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Table of Contents
ORIGINAL ARTICLE
Year : 2015  |  Volume : 2  |  Issue : 2  |  Page : 16-18

Study about genetic variability of SE33 locus


1 Studio Indagini Mediche E Forensi (SIMEF), Reggio Calabria, Italy
2 MLS BioDNA, Paola, Malta

Date of Web Publication5-Jul-2017

Correspondence Address:
A Barbaro
WAWFE President Chief Forensic Genetics, Department at SIMEF Studio Indagini Mediche E Forensi (SIMEF), Via Nicolò da Reggio 4, Reggio Calabria
Italy
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Source of Support: None, Conflict of Interest: None


DOI: 10.5530/ami.2015.2.5

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  Abstract 


Introduction: The HUMACTBP2 (SE33) locus is one of the most polymorphic markers commonly used in forensic human identification. Variability of SE33 was studied in 2 Calabria and Malta populations using the AmpFlSTR NGM SElect™ PCR Amplification Kit (Applied Biosystems) and the PowerPlex ESI 17 (Promega). Material & Methods: A total of 41 different alleles were observed in the 2 examined populations with no allele being more frequent than 10,5%. In the Maltese population more intermediate alleles than in Calabria were found. Allelic frequencies and statistical parameters of forensic interest (Dp,PE, RMP) were calculated using PowerStats v.1.2 software. Hardy-Weinberg equilibrium and other population parameters were calculated using Arlequin v.3.1 and TFPGA v1.3 softwares. Results: No significant deviations from Hardy–Weinberg equilibrium were found. Calabria and Malta allelic frequencies were compared to previously published population data and no significant differences were found. When comparing with Sicily no overall significant genetic distances were found, while comparison to other populations showed significant ones. Moreover comparison with non-European population showed no big distances between Germany and Morocco and between Hungary and Turkey. Conclusion: confirmed the locus is effectively highly polymorphic and useful not only for forensic identification but also in paternity cases in addition to the set of STRs loci commonly used.

Keywords: Allele, Hardy–Weinberg equilibrium, SE33 Locus


How to cite this article:
Barbaro A, Cassar M, Cormaci P, Grech J C. Study about genetic variability of SE33 locus. Acta Med Int 2015;2:16-8

How to cite this URL:
Barbaro A, Cassar M, Cormaci P, Grech J C. Study about genetic variability of SE33 locus. Acta Med Int [serial online] 2015 [cited 2019 Jul 20];2:16-8. Available from: http://www.actamedicainternational.com/text.asp?2015/2/2/16/209635




  Introduction Top


The HUMACTBP2 (SE33) locus is one of the most polymorphic markers commonly used in forensic human identification.[1],[2]

The genetic variability of SE33 in Calabria (Southern Italy) and Malta has been compared to the one of other Mediterranean and not-Mediterranean populations in order to evaluate significant genetic distances.

Both laboratories performing this study are accredited UNI CEI/EN ISO 17025 and participate in the quality control/proficiency testing of the GEP-ISFG WG (www. gep-isfg.org), College of American Pathologists (CAP) and Collaborative Testing Services (CTS).


  Materials and Methods Top


SE33 data from Calabria and Malta were obtained from blood or saliva samples of 200 unrelated healthy donors belonging to the correspondent population from at least 3 generations.

Samples were taken from donors with previously obtained informed consent for population studies.

DNA was extracted by rapid resin (IstaGene Matrix System-Biorad) and silica columns (AccuPrep Genomic DNA Extraction Kit- Bioneer) and then quantified with the Quantifiler™ Human DNA Quantification Kit using a 7300 Real Time System kit.[3]

SE33 amplification was performed using NGM SElect™ (Applied Biosystems) and PowerPlex® ESI 17 (Promega).[4],[5] Positive and negative controls were used during all amplification steps.

PCR products were analyzed by capillary electrophoresis with an AB 3130 genetic analyzer and allele assignment was carried out by comparison with the reference allelic ladders available in the kits using GeneMapper 3.2 software.


  Results and Discussion Top


Allelic frequencies and statistical parameters of forensic interest (Dp: power of discrimination, PE: power of exclusion, RMP: random matching probability, etc.) were calculated using PowerStats v.1.2 software.[6]

Allele frequencies are showed in [Figure 1]. Statistical parameters are given in [Table 1] and [Table 2].
Figure 1: Alleles frequencies

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Table 1: Forensic parameters

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Table 2: Statistical parameters

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Hardy-Weinberg equilibrium and other population parameters were calculated using Arlequin software v.3.1[7] and TFPGA v1.3.[8]

A total of 41 different alleles were observed in the 2 examined populations with no allele being more frequent than 10,5%. In the Maltese population more intermediate alleles than in Calabria were found; moreover 6 out of ladder alleles (17.3, 18.3, 20.3,32,33,34) were present.

The high number of alleles observed at SE33 locus confirmed the high degree of polymorphism.

No significant deviations from Hardy–Weinberg equilibrium were found.

Based on heterozygosity (greater than 0.7) and polymorphic information content PIC (greater than 0.9), SE33 could be considered as an informative locus in both populations.

Even if it shows a low exclusion power (PE) degree when used individually, however combined PE with the other 5 ESS new STRs is increased to 0.999 in both populations and the combined power of discrimination (PD) was 0.999999.

This means when used together these loci can distinguish samples from different individuals from Calabria with a probability of 99,9999%.

Allelic frequencies of SE33 were compared to previously published population data and no significant differences were found.[9],[10],[11],[12],[13]

When comparing Calabria and Malta data with the one of Sicily no overall significant genetic distances were found, while comparison to other populations showed significant ones.

Moreover comparison with non-European population showed no big distances between Germany and Morocco and between Hungary and Turkey.

Data of populations comparisons analysis are outlined in [Figure 2] and [Figure 3].
Figure 2: Matrix of pairwise Fst

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Figure 3: Average number of pairwise differences

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  Conclusions Top


SE33 showed a similar variability in Calabria and Malta in comparison with other European populations: a total of 41 different alleles were observed in the above populations with no allele being more frequent than 10,5%.This confirmed the locus is effectively highly polymorphic in all evaluated populations and useful not only for forensic identification but also in paternity cases in addition to the set of STRs loci commonly used.


  Ethical Standards Top


The study described in the present paper have been carried out using samples taken from people where informed consent had been previously obtained for research studies in accordance with Italian and Maltese Laws and to both labs approved UNI EN ISO 17025 procedures.


  Conflict of Interest Top


None



 
  References Top

1.
Rolf B, Schürenkamp M, Junge A, Brinkmann B, Sequence polymorphism at the tetranucleotide repeat of the human beta-actin related pseudogene H-beta-Ac-psi-2 (ACTBP2) locus, Int. J. Leg. Med. 110 (1997) 69–72.  Back to cited text no. 1
    
2.
Wenda S, Dauber EM, Schwartz M, Jungbauer C, Weirich V, Wegener R, Mayr WR, ACTBP2 (alias ACTBP8) is localized on chromosome 6 (band 6q14), Forensic Sci. Int. Volume 148, Issues 2-3, 10 March 2005, Pages 207–209.  Back to cited text no. 2
    
3.
Walsh PS, Metzger DA, Higuchi R, Chelex 100 as a medium for the simple extraction of DNA for PCR-based typing from forensic materials, Biotechniques 10 (1991) 506–513.  Back to cited text no. 3
    
4.
Gill P, Fereday L, Morling N, Schneider PM, The evolution of DNA databases recommendations for new European STR loci, Forensic Sci. Int. 156 (2006) 242–244.  Back to cited text no. 4
    
5.
Gill P, Fereday L, Morling N, Schneider PM, New multiplexes for Europe. Amendments and clarification of strategic development, Forensic Sci. Int. 163 (2006) 155–157.  Back to cited text no. 5
    
6.
Tereba A, Tools for analysis of population statistics, Profile in DNA (1999) 14–16 (free software distributed at http://www.promega. com/geneticidtools/).  Back to cited text no. 6
    
7.
Excoffier L, Laval G, Schneider S, Arlequin ver. 3.0: an integrated software package for population genetics data analysis, Evol. Bioinform. (Online) 1 (2005) 47–50.  Back to cited text no. 7
    
8.
Miller MP,TFPGA (genetic data analysis software) http://herb.bio. nau.edu/miller/tfpga.htm.  Back to cited text no. 8
    
9.
Barbaro A, Phillips C, Formoso LF, Lareu MV, Carracedo Á, Distribution of allele frequencies of 20 STRs loci in a population sample from Calabria, Southern Italy, Forensic Sci. Int. Genet. 6 (2012) 149–150.  Back to cited text no. 9
    
10.
Berti A,Brisighelli F, Bosetti A, Pilli E, Trapani C, Tullio V, Franchi C, Lago G, Capelli C, Allele frequencies of the new European Standard Set (ESS) loci in the Italian population, Forensic Sci Int Genet. (2011) 548–9.  Back to cited text no. 10
    
11.
Cruz C, Vieira-Silva C, Ribeiro T, Espinheira R, Genetic data for the locus SE33 in a south Portuguese population with Powerplex ES System, ICS 1288 (2006) 427–429.  Back to cited text no. 11
    
12.
Lászik A, Sótonyi P, Rand S, Hohof C, Frequency data for the STR locus ACTBP2 (SE33) in eight populations, Int J Legal Med 115 (2001) 94–96.  Back to cited text no. 12
    
13.
Krause M, Heide KG, Krawczak M,SE33 allele and genotype frequencies in the population of Schleswig-Holstein (Northern Germany),ICS 1288 (2006) 400–402.  Back to cited text no. 13
    


    Figures

  [Figure 1], [Figure 2], [Figure 3]
 
 
    Tables

  [Table 1], [Table 2]



 

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