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Population genetic analysis of Moroccans residing in Belgium using 16 autosomal STRs of the PowerPlex ESI 17 multiplex
Forensic Science International: Genetics 5 (2011) 352–353
Contents lists available at ScienceDirect
Forensic Science International: Genetics journal homepage: www.elsevier.com/locate/fsig
Letter to the Editor Population genetic analysis of Moroccans residing in Belgium using 16 autosomal STRs of the PowerPlex ESI 17 multiplex
Dear Editor, As a consequence of immigration starting in the 1960s, about 265,000 people of Moroccan origin presently reside in Belgium, thus constituting the most numerous group of non-indigenous inhabitants [1]. Most Moroccan immigrants in Belgium as well as the Netherlands and Germany belong to the Berber (Imazighen) ethnic group and originate from the Rif area, a mountainous region of northern Morocco. Because of socio-economic issues beyond the scope of this journal, they are over-represented in forensic as well as paternity testing statistics. We tested a sample of 239 apparently unrelated Moroccans (134 males, 105 females), representing the mothers and alleged fathers from paternity cases. All had consented to the anonymous use of their data for a population genetic study. Buccal swabs were collected from which DNA was extracted using the Qiamp DNA kit (Qiagen). Multiplex PCR was performed on approximately 0.5 ng of DNA using the PowerPlex ESI (European Standard Investigator) 17 System (Promega) following the manufacturer’s instructions, in a GeneAmp PCR System 9700 (Applied Biosystems). The ESI 17 configuration contains 7 loci as mini-STRs of the European Standard Set (D3S1358, D8S1179, D18S51, D21S11, FGA, TH01, vWA), 5 new ENFSI recommended loci with normal sized amplicons (D2S441, D10S1248, D22S1045, D1S1656, D12S399), 4 other routinely tested loci (D2S1358, D16S539, D19S433, SE33) and the amelogenin sex marker. Amplification products were separated and detected on the ABI 3130 Genetic Analyzer (Applied Biosystems). Alleles were called using the ladder included in the kit and GeneMapperID V3.2.1 software (Applied Biosystems). Results are summarised in Table 1 which shows the allelic frequencies for the 16 STRs of the ESI 17 system, together with the data on Hardy–Weinberg equilibrium (HWE) and the parameters relevant for forensic and paternity casework. In Table 2 the 16locus genotypes of the 239 tested Moroccans are given. Stored DNA from samples previously sent by the English Speaking Working Group of International Society for Forensic Genetics for quality control testing, was retested with the ESI 17 kit. Allelic frequencies were estimated by direct gene counting. Conformity of the observed genotype frequencies with Hardy– Weinberg expectations was examined by the exact test from Guo and Thompson [2] using the Arlequin V3.01 software [3]. The matching probability (MP), power of discrimination (PD), polymorphism information content (PIC) and power of exclusion (PE) were calculated with the Powerstats V12 worksheet (Promega) [4]. Regarding the test results for HWE, a p value > 0.05 was obtained for 1872-4973/$ – see front matter ß 2010 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.fsigen.2010.01.008
all STRs except for D22S1045 where the exact test yielded a p value of 0.0497. Considering the Bonferroni [5] procedure and the fact that 16 tests for HWE were simultaneously performed on the same population sample, the significance threshold is adjusted from a = 0.05 to a = 0.05/16 = 0.0031 which is clearly below the p value of 0.0497 observed for D22S1045. Hence this single p value gives no reason to reject the null hypothesis. Combined, the 16 STRs result in a MP of 1 in 4.43 1020 and a PE of 99.999998%, which should be effective in the resolution of most forensic and paternity cases. One tri-allelic pattern was observed in D12S391, with alleles 14, 17 and 24. The height of the three peaks was uneven and the sum of the height of peaks 17 and 24 was equal to the height of peak 17, making it an example of a ‘‘type I’’ tri-allelic pattern according to the nomenclature of Clayton et al. [6]. We also observed an example of the rare 7.3 allele in SE33, which is among the shortest allelic variants of this highly polymorphic and complex locus. It was first described in an Austrian Caucasian by Dauber et al. [7] and its rarity is illustrated by the fact that it was not encountered a single time among 1443 U.S. Caucasian, African American, Hispanic and Asian samples published by Butler et al. [8]. Due to the relative novelty of the ESI 17 multiplex, we found no data on relevant populations with which to compare this Moroccan population. This paper follows the guidelines for publication of population data for forensic purposes requested by the journal [9]. Appendix A. Supplementary data Supplementary data associated with this article can be found, in the online version, at doi:10.1016/j.fsigen.2010.01.008. References [1] R. Schittecatte, Moroccans surpass Italians as most numerous foreigners in Belgium, Nat. Inst. Stat. (2007) http://www.npdata.be/. [2] S.W. Guo, E.A. Thompson, Performing the exact test of Hardy–Weinberg proportion for multiple alleles, Biometrics 48 (1992) 361–372. [3] L. Excoffier, G. Laval, S. Schneider, Arlequin ver. 3.0: an integrated software package for population genetics data analysis, Evol. Bioinform. Online 1 (2005) 47–50. [4] www.promega.com/geneticidtools/powerstats/PowerStatsV12.xls. [5] C.E. Bonferroni, Teoria statistica delle classi e calculo delle probabilita, Pubblicazioni del Instituto Superiore di Scienze Economiche e Commerciali de Firenze 8 (1936) 3–62. [6] T.M. Clayton, J.L. Guest, A.J. Urquhart, P.D. Gill, A genetic basis for anomalous band patterns encountered during DNA STR profiling, J. Forensic Sci. 49 (2004) 1207– 1214. [7] E.M. Dauber, W. Ba¨r, M. Klintschar, F. Neuhuber, W. Parson, E. Mueller-van der Spruit, W.R. Mayr, New sequence data of allelic variants at the STR loci ACTBP2 (SE33), D21S11, FGA, vWA, CSF1PO, D2S1338, D16S539, D18S51 and D19S433 in Caucasoids, International Congress Series, Progress Forensic Genet. 10 (2004) 191– 193. [8] J.M. Butler, C.R. Hill, M.C. Kline, D.L. Duewer, C.J. Sprecher, R.S. McLaren, D.R. Rabbach, B.E. Krenke, D.R. Storts, The single most polymorphic STR locus: SE33 performance in U.S. populations, Forensic Sci. Int.: Genet. 4 (2009) e39–e40. [9] 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., (2010), in press.
Letter to the Editor / Forensic Science International: Genetics 5 (2011) 352–353
Gerhard Mertens* Steven Rand Katleen Moordtgat Els Cardoen Isabelle De Bruyn Nadia Mommers Gitte Leijnen Els Jehaes
353
Werner Jacobs Forensic DNA Laboratory, Antwerp University Hospital, University of Antwerp, Wilrijkstaat 10, B-2650 Edegem, Belgium *Corresponding author. Tel.: +32 3 821 39 46 E-mail address: [email protected] (G. Mertens) 11 January 2010
Contents lists available at ScienceDirect
Forensic Science International: Genetics journal homepage: www.elsevier.com/locate/fsig
Letter to the Editor Population genetic analysis of Moroccans residing in Belgium using 16 autosomal STRs of the PowerPlex ESI 17 multiplex
Dear Editor, As a consequence of immigration starting in the 1960s, about 265,000 people of Moroccan origin presently reside in Belgium, thus constituting the most numerous group of non-indigenous inhabitants [1]. Most Moroccan immigrants in Belgium as well as the Netherlands and Germany belong to the Berber (Imazighen) ethnic group and originate from the Rif area, a mountainous region of northern Morocco. Because of socio-economic issues beyond the scope of this journal, they are over-represented in forensic as well as paternity testing statistics. We tested a sample of 239 apparently unrelated Moroccans (134 males, 105 females), representing the mothers and alleged fathers from paternity cases. All had consented to the anonymous use of their data for a population genetic study. Buccal swabs were collected from which DNA was extracted using the Qiamp DNA kit (Qiagen). Multiplex PCR was performed on approximately 0.5 ng of DNA using the PowerPlex ESI (European Standard Investigator) 17 System (Promega) following the manufacturer’s instructions, in a GeneAmp PCR System 9700 (Applied Biosystems). The ESI 17 configuration contains 7 loci as mini-STRs of the European Standard Set (D3S1358, D8S1179, D18S51, D21S11, FGA, TH01, vWA), 5 new ENFSI recommended loci with normal sized amplicons (D2S441, D10S1248, D22S1045, D1S1656, D12S399), 4 other routinely tested loci (D2S1358, D16S539, D19S433, SE33) and the amelogenin sex marker. Amplification products were separated and detected on the ABI 3130 Genetic Analyzer (Applied Biosystems). Alleles were called using the ladder included in the kit and GeneMapperID V3.2.1 software (Applied Biosystems). Results are summarised in Table 1 which shows the allelic frequencies for the 16 STRs of the ESI 17 system, together with the data on Hardy–Weinberg equilibrium (HWE) and the parameters relevant for forensic and paternity casework. In Table 2 the 16locus genotypes of the 239 tested Moroccans are given. Stored DNA from samples previously sent by the English Speaking Working Group of International Society for Forensic Genetics for quality control testing, was retested with the ESI 17 kit. Allelic frequencies were estimated by direct gene counting. Conformity of the observed genotype frequencies with Hardy– Weinberg expectations was examined by the exact test from Guo and Thompson [2] using the Arlequin V3.01 software [3]. The matching probability (MP), power of discrimination (PD), polymorphism information content (PIC) and power of exclusion (PE) were calculated with the Powerstats V12 worksheet (Promega) [4]. Regarding the test results for HWE, a p value > 0.05 was obtained for 1872-4973/$ – see front matter ß 2010 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.fsigen.2010.01.008
all STRs except for D22S1045 where the exact test yielded a p value of 0.0497. Considering the Bonferroni [5] procedure and the fact that 16 tests for HWE were simultaneously performed on the same population sample, the significance threshold is adjusted from a = 0.05 to a = 0.05/16 = 0.0031 which is clearly below the p value of 0.0497 observed for D22S1045. Hence this single p value gives no reason to reject the null hypothesis. Combined, the 16 STRs result in a MP of 1 in 4.43 1020 and a PE of 99.999998%, which should be effective in the resolution of most forensic and paternity cases. One tri-allelic pattern was observed in D12S391, with alleles 14, 17 and 24. The height of the three peaks was uneven and the sum of the height of peaks 17 and 24 was equal to the height of peak 17, making it an example of a ‘‘type I’’ tri-allelic pattern according to the nomenclature of Clayton et al. [6]. We also observed an example of the rare 7.3 allele in SE33, which is among the shortest allelic variants of this highly polymorphic and complex locus. It was first described in an Austrian Caucasian by Dauber et al. [7] and its rarity is illustrated by the fact that it was not encountered a single time among 1443 U.S. Caucasian, African American, Hispanic and Asian samples published by Butler et al. [8]. Due to the relative novelty of the ESI 17 multiplex, we found no data on relevant populations with which to compare this Moroccan population. This paper follows the guidelines for publication of population data for forensic purposes requested by the journal [9]. Appendix A. Supplementary data Supplementary data associated with this article can be found, in the online version, at doi:10.1016/j.fsigen.2010.01.008. References [1] R. Schittecatte, Moroccans surpass Italians as most numerous foreigners in Belgium, Nat. Inst. Stat. (2007) http://www.npdata.be/. [2] S.W. Guo, E.A. Thompson, Performing the exact test of Hardy–Weinberg proportion for multiple alleles, Biometrics 48 (1992) 361–372. [3] L. Excoffier, G. Laval, S. Schneider, Arlequin ver. 3.0: an integrated software package for population genetics data analysis, Evol. Bioinform. Online 1 (2005) 47–50. [4] www.promega.com/geneticidtools/powerstats/PowerStatsV12.xls. [5] C.E. Bonferroni, Teoria statistica delle classi e calculo delle probabilita, Pubblicazioni del Instituto Superiore di Scienze Economiche e Commerciali de Firenze 8 (1936) 3–62. [6] T.M. Clayton, J.L. Guest, A.J. Urquhart, P.D. Gill, A genetic basis for anomalous band patterns encountered during DNA STR profiling, J. Forensic Sci. 49 (2004) 1207– 1214. [7] E.M. Dauber, W. Ba¨r, M. Klintschar, F. Neuhuber, W. Parson, E. Mueller-van der Spruit, W.R. Mayr, New sequence data of allelic variants at the STR loci ACTBP2 (SE33), D21S11, FGA, vWA, CSF1PO, D2S1338, D16S539, D18S51 and D19S433 in Caucasoids, International Congress Series, Progress Forensic Genet. 10 (2004) 191– 193. [8] J.M. Butler, C.R. Hill, M.C. Kline, D.L. Duewer, C.J. Sprecher, R.S. McLaren, D.R. Rabbach, B.E. Krenke, D.R. Storts, The single most polymorphic STR locus: SE33 performance in U.S. populations, Forensic Sci. Int.: Genet. 4 (2009) e39–e40. [9] 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., (2010), in press.
Letter to the Editor / Forensic Science International: Genetics 5 (2011) 352–353
Gerhard Mertens* Steven Rand Katleen Moordtgat Els Cardoen Isabelle De Bruyn Nadia Mommers Gitte Leijnen Els Jehaes
353
Werner Jacobs Forensic DNA Laboratory, Antwerp University Hospital, University of Antwerp, Wilrijkstaat 10, B-2650 Edegem, Belgium *Corresponding author. Tel.: +32 3 821 39 46 E-mail address: [email protected] (G. Mertens) 11 January 2010