- Email: [email protected]
Allele frequencies for the new European Standard Set (ESS) loci and D1S1677 in the Belgian population
Forensic Science International: Genetics 6 (2012) e75–e77
Contents lists available at ScienceDirect
Forensic Science International: Genetics journal homepage: www.elsevier.com/locate/fsig
Forensic Population Genetics - Letter to the Editor Allele frequencies for the new European Standard Set (ESS) loci and D1S1677 in the Belgian population
Dear Editor, The nine Belgian laboratories, officially recognized by the Belgian Minister of Justice for performing DNA analysis in criminal cases, have jointly decided to use a common local population database for statistical calculations. A first database has been set up for the loci covered in AmpFlSTR1 IdentifilerTM and PowerPlex1 16 [1,2]. With the decision of ENFSI and EDNAP to extend the current ESS loci (D3S1358, vWA, D8S1179, D21S11, D18S51, THO1 and FGA) with new loci (D1S1656, D2S441, D10S1248, D12S391 and D22S1045), there was a need to obtain also data for these loci within the Belgian population [3,4]. Here, we present the allele frequencies and forensic efficiency data for the new ESS loci and one additional miniSTR, D1S1677. Buccal swab samples were collected with the Clue C.D.S. Swab Safe1 kit (Swiss Forensic) from 205 unrelated individuals after informed consent, hereafter referred as the Brussels sample set. Genomic DNA was isolated using the QIAamp DNA Mini KitTM (Qiagen, Germany) or the NucleoMag 96 Trace kit (MachereyNagel, Germany) on the KingFisher automatic extraction platform (Thermo Scientific, USA) and DNA was quantified with the Plexor HY KitTM (Promega Corporation, USA). The Leuven sample set consisted of 196 unrelated individuals from the Leuven Blood Bank previously used for obtaining allele frequencies for PowerPlex1 16 [2]. The Brussels sample set was amplified with PowerPlex1 ESI 17 System (Promega Corporation, USA) and AmpFlSTR1 NGMTM PCR Amplification Kit (Applied Biosystems, USA) using the reaction conditions as described by each manufacturer. The samples were amplified in a GeneAmp PCR System 9700 (Applied Biosystems, USA). The Leuven sample set was amplified with an in-house developed multiplex (MiniPlex-9) consisting of D1S1677 [5], D1S1656 [6], D2S441 [5], D10S1248 [5], D12S391 [7], D22S1045 [5], D21S11 [8], D18S51 [8], FGA [9] and the Amelogenin locus [10,11]. Samples were amplified using 0.5–1 ng target DNA in 25 ml reactions of QIAGEN Multiplex PCR Kit (Qiagen, Germany) in a GeneAmp PCR System 9700 (Applied Biosystems, USA) using the following reaction conditions: 95 8C for 15 min followed by 30 cycles of 30 s at 94 8C, 60 s at 57 8C and 60 s at 72 8C, and a final incubation of 45 min at 60 8C. The amplified products of the Brussels sample set were detected on the ABI PRISM 3130xl Genetic Analyzer (Applied Biosystems, USA) using internal size standard, filter set and conditions recommended by each manufacturer except for the amount of PCR product used on the capillary sequencer (2 ml instead of the recommended 1 ml). Allele calling was performed using GeneMapper ID-X software (Applied Biosystems, USA). The amplified products of the Leuven sample set were purified with 1872-4973/$ – see front matter ß 2011 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.fsigen.2011.05.003
BigDye1 XTerminatorTM (Applied Biosystems, USA) according to Janssen et al. [12] and 1 ml was used for detection on the ABI PRISM 3130xl Genetic Analyzer (Applied Biosystems, USA) using GeneScan1 500 [LIZ] as internal size standard and filter set G5 for discriminating the different dyes (6-FAM, VIC, NED, PET and LIZ). Allele calling was performed using GeneMapper ID v3.2 (Applied Biosystems, USA). The Laboratory of Forensic Genetics and Molecular Archaeology (Leuven) and the National Institute of Criminalistics and Criminology (Brussels) are accredited according to ISO/IEC 17025 and participate in CTS (Collaborative Testing Services Inc., USA) and GEDNAP proficiency tests. SRM 2391b (National Institute of Standards and Technology, USA) and DNA from control cell lines 9947A, 9948 and 007 were used for verification of the MiniPlex-9 genotyping. Observed heterozygosity (Ho), expected heterozygosity (He), Hardy–Weinberg equilibrium (exact test) and population differentiation (genic and genotypic) were calculated with Genepop v4 software (http://genepop.curtin.edu.au/) [13,14]. The power of discrimination (PD) and the power of exclusion were calculated for each locus [15,16]. In order to assess the different genetic distribution between the populations analyzed with respect to other published population data [17–29], population pairwise genetic distances FST were calculated using Arlequin v3.01 software [30]. For data published before 2008, we adapted the alleles to the current nomenclature [31]. Regarding D12S391, most authors do not mention micro-variants (.1 alleles). Therefore, we combined these micro-variants with the nearest alleles (.0) in each population for comparison purposes [22]. The statistical significance of the pairwise FST estimates was determined with 10,000 permutation tests. No significant difference in allele nor genotype frequencies were observed between the two population sets for the 8 common STR loci. Therefore, both data sets were combined for determination of the allele frequencies, forensic efficiency data and Hardy– Weinberg equilibrium (p-values; Table 1). No evidence for deviation from Hardy–Weinberg equilibrium was found except for D2S441 which could be rejected after Bonferroni correction. The allele frequencies of all tested STRs were significantly different between the Belgian population and the populations from Ghana, Madagascar and Korea. Moreover, there are few significant differences between Belgium with all other tested populations for one or more loci (especially D2S441), except between the Belgian and the Italian, Swedish, Polish and North German populations. All FST genetic distances are reported in supplementary Table 2. Evaluation of the concordance in the Leuven data set between MiniPlex-9 and PowerPlex1 16 [2] for the common loci D18S51, D21S11 and FGA revealed no difference. The Brussels data set showed one discordance: a heterozygous genotype (14,15) for D19S433 with AmpFlSTR1 NGMTM and a homozygous genotype
Letter to the Editor / Forensic Science International: Genetics 6 (2012) e75–e77
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Table 1 Allele frequency data for the Belgian population. Allele 9 10 11 11.3 12 12.3 13 13.3 14 14.3 15 15.3 16 16.3 17 17.1 17.3 18 18.3 19 19.3 20 21 22 23 24 25 26 N Obs. He. Exp. He. P-value SE PD PE
D1S1677
D1S1656
0.00256 0.00513
0.08875
0.06923
0.13000
0.25385
0.05250 0.00125 0.09125 0.00125 0.13500 0.06625 0.12500 0.05125 0.05625 0.00250 0.12000 0.00625 0.05875
0.31282 0.28205 0.06410 0.01026
D2S441 0.00125 0.17000 0.36125 0.04375 0.05125 0.00375 0.02875
D10S1248
400 0.9125 0.9032 0.6699 0.0303 0.9821 0.8009
D22S1045
0.00125 0.13875 0.02750
0.00625
0.28250
0.00500
0.28625
0.34375
0.05000
0.05000
0.17000
0.04625
0.37125
0.00375
0.14250
0.02625
0.34750
0.02750
0.08500
0.07250
0.00500
0.01250 0.00125
195 0.8205 0.7510 0.6613 0.0186 0.8942 0.5177
D12S391
400 0.7550 0.7517 0.0113 0.0043 0.9004 0.6265
400 0.7300 0.7522 0.4584 0.0240 0.8979 0.5256
0.01500 0.20000 0.02125 0.12625 0.01500 0.12000 0.12000 0.08750 0.07750 0.04000 0.01625 0.00375 400 0.8850 0.8898 0.4732 0.0297 0.9777 0.7770
0.00875
400 0.7425 0.7152 0.8946 0.0107 0.8707 0.4756
N = number of individuals; Obs. He. = observed heterozygosity; Exp. He. = expected heterozygosity; P-value = probability values of the Hardy–Weinberg equilibrium exact test (100 batches and 1000 iterations); SE = standard error of P-value; PD = probability of discrimination; PE = probability of exclusion.
(15,15) with PowerPlex1 ESI 17 System. This discordant result was confirmed by re-testing the sample with the respective kits, and is probably due to a mutation at the primer binding site positions [32]. A different null allele (15) at D19S433 was also observed by Tucker et al. [29] with PowerPlex1 ESI 17 System in a population study of 242 Caucasians and 64 Indo-Pakistani. This paper follows the guidelines for publication of population data requested by the journal [33].
Appendix A. Supplementary data Supplementary data associated with this article can be found, in the online version, at doi:10.1016/j.fsigen.2011.05.003. References [1] R. Decorte, M. Engelen, L. Larno, K. Nelissen, A. Gilissen, J.J. Cassiman, Belgian population data for 15 STR loci (AmpFlSTR SGM Plus and AmpFlSTR profiler PCR amplification kit), Forensic Sci. Int. 13 (9) (2004) 211–213. [2] R. Decorte, E. Verhoeven, E. Vanhoutte, K. Knaepen, J.J. Cassiman, Allele frequency data for 19 short tandem repeats (PowerPlex 16 and FFFl) in a Belgian population sample, J. Forensic Sci. 51 (2006) 436–437. [3] P. Gill, L. Fereday, N. Morling, P.M. Schneider, The evolution of DNA databases— recommendations for new European STR loci, Forensic Sci. Int. 15 (6) (2006) 242– 244. [4] P. Gill, L. Fereday, N. Morling, P.M. Schneider, New multiplexes for Europeamendments and clarification of strategic development, Forensic Sci. Int. 16 (3) (2006) 155–157. [5] M.D. Coble, J.M. Butler, Characterization of new miniSTR loci to aid analysis of degraded DNA, J. Forensic Sci. 50 (2005) 43–53. [6] 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. 11 (1) (1998) 244–247.
[7] M.V. Lareu, C. Pestoni, M. Schrenkamp, S. Rand, B. Brinkmann, A. Carracedo, A highly variable STR at the D12S391 locus, Int. J Legal Med. 109 (1996) 134–138. [8] J.M. Butler, Y. Shen, B.R. McCord, The development of reduced size STR amplicons as tools for analysis of degraded DNA, J. Forensic Sci. 48 (2003) 1054–1064. [9] P. Grubwieser, R. Muhlmann, B. Berger, H. Niederstatter, M. Pavlic, W. Parson, A new miniSTR-multiplex displaying reduced amplicon lengths for the analysis of degraded DNA, Int. J. Legal Med. 12 (0) (2006) 115–120. [10] K.M. Sullivan, A. Mannucci, C.P. Kimpton, P. Gill, A rapid and quantitative DNA sex test: fluorescence-based PCR analysis of X-Y homologous gene amelogenin, Biotechniques 15 (1993), 636–638, 640–641. [11] B.E. Krenke, A. Tereba, S.J. Anderson, E. Buel, S. Culhane, C.J. Finis, C.S. Tomsey, J.M. Zachetti, A. Masibay, D.R. Rabbach, E.A. Amiott, C.J. Sprecher, Validation of a 16locus fluorescent multiplex system, J. Forensic Sci. 47 (2002) 773–785. [12] L. Janssen, M. Jacobs, N. Vanderheyden, B. Bekaert, W. Van de Voorde, R. Decorte, Increased sensitivity for amplified STR alleles on capillary sequencers with BigDye1 XTerminatorTM, Forensic Sci. Int. Genet. Sup. Ser. 2 (2009) 123–124. [13] M. Raymond, F. Rousset, GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism, J. Hered. 86 (1995) 248–249. [14] F. Rousset, Genepop’007: a complete reimplementation of the Genepop sofware for exact tests for Windows and Linux, Mol. Ecol. Resour. 8 (2008) 103–106. [15] D.A. Jones, Blood samples: probability of discrimination, J. Forensic Sci. Soc. 12 (1972) 355–359. [16] R.A. Fisher, Standard calculations for evaluating a blood-group system, Heredity 5 (1951) 95–102. [17] P. Martin, O. Garcia, C. Albarran, P. Garcia, I. Yurrebaso, A. Alonso, Allele frequencies of six miniSTR loci (D10S1248, D14S1434 D22S1045, D4S2364, D2S441 and D1S1677) in a Spanish population, Forensic Sci. Int. 169 (2007) 252–254. [18] M. Reichert, R. Pawlowski, Population genetics of six miniSTR loci (D1S1677, D2S441 D4S2364, D10S1248, D14S1434, D22S1045) in a Polish population, Leg. Med. (Tokyo) 11 (2009) 147–148. [19] M.S. Han, Y.S. Kim, H.J. Jin, J.J. Kim, K.D. Kwak, J.E. Lee, J.M. Song, W. Kim, Forensic genetic analysis of nine miniSTR loci in the Korean population, Leg. Med. (Tokyo) 11 (2009) 209–212. [20] C. Vullo, A. Borosky, C. Romanini, L. Catelli, T. Yamamoto, Frequency data for 12 mini STR loci in Argentina, Forensic Sci. Int. Genet. 4 (2010) e79–81. [21] M. Poetsch, K. Bayer, Z. Ergin, M. Milbrath, T. Schwark, N. von Wurmb-Schwark, First experiences using the new Powerplex1 ESX17 and ESI17 kits in casework analysis and allele frequencies for two different regions in Germany, Int. J. Legal Med. (2010), doi:10.1007/s00414-010-0480-2.
Letter to the Editor / Forensic Science International: Genetics 6 (2012) e75–e77 [22] M. Poetsch, Z. Ergin, K. Bayer, D. El-Mostaqim, N. Rakotomavo, E.N. Browne, C. Timmann, R.D. Horstmann, T. Schwark, N. von Wurmb-Schwark, The new Powerplex1 ESX17 and ESI17 kits in paternity and maternity analyses involving people from Africa–including allele frequencies for three African populations, Int. J. Legal Med. 12 (5) (2011) 149–154. [23] A. Berti, F. Brisighelli, A. Bosetti, E. Pilli, C. Trapani, V. Tullio, C. Franchi, G. Lago, C. Capelli, Allele frequencies of the new European Standard Set (ESS) loci in the Italian population, Forensic Sci. Int. Genet. (2010), doi:10.1016/j.fsigen.2010.01.006. [24] V. Cortellini, N. Cerri, A. Verzeletti, Population data on 5 non-CODIS STR loci (D10S1248, D22S1045 D2S441, D1S1656, D12S391) in a population sample from Brescia county (Northern Italy), Forensic Sci. Int. Genet. 5 (2011) e97–98. [25] L. Albinsson, L. Noren, R. Hedell, R. Ansell, Swedish population data and concordance for the kits PowerPlex1 ESX 16 System, PowerPlex1 ESI 16 System AmpFlSTR1 NGM, AmpFlSTR1 SGM Plus and Investigator ESSplex, Forensic Sci. Int. Genet. 5 (2011) e89–92. [26] I. Yurrebaso, J.A. Ajuriagerra, A. Alday, I. Lezama, J.A. Perez, E. Romon, I. Uriarte, O. Garcia, Allele frequencies and concordance study between the Identifiler and the PowerPlex ESX17 systems in the Basque Country population, Forensic Sci. Int. Genet. 5 (2011) e79–80. [27] G. Mertens, S. Rand, K. Moordtgat, E. Cardoen, I. De Bruyn, N. Mommers, G. Leijnen, E. Jehaes, W. Jacobs, Population genetic analysis of Moroccans residing in Belgium using 16 autosomal STRs of the PowerPlex ESI 17 multiplex, Forensic Sci. Int. Genet. (2010), doi:10.1016/j.fsigen.2010.01.008. [28] A. Molnar, A. Zalan, G. Horvath, H. Pamjav, Allele distribution of the new European Standard Set (ESS) loci in the Hungarian population, Forensic Sci. Int. Genet. (2010), doi:10.1016/j.fsigen.2010.06.002. [29] V.C. Tucker, A.J. Hopwood, C.J. Sprecher, R.S. McLaren, D.R. Rabbach, M.G. Ensenberger, J.M. Thompson, D.R. Storts, Developmental validation of the PowerPlex1 ESI 16 and PowerPlex1 ESI 17 Systems: STR multiplexes for the new European standard, Forensic Sci. Int. Genet. (2010), doi:10.1016/j.fsigen.2010.09.004. [30] L. Excoffier, G. Laval, S. Schneider, Arlequin (version 3.0): an integrated software package for population genetics data analysis, Evol. Bioinform. Online 1 (2005) 47–50. [31] T. Lederer, G. Braunschweiger, Commentary on: Coble MD, Butler JM. Characterization of new miniSTR loci to aid analysis of degraded DNA, J. Forensic Sci. 50 (2005) 43–53, J. Forensic Sci. 52 (2007) 493; author reply 494. [32] C.R. Hill, D.L. Duewer, M.C. Kline, C.J. Sprecher, R.S. McLaren, D.R. Rabbach, B.E. Krenke, M.G. Ensenberger, P.M. Fulmer, D.R. Storts, J.M. Butler, Concordance and population studies along with stutter and peak height ratio analysis for the PowerPlex1 ESX 17 and ESI 17 Systems, Forensic Sci. Int. Genet. (2010), doi:10.1016/j.fsigen.2010.03.014. [33] 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) 145–147.
Sophie Dognaux1 National Institute of Criminalistics and Criminology, Brussels, Belgium
a
e77
Maarten H.D. Larmuseauabc1 Laboratory of Forensic Genetics and Molecular Archaeology, University Hospitals Leuven, Leuven, Belgium b
Center for Human Genetics, K.U. Leuven, Leuven, Belgium
c
Laboratory of Animal Diversity and Systematics, K.U. Leuven, Leuven, Belgium Lynn Jansen1 Laboratory of Forensic Genetics and Molecular Archaeology, University Hospitals Leuven, Leuven, Belgium Tom Heylen National Institute of Criminalistics and Criminology, Brussels, Belgium Nancy Vanderheyden Bram Bekaert Laboratory of Forensic Genetics and Molecular Archaeology, University Hospitals Leuven, Leuven, Belgium Fabrice Noel National Institute of Criminalistics and Criminology, Brussels, Belgium
a
Ronny Decorteab* Laboratory of Forensic Genetics and Molecular Archaeology, University Hospitals Leuven, Leuven, Belgium b
Center for Human Genetics, K.U. Leuven, Leuven, Belgium
*Corresponding author at: Laboratory for Forensic Genetics and Molecular Archaeology, University Hospitals Leuven, Campus Sint-Rafae¨l, Kapucijnenvoer 33, B-3000 Leuven, Belgium, Tel.: +32 16 345860; fax: +32 16 345997 E-mail address: [email protected] (R. Decorte). 1
These three authors contributed equally to this study.
Contents lists available at ScienceDirect
Forensic Science International: Genetics journal homepage: www.elsevier.com/locate/fsig
Forensic Population Genetics - Letter to the Editor Allele frequencies for the new European Standard Set (ESS) loci and D1S1677 in the Belgian population
Dear Editor, The nine Belgian laboratories, officially recognized by the Belgian Minister of Justice for performing DNA analysis in criminal cases, have jointly decided to use a common local population database for statistical calculations. A first database has been set up for the loci covered in AmpFlSTR1 IdentifilerTM and PowerPlex1 16 [1,2]. With the decision of ENFSI and EDNAP to extend the current ESS loci (D3S1358, vWA, D8S1179, D21S11, D18S51, THO1 and FGA) with new loci (D1S1656, D2S441, D10S1248, D12S391 and D22S1045), there was a need to obtain also data for these loci within the Belgian population [3,4]. Here, we present the allele frequencies and forensic efficiency data for the new ESS loci and one additional miniSTR, D1S1677. Buccal swab samples were collected with the Clue C.D.S. Swab Safe1 kit (Swiss Forensic) from 205 unrelated individuals after informed consent, hereafter referred as the Brussels sample set. Genomic DNA was isolated using the QIAamp DNA Mini KitTM (Qiagen, Germany) or the NucleoMag 96 Trace kit (MachereyNagel, Germany) on the KingFisher automatic extraction platform (Thermo Scientific, USA) and DNA was quantified with the Plexor HY KitTM (Promega Corporation, USA). The Leuven sample set consisted of 196 unrelated individuals from the Leuven Blood Bank previously used for obtaining allele frequencies for PowerPlex1 16 [2]. The Brussels sample set was amplified with PowerPlex1 ESI 17 System (Promega Corporation, USA) and AmpFlSTR1 NGMTM PCR Amplification Kit (Applied Biosystems, USA) using the reaction conditions as described by each manufacturer. The samples were amplified in a GeneAmp PCR System 9700 (Applied Biosystems, USA). The Leuven sample set was amplified with an in-house developed multiplex (MiniPlex-9) consisting of D1S1677 [5], D1S1656 [6], D2S441 [5], D10S1248 [5], D12S391 [7], D22S1045 [5], D21S11 [8], D18S51 [8], FGA [9] and the Amelogenin locus [10,11]. Samples were amplified using 0.5–1 ng target DNA in 25 ml reactions of QIAGEN Multiplex PCR Kit (Qiagen, Germany) in a GeneAmp PCR System 9700 (Applied Biosystems, USA) using the following reaction conditions: 95 8C for 15 min followed by 30 cycles of 30 s at 94 8C, 60 s at 57 8C and 60 s at 72 8C, and a final incubation of 45 min at 60 8C. The amplified products of the Brussels sample set were detected on the ABI PRISM 3130xl Genetic Analyzer (Applied Biosystems, USA) using internal size standard, filter set and conditions recommended by each manufacturer except for the amount of PCR product used on the capillary sequencer (2 ml instead of the recommended 1 ml). Allele calling was performed using GeneMapper ID-X software (Applied Biosystems, USA). The amplified products of the Leuven sample set were purified with 1872-4973/$ – see front matter ß 2011 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.fsigen.2011.05.003
BigDye1 XTerminatorTM (Applied Biosystems, USA) according to Janssen et al. [12] and 1 ml was used for detection on the ABI PRISM 3130xl Genetic Analyzer (Applied Biosystems, USA) using GeneScan1 500 [LIZ] as internal size standard and filter set G5 for discriminating the different dyes (6-FAM, VIC, NED, PET and LIZ). Allele calling was performed using GeneMapper ID v3.2 (Applied Biosystems, USA). The Laboratory of Forensic Genetics and Molecular Archaeology (Leuven) and the National Institute of Criminalistics and Criminology (Brussels) are accredited according to ISO/IEC 17025 and participate in CTS (Collaborative Testing Services Inc., USA) and GEDNAP proficiency tests. SRM 2391b (National Institute of Standards and Technology, USA) and DNA from control cell lines 9947A, 9948 and 007 were used for verification of the MiniPlex-9 genotyping. Observed heterozygosity (Ho), expected heterozygosity (He), Hardy–Weinberg equilibrium (exact test) and population differentiation (genic and genotypic) were calculated with Genepop v4 software (http://genepop.curtin.edu.au/) [13,14]. The power of discrimination (PD) and the power of exclusion were calculated for each locus [15,16]. In order to assess the different genetic distribution between the populations analyzed with respect to other published population data [17–29], population pairwise genetic distances FST were calculated using Arlequin v3.01 software [30]. For data published before 2008, we adapted the alleles to the current nomenclature [31]. Regarding D12S391, most authors do not mention micro-variants (.1 alleles). Therefore, we combined these micro-variants with the nearest alleles (.0) in each population for comparison purposes [22]. The statistical significance of the pairwise FST estimates was determined with 10,000 permutation tests. No significant difference in allele nor genotype frequencies were observed between the two population sets for the 8 common STR loci. Therefore, both data sets were combined for determination of the allele frequencies, forensic efficiency data and Hardy– Weinberg equilibrium (p-values; Table 1). No evidence for deviation from Hardy–Weinberg equilibrium was found except for D2S441 which could be rejected after Bonferroni correction. The allele frequencies of all tested STRs were significantly different between the Belgian population and the populations from Ghana, Madagascar and Korea. Moreover, there are few significant differences between Belgium with all other tested populations for one or more loci (especially D2S441), except between the Belgian and the Italian, Swedish, Polish and North German populations. All FST genetic distances are reported in supplementary Table 2. Evaluation of the concordance in the Leuven data set between MiniPlex-9 and PowerPlex1 16 [2] for the common loci D18S51, D21S11 and FGA revealed no difference. The Brussels data set showed one discordance: a heterozygous genotype (14,15) for D19S433 with AmpFlSTR1 NGMTM and a homozygous genotype
Letter to the Editor / Forensic Science International: Genetics 6 (2012) e75–e77
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Table 1 Allele frequency data for the Belgian population. Allele 9 10 11 11.3 12 12.3 13 13.3 14 14.3 15 15.3 16 16.3 17 17.1 17.3 18 18.3 19 19.3 20 21 22 23 24 25 26 N Obs. He. Exp. He. P-value SE PD PE
D1S1677
D1S1656
0.00256 0.00513
0.08875
0.06923
0.13000
0.25385
0.05250 0.00125 0.09125 0.00125 0.13500 0.06625 0.12500 0.05125 0.05625 0.00250 0.12000 0.00625 0.05875
0.31282 0.28205 0.06410 0.01026
D2S441 0.00125 0.17000 0.36125 0.04375 0.05125 0.00375 0.02875
D10S1248
400 0.9125 0.9032 0.6699 0.0303 0.9821 0.8009
D22S1045
0.00125 0.13875 0.02750
0.00625
0.28250
0.00500
0.28625
0.34375
0.05000
0.05000
0.17000
0.04625
0.37125
0.00375
0.14250
0.02625
0.34750
0.02750
0.08500
0.07250
0.00500
0.01250 0.00125
195 0.8205 0.7510 0.6613 0.0186 0.8942 0.5177
D12S391
400 0.7550 0.7517 0.0113 0.0043 0.9004 0.6265
400 0.7300 0.7522 0.4584 0.0240 0.8979 0.5256
0.01500 0.20000 0.02125 0.12625 0.01500 0.12000 0.12000 0.08750 0.07750 0.04000 0.01625 0.00375 400 0.8850 0.8898 0.4732 0.0297 0.9777 0.7770
0.00875
400 0.7425 0.7152 0.8946 0.0107 0.8707 0.4756
N = number of individuals; Obs. He. = observed heterozygosity; Exp. He. = expected heterozygosity; P-value = probability values of the Hardy–Weinberg equilibrium exact test (100 batches and 1000 iterations); SE = standard error of P-value; PD = probability of discrimination; PE = probability of exclusion.
(15,15) with PowerPlex1 ESI 17 System. This discordant result was confirmed by re-testing the sample with the respective kits, and is probably due to a mutation at the primer binding site positions [32]. A different null allele (15) at D19S433 was also observed by Tucker et al. [29] with PowerPlex1 ESI 17 System in a population study of 242 Caucasians and 64 Indo-Pakistani. This paper follows the guidelines for publication of population data requested by the journal [33].
Appendix A. Supplementary data Supplementary data associated with this article can be found, in the online version, at doi:10.1016/j.fsigen.2011.05.003. References [1] R. Decorte, M. Engelen, L. Larno, K. Nelissen, A. Gilissen, J.J. Cassiman, Belgian population data for 15 STR loci (AmpFlSTR SGM Plus and AmpFlSTR profiler PCR amplification kit), Forensic Sci. Int. 13 (9) (2004) 211–213. [2] R. Decorte, E. Verhoeven, E. Vanhoutte, K. Knaepen, J.J. Cassiman, Allele frequency data for 19 short tandem repeats (PowerPlex 16 and FFFl) in a Belgian population sample, J. Forensic Sci. 51 (2006) 436–437. [3] P. Gill, L. Fereday, N. Morling, P.M. Schneider, The evolution of DNA databases— recommendations for new European STR loci, Forensic Sci. Int. 15 (6) (2006) 242– 244. [4] P. Gill, L. Fereday, N. Morling, P.M. Schneider, New multiplexes for Europeamendments and clarification of strategic development, Forensic Sci. Int. 16 (3) (2006) 155–157. [5] M.D. Coble, J.M. Butler, Characterization of new miniSTR loci to aid analysis of degraded DNA, J. Forensic Sci. 50 (2005) 43–53. [6] 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. 11 (1) (1998) 244–247.
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Sophie Dognaux1 National Institute of Criminalistics and Criminology, Brussels, Belgium
a
e77
Maarten H.D. Larmuseauabc1 Laboratory of Forensic Genetics and Molecular Archaeology, University Hospitals Leuven, Leuven, Belgium b
Center for Human Genetics, K.U. Leuven, Leuven, Belgium
c
Laboratory of Animal Diversity and Systematics, K.U. Leuven, Leuven, Belgium Lynn Jansen1 Laboratory of Forensic Genetics and Molecular Archaeology, University Hospitals Leuven, Leuven, Belgium Tom Heylen National Institute of Criminalistics and Criminology, Brussels, Belgium Nancy Vanderheyden Bram Bekaert Laboratory of Forensic Genetics and Molecular Archaeology, University Hospitals Leuven, Leuven, Belgium Fabrice Noel National Institute of Criminalistics and Criminology, Brussels, Belgium
a
Ronny Decorteab* Laboratory of Forensic Genetics and Molecular Archaeology, University Hospitals Leuven, Leuven, Belgium b
Center for Human Genetics, K.U. Leuven, Leuven, Belgium
*Corresponding author at: Laboratory for Forensic Genetics and Molecular Archaeology, University Hospitals Leuven, Campus Sint-Rafae¨l, Kapucijnenvoer 33, B-3000 Leuven, Belgium, Tel.: +32 16 345860; fax: +32 16 345997 E-mail address: [email protected] (R. Decorte). 1
These three authors contributed equally to this study.