S.W. Guo, E.A. Thompson, Performing the exact test of HardyWeinberg proportion for multiple alleles, Biometrics 48 (1992) 361372. [7] M. Nei, Molecular Evolutionary Genetics, Columbia University Press, New York, 1987. [8] M. Raymond, F. Rousset, An exact test for population differentiation, Evolution 49 (1995) 12801283. [9] B.S. Weir, Genetic Data Analysis II: Methods for Discrete Population Genetic Data, Sinauer Assoc., Inc., Sunderland, MA, 1996. [10] L. Kejun, V.M. Spencer, PowerMarker: an integrated analysis environment for genetic marker analysis, Bioinformatics 21 (2005) 21282129. [11] A. Tereba, Tools for analysis of population statistics, Proles DNA 3 (1999) 1416. [12] A. Carracedo, J.M. Butler, L. Gusmao, W. Parson, L. Roewer, P.M. Schneider, Publication of population data for forensic purposes, Forensic Sci. Int. Genet. 4 (2010) 145147. [13] B. Olaisen, W. Bar, B. Brinkmann, B. Budowle, A. Carracedo, P. Gill, P. Lincoln, W.R. Mayr, S. Vox Sang Rand, DNA recommendations 1997 of the International Society for Forensic Genetics, Vox Sang. 74 (1) (1998) 6163.

Please cite this article in press as: Z. Jakovski, et al., Allele frequencies of the new European Standard Set (ESS) loci plus SE33 locus in a population from the Republic of Macedonia, Book review. Forensic Sci. Int. Genet. (2011), doi:10.1016/j.fsigen.2011.07.004

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Letter to the Editor / Forensic Science International: Genetics xxx (2011) xxxxxx [14] P. Gill, L. Fereday, N. Morling, P.M. Schneider, The evolution of DNA databases recommendations for new European STR loci, Forensic Sci. Int. 156 (2006) 242244. 3

Zlatko Jakovski* Ksenija Nikolova Renata Jankova-Ajanovska Biljana Janeska Institute of Forensic Medicine and Criminology, School of Medicine, University Ss. Cyril and Methodious, Skopje, Macedonia Naris Pojskic Institute for Genetic Engineering and Biotechnology, Sarajevo, Bosnia and Herzegovina

Damir Marjanovicab Institute for Genetic Engineering and Biotechnology, Sarajevo, Bosnia and Herzegovina b Genos, Planinska 1, 10000 Zagreb, Croatia
*Corresponding

author. Tel.: +389 2 3 177 044; fax: +389 2 1 178 831

E-mail address: zlatedr@yahoo.com (Z. Jakovski). 24 December 2010

Please cite this article in press as: Z. Jakovski, et al., Allele frequencies of the new European Standard Set (ESS) loci plus SE33 locus in a population from the Republic of Macedonia, Book review. Forensic Sci. Int. Genet. (2011), doi:10.1016/j.fsigen.2011.07.004