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Population data of 5 next generation STRs in Southern Italy
Forensic Science International: Genetics Supplement Series 2 (2009) 386–387
Contents lists available at ScienceDirect
Forensic Science International: Genetics Supplement Series journal homepage: www.elsevier.com/locate/FSIGSS
Research article
Population data of 5 next generation STRs in Southern Italy A. Barbaro a,b,*, C. Phillips b, L. Fernandez Formoso b, A´. Carracedo b, M.V. Lareu b a b
Department of Forensic Genetics, SIMEF, Reggio Calabria, Italy Institute of Legal Medicine, University of Santiago de Compostela, Spain
A R T I C L E I N F O
A B S T R A C T
Article history: Received 14 August 2009 Accepted 24 August 2009
MiniSTRs analysis has been demonstrated useful to increase the success rate of degraded samples typing. In the present study we investigated the distribution of D10S1248, D12S391, D1S1656, D22S1045, and D2S441 in a population from Southern Italy (Calabria). Saliva/blood samples were obtained from around 150 unrelated healthy individuals belonging to tested population since at least 3 generations. Statistical analysis was performed and results obtained showed that all loci met Hardy–Weinberg expectations. ß 2009 Elsevier Ireland Ltd. All rights reserved.
Keywords: Allelic frequencies 5-Plex Italy
1. Introduction The suitability of miniSTRs in degraded DNA analysis has been well demonstrated [1]. In the present study we investigated the distribution of D10S1248, D12S391, D1S1656, D22S1045, and D2S441 in a population from Southern Italy (Calabria) using saliva/blood samples collected from around 150 unrelated healthy individuals belonging to the tested population since at least 3 generations. Statistical analysis was performed and results showed that all loci met Hardy–Weinberg expectations.
STRs amplification was carried out by GeneAmp PCR Systems 9700, 2400, 2720 thermal cyclers, using a pentaplex we designed for the purpose including for D2, D10 and D22 primers detailed by NIST developers [1] together with those described by Lareu et al. [4,5] for D1 and D12. Female and Male Positive controls and negative controls were used during all amplification steps. PCR products were analyzed by capillary electrophoresis on an ABI PRISM 3130 Genetic Analyzer employing GeneMapper 3.2 software with reference to sequenced allelic ladders assembled in-house. Allele designations were determined following the changes noted by Coble and Butler [2]. 3. Results and discussion
2. Materials and methods In order to minimize the possibility of contamination, all extractions were set up in a laminar flow cabinet in a dedicated extraction laboratory. DNA was extracted from donors blood/saliva samples using the IstaGene Matrix System. DNA extracted from samples was quantified by the QuantifilerTM Human DNA Quantification Kit using a 7300 Real Time System kit following the manufacturer protocol. Amplification was carried out in a laboratory different from the one dedicated to the extraction, so that amplified products never entered the extraction laboratory.
* Corresponding author at: Department of Forensic Genetics, SIMEF, Reggio Calabria, Italy. E-mail address: [email protected] (A. Barbaro). 1875-1768/$ – see front matter ß 2009 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.fsigss.2009.08.130
The distribution of the allele frequency for each locus is represented in Fig. 1 and it is close to that found in Caucasian [3]. Different bio-statistical values of forensic interest were calculated for the loci examined in the present study as summarized in Table 1. The test for Hardy–Weinberg equiliTable 1 Forensic statistical parameters. PIC HET PD MEC HW equilibrium X2 (sum) X2 (table) Degree freedom
0.6961 0.7389 0.8383 0.5081 Proven. 25.68167 50.9985 36
0.8618 0.8740 0.9646 0.7493 Proven. 190.9585 260.9921 225
0.8759 0.8865 0.9719 0.7713 Proven. 121.5608 200.334 169
0.7516 0.7830 0.8900 0.5822 Proven. 55.3789 66.3386 49
0.7086 0.7412 0.8316 0.5343 Proven. 35.9073 83.6753 64
PIC = polymorphic information content; HET = heterozygote; PD = discrimination power; MEC = mean exclusion chance.
A. Barbaro et al. / Forensic Science International: Genetics Supplement Series 2 (2009) 386–387
387
Fig. 1. Allele frequencies for all examined loci.
brium showed that the genotype distribution was correspondent with the expected.
Conflict of interest statement None.
4. Conclusions Degraded DNA samples are commonly observed in the forensic analysis of biological evidence from a crime scene. In these cases suitability of miniSTRs typing has been clearly demonstrated. Data obtained in this study showed that all loci analyzed met Hardy–Weinberg expectations and provided better informativeness compared to SGM+/Identifiler STR sets as well as the opportunity to enhance identification of highly degraded DNA.
References [1] M.D. Coble, J.M. Butler, Characterization of new mini STR loci to aid analysis of degraded DNA, J. Forensic Sci. 50 (1) (2005) 43–53. [2] J.M. Butler, M.D. Coble, Authors’ response, J. Forensic Sci. 52 (2) (2007) 494. [3] C.R. Hill, et al., Characterization of 26 New miniSTR Loci, in: 17th International Symposium on Human Identification, Nashville, TN, October 10–12, 2006. [4] M.V. Lareu, C. Pestoni, M. Schu¨renkamp, S. Rand, B. Brinkmann, A´. Carracedo, A highly variable STR at the D12S391 locus, Int. J. Legal Med. 109 (1996) 134–138. [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 (1998) 244–247.
Contents lists available at ScienceDirect
Forensic Science International: Genetics Supplement Series journal homepage: www.elsevier.com/locate/FSIGSS
Research article
Population data of 5 next generation STRs in Southern Italy A. Barbaro a,b,*, C. Phillips b, L. Fernandez Formoso b, A´. Carracedo b, M.V. Lareu b a b
Department of Forensic Genetics, SIMEF, Reggio Calabria, Italy Institute of Legal Medicine, University of Santiago de Compostela, Spain
A R T I C L E I N F O
A B S T R A C T
Article history: Received 14 August 2009 Accepted 24 August 2009
MiniSTRs analysis has been demonstrated useful to increase the success rate of degraded samples typing. In the present study we investigated the distribution of D10S1248, D12S391, D1S1656, D22S1045, and D2S441 in a population from Southern Italy (Calabria). Saliva/blood samples were obtained from around 150 unrelated healthy individuals belonging to tested population since at least 3 generations. Statistical analysis was performed and results obtained showed that all loci met Hardy–Weinberg expectations. ß 2009 Elsevier Ireland Ltd. All rights reserved.
Keywords: Allelic frequencies 5-Plex Italy
1. Introduction The suitability of miniSTRs in degraded DNA analysis has been well demonstrated [1]. In the present study we investigated the distribution of D10S1248, D12S391, D1S1656, D22S1045, and D2S441 in a population from Southern Italy (Calabria) using saliva/blood samples collected from around 150 unrelated healthy individuals belonging to the tested population since at least 3 generations. Statistical analysis was performed and results showed that all loci met Hardy–Weinberg expectations.
STRs amplification was carried out by GeneAmp PCR Systems 9700, 2400, 2720 thermal cyclers, using a pentaplex we designed for the purpose including for D2, D10 and D22 primers detailed by NIST developers [1] together with those described by Lareu et al. [4,5] for D1 and D12. Female and Male Positive controls and negative controls were used during all amplification steps. PCR products were analyzed by capillary electrophoresis on an ABI PRISM 3130 Genetic Analyzer employing GeneMapper 3.2 software with reference to sequenced allelic ladders assembled in-house. Allele designations were determined following the changes noted by Coble and Butler [2]. 3. Results and discussion
2. Materials and methods In order to minimize the possibility of contamination, all extractions were set up in a laminar flow cabinet in a dedicated extraction laboratory. DNA was extracted from donors blood/saliva samples using the IstaGene Matrix System. DNA extracted from samples was quantified by the QuantifilerTM Human DNA Quantification Kit using a 7300 Real Time System kit following the manufacturer protocol. Amplification was carried out in a laboratory different from the one dedicated to the extraction, so that amplified products never entered the extraction laboratory.
* Corresponding author at: Department of Forensic Genetics, SIMEF, Reggio Calabria, Italy. E-mail address: [email protected] (A. Barbaro). 1875-1768/$ – see front matter ß 2009 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.fsigss.2009.08.130
The distribution of the allele frequency for each locus is represented in Fig. 1 and it is close to that found in Caucasian [3]. Different bio-statistical values of forensic interest were calculated for the loci examined in the present study as summarized in Table 1. The test for Hardy–Weinberg equiliTable 1 Forensic statistical parameters. PIC HET PD MEC HW equilibrium X2 (sum) X2 (table) Degree freedom
0.6961 0.7389 0.8383 0.5081 Proven. 25.68167 50.9985 36
0.8618 0.8740 0.9646 0.7493 Proven. 190.9585 260.9921 225
0.8759 0.8865 0.9719 0.7713 Proven. 121.5608 200.334 169
0.7516 0.7830 0.8900 0.5822 Proven. 55.3789 66.3386 49
0.7086 0.7412 0.8316 0.5343 Proven. 35.9073 83.6753 64
PIC = polymorphic information content; HET = heterozygote; PD = discrimination power; MEC = mean exclusion chance.
A. Barbaro et al. / Forensic Science International: Genetics Supplement Series 2 (2009) 386–387
387
Fig. 1. Allele frequencies for all examined loci.
brium showed that the genotype distribution was correspondent with the expected.
Conflict of interest statement None.
4. Conclusions Degraded DNA samples are commonly observed in the forensic analysis of biological evidence from a crime scene. In these cases suitability of miniSTRs typing has been clearly demonstrated. Data obtained in this study showed that all loci analyzed met Hardy–Weinberg expectations and provided better informativeness compared to SGM+/Identifiler STR sets as well as the opportunity to enhance identification of highly degraded DNA.
References [1] M.D. Coble, J.M. Butler, Characterization of new mini STR loci to aid analysis of degraded DNA, J. Forensic Sci. 50 (1) (2005) 43–53. [2] J.M. Butler, M.D. Coble, Authors’ response, J. Forensic Sci. 52 (2) (2007) 494. [3] C.R. Hill, et al., Characterization of 26 New miniSTR Loci, in: 17th International Symposium on Human Identification, Nashville, TN, October 10–12, 2006. [4] M.V. Lareu, C. Pestoni, M. Schu¨renkamp, S. Rand, B. Brinkmann, A´. Carracedo, A highly variable STR at the D12S391 locus, Int. J. Legal Med. 109 (1996) 134–138. [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 (1998) 244–247.