Skip to content

Advertisement

  • Short Report
  • Open Access

Allele frequencies distribution of 16 forensic STR loci in a Western Sicilian population sample

  • 1Email author,
  • 2,
  • 1,
  • 2,
  • 1,
  • 2 and
  • 1
Egyptian Journal of Forensic Sciences20177:13

https://doi.org/10.1186/s41935-017-0013-y

  • Received: 13 April 2017
  • Accepted: 12 July 2017
  • Published:

Abstract

The PowerPlex® ESI 17 Fast and ESX 17 Fast Systems represent faster cycling versions released by Promega® to follow the requirements of ENFSI and EDNAP groups’ for new STR genotyping systems in Europe. Allele frequencies and forensic parameters were estimated in a population sample of 120 unrelated healthy individuals living in Sicily (Western Sicilian population sample) using PowerPlex® ESI 17 Fast and PowerPlex® 17 Fast Systems. Full concordance of the results for both systems was observed. No significant deviation from Hardy-Weinberg equilibrium was detected. The observed heterozygosity changed from 0.85833 for FGA to 0.95 for TH01. The combined power of discrimination for the 16 loci was >0.999999.

Keywords

  • Allele frequencies
  • Str
  • Italian population
  • DNA database
  • PowerPlex

Introduction

The International Scientific Community establishes the crucial role of the population studies on allele frequencies and the importance to extend DNA database for forensic purposes. This study analyzed the allele frequencies and genetic parameters of 16 STR loci in a Western Sicilian population sample.

Western Sicily has been the object of many denominations. 120 unrelated Sicilian individuals have been selected for at least 3 generations. This study belongs to the only Western Sicilian population.

Sicily is the biggest and one of the most populated regions in Italy. The Sicilian population amounts approximately to 5,077,487 people (2015), in which only 162,000 are foreigners.

The population study is performed by PowerPlex ESI 17 Fast and ESX 17 Fast Systems designed with the new loci recommended by the European Network of Forensic Science Institutes (ENFSI) and European DNA Profiling Group (EDNAP) (McLaren et al. 2014; Tucker et al. 2011, 2012; Gill et al. 2006).

Materials and methods

DNA extraction

Blood samples and buccal swabs were collected from 120 unrelated occidental Sicilian individuals. DNA was extracted using Prepfiler Forensic DNA Extraction kit (Applied Biosystems – Life Technologies) and a Nanodrop-1000 spectrophotometer (Thermo Scientific, Waltham, MA) was employed to measure the DNA concentration.

Blood samples and buccal swabs were collected anonymously from 120 unrelated healthy individuals living in Western Sicily acquiring their informed consents.

DNA extraction was performed using the Prepfiler Forensic DNA Extraction kit (Applied Biosystems – Life Technologies) according to the manufacturer’s instructions.

Amplification

Approximately 1 ng/μl of template DNA was amplified using PowerPlex ESI and ESX 17 fast System (Promega). The PCR amplification was performed using the GeneAmp PCR System 9700 thermocycler (Applied Biosystems) on the basis of the suggested manufacturer guidelines of the STR kit tested in this study. PCR products were analyzed by capillary electrophoresis and positive and negative controls were carried out as specified in the PowerPlex ESI® and ESX 17® fast System (Promega) user’s manual.

DNA electrophoresis and analysis

All the amplification products were detected by capillary electrophoresis and genotyping was carried out on the ABI PRISM 310 Genetic Analyzer (Applied Biosystems). Data obtained were analyzed using GeneMapper ID v3.2.1 Software (Applied Biosystems).

Population study

Allelic frequencies for all loci and additional relevant forensic parameters such as expected heterozygosity (He) and observed heterozygosity (Ho), polymorphic information content (PIC), power of discrimination (PD) and power of exclusion (PE) were calculated by GenePop (v.4.5.1) software (Rousset 2008). The Hardy–Weinberg equilibrium was tested by the p-value obtained by setting 100 batches with 5000 interactions per batch in the Markov chain method (Guo and Thompson 1992). Allele frequencies of 16 STR and parameters of forensic interest are summarized in Tables 1 and 2.
Table 1

Allele frequency distribution of 16 STR in the studied population

Allele

D1S1656

D2S441

D2S1338

D3S1358

D8S1179

D10S1248

D12S391

D16S539

D18S51

D19S433

D21S11

D22S1045

FGA

TH01

VWA

SE33

6

             

0.254

  

7

             

0.179

  

8

    

0.033

  

0.054

     

0.167

  

9

 

0.004

  

0.029

  

0.150

     

0.192

  

9.3

             

0.179

  

10

0.013

0.146

  

0.092

  

0.038

0.017

    

0.029

 

0.004

11

0.079

0.363

  

0.075

  

0.279

0.017

0.013

 

0.113

    

11.3

 

0.083

     

0.004

        

12

0.108

0.058

  

0.088

0.025

0.004

0.300

0.175

0.150

 

0.004

  

0.008

0.008

12.2

         

0.004

     

0.004

13

0.058

0.025

0.013

0.004

0.308

0.283

 

0.154

0.154

0.175

 

0.004

   

0.004

13.2

         

0.008

      

13.3

 

0.004

              

14

0.063

0.292

0.008

0.046

0.204

0.283

 

0.017

0.179

0.321

 

0.058

0.004

 

0.100

0.029

14,2

 

0.021

       

0.046

      

15

0.167

  

0.213

0.117

0.204

0.042

0.004

0.096

0.167

 

0.425

  

0.104

0.042

15.2

         

0.021

     

0.004

15.3

0.079

               

16

0.121

0.004

0.058

0.300

0.038

0.129

0.017

 

0.142

0.067

 

0.288

  

0.221

0.063

16,2

         

0.025

     

0.008

16.3

0.050

               

17

0.046

 

0.242

0.250

0.017

0.063

0.096

 

0,092

  

0.092

  

0.292

0.071

17,2

         

0.004

      

17.3

0.146

     

0.004

         

18

0.004

 

0.079

0.179

 

0.013

0.242

 

0.058

  

0.017

0.021

 

0.233

0.083

18.1

      

0.004

         

18.2

               

0.004

18.3

0.063

     

0.025

         

19

  

0.096

0.008

  

0.088

 

0.042

   

0.058

 

0.029

0,075

19,2

               

0.004

19.3

0.004

 

0.008

   

0.008

         

20

  

0.158

   

0.146

 

0.025

   

0.108

 

0.013

0.075

20.2

               

0,103

21

  

0.025

   

0.104

     

0.158

  

0.021

21.2

            

0.004

  

0.013

22

  

0.046

   

0.075

     

0.158

  

0.013

22.2

            

0.008

  

0.013

22.3

            

0.013

   

23

  

0.113

   

0.067

     

0.183

   

23,2

               

0.042

23.3

  

0.004

             

24

  

0.050

   

0.050

 

0.004

   

0.154

  

0.004

24.2

            

0.004

  

0.025

24.3

            

0.004

   

25

  

0.075

   

0.017

     

0.104

   

25.2

               

0.021

26

  

0.021

   

0.013

   

0.004

 

0.013

   

26.2

               

0.042

27

  

0.004

       

0.017

    

0.004

27.2

               

0.046

28

          

0.146

 

0.004

  

0.004

28.2

               

0.063

29

          

0.225

     

29.2

          

0.004

    

0.050

30

          

0.192

     

30.2

          

0.021

    

0.054

31

          

0.083

     

31.2

          

0.158

    

0.029

32

          

0.008

    

0.004

32.2

          

0.113

    

0.013

33

               

0.008

33.2

          

0.029

     
Table 2

Parameters of forensic interest for the Sicilian population

Allele

D1S1656

D2S441

D2S1338

D3S1358

D8S1179

D10S1248

D12S391

D16S539

D18S51

D19S433

D21S11

D22S1045

FGA

TH01

VWA

SE33

Ho

.883333

.916

.866667

.941666

.916666

.941666

.89167

.9200

.9000

.9000

.9000

.933333

.85833

.9500

.933333

.93333

He

.895889

.750

.873246

.767894

.824335

.776802

.87915

.7800

.869426

.808009

.843322

.711513

.86844

.805808

.789716

.95073

PD

.972222

.898888

.999991

.898333

.941666

.911666

.999991

.907222

.965000

.933888

.940833

.861250

.9999907

.925972

.930972

.999996

PI

2.77777

.101111

8.802362

.101666

5.83334

8.833334

8.577639

9.277778

3.499999

6.611113

5.916666

.13875

9.298611

7.402778

6.902778

3.779931

PE

.790545

.534698

.750358

.544739

.663827

.565503

.758939

.577143

.737705

.631701

.689461

.481865

.7273922

.610151

.588902

.9001

PIC

.886764

.713072

.861394

.729116

.804562

.741838

.861050

.748654

.855482

.784013

.826062

.668039

.8512339

.776450

.758317

.970524

P-value

.1673

.00002

.00077

.6824

.1371

.9507

0.02107

.0009

.7550

.7891

.0092

.8601

0.68866

.6264

.5312

0.02533

Ho observed heterozygosity, He expected heterozygosity, PD power of discrimination, PIC polymorphism information content, PE power of exclusion, PI typical paternity index, p probability of deviation from Hardy-Weinberg equilibrium

Results and discussion

All loci exhibited an observed heterozygosity (Ho) greater than 0.85833 (FGA), with the highest value at 0.95 for TH01 and values of polymorphism information content (PIC) ranging between 0.668039 for D22S1045 and 0.970524 for SE33.

The lower power discrimination (PD) was observed for D22S1045 (0.861250) and the highest for D2S1338, D12S391 and SE33 (0.99999) The power of exclusion (PE) ranged from 0.481865 for D22S1045 to 0.9001 for SE33.

The study confirmed that all the markers were useful for forensic purposes: the combined power of discrimination was >0.999999. No significant deviation from Hardy-Weinberg expectations was found. Full concordance at all autosomal loci and amelogenin for both systems was observed.

Allele frequencies for studied 16 STR loci were compared to Italian population data (Berti et al. 2011). The data from Sicilian population was not significantly different from the Italian ones, except for the highest power of discrimination that was observed also for D2S1338 and D12S391.

In conclusion, we report the allele frequencies and forensic statical parameters in a Southern Italian population (Western Sicily). The results contribute to extending knowledge on DNA population data in Italy for forensic purposes. Our data on PowerPlex ESX 17 Fast System and PowerPlex ESI 17 Fast System demonstrate that both systems represent very remarkable tools for forensic human identification and kinship relationship.

Declarations

Funding

No funding for the study.

Authors’ contributions

Study concept and design: EVS, CM, SP. Acquisition of data: SP, SZ, AAsmundo, AArgo. Analysis and interpretation of data: SM, CM, EVS. Drafting of the manuscript: EVS, CM. Study supervision: EVS, CM. All authors read and approved the final manuscript.

Competing interests

The authors declare that they have no competing interests.

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

Authors’ Affiliations

(1)
Legal Medicine Section – Department for Health Promotion and Mother-Child Care, University of Palermo, Via del Vespro 129, 90127 Palermo, Italy
(2)
Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, via Consolare Valeria, 1, 98125 Messina, Italy

References

  1. Berti A, Brisighelli F, Bosetti A, Pilli E, Trapani C, Tullio V, Franchi C, Lago G, Capelli C (2011) Allele frequencies of the new European standard set (ESS) loci in the Italian population. Forensic Sci Int Genet 5(5):548–549View ArticlePubMedGoogle Scholar
  2. Gill P, Fereday L, Morling N. Schneider PM. The evolution of DNA databases- recommendations for new European STR loci. Forensic Sci Int 2006;156(2–3):242-244Google Scholar
  3. Guo SW, Thompson EA (1992) Performing the exact test of hardy-Weinberg proportion for multiple alleles. Biometrics 48(2):361–372View ArticlePubMedGoogle Scholar
  4. McLaren RS, Bourdeau-Heller J, Patel J, Thompson JM, Pagram J, Loake T, Beesley D, Pirttimaa M, Hill CR, Duewer DL, Kline MC, Butler JM, Storts DR (2014) Developmental validation of the PowerPlex® ESI 16/17 fast and PowerPlex® ESX 16/17 fast systems. Forensic Sci Int Genet. 13:195–205View ArticlePubMedGoogle Scholar
  5. Rousset F (2008) Genepop'007: a complete re-implementation of the genepop software for windows and Linux. Mol Ecol Resour 8(1):103–106View ArticlePubMedGoogle Scholar
  6. Tucker VC, Hopwood AJ, Sprecher CJ, McLaren RS, Rabbach DR, Ensenberger MG, Thompson JM, Storts DR (2011) Developmental validation of the PowerPlex® ESI 16 and PowerPlex® ESI 17 systems: STR multiplexes for the new European standard. Forensic Sci Int Genet. 5(5):436–448View ArticlePubMedGoogle Scholar
  7. Tucker VC, Hopwood AJ, Sprecher CJ, McLaren RS, Rabbach DR, Ensenberger MG, Thompson JM, Storts DR (2012) Developmental validation of the PowerPlex® ESX 16 and PowerPlex® ESX 17 system. Forensic Sci Int Genet 6(1):124–131View ArticlePubMedGoogle Scholar

Copyright

© The Author(s) 2017

Advertisement