Forensic Science International: Genetics
Volume 6, Issue 1 , Pages e44-e45, January 2012

Genetic data of 15 STR loci in five populations from Afghanistan

UMR 6578 (Anthropologie Bioculturelle), Université de la Méditerranée, CNRS, EFS; 51 bd Pierre Dramard, 13916 Marseille, France

Laboratoire d’Anthropologie, Université de Genève, 12, rue Gustave-Revilliod, 1227 Genève, Switzerland

Department of biochemistry, Kabul Medical University, Kabul, Afghanistan

UMR 6578 (Anthropologie Bioculturelle), Université de la Méditerranée, CNRS, EFS; 51 bd Pierre Dramard, 13916 Marseille, France

Received 7 October 2010 published online 13 April 2011.

Article Outline

 

Dear Editor,

The variability of 15 hyper-variable autosomal STR loci included in the AmpFlSTR Identifiler™ PCR amplification kit (Applied Biosystems) was analyzed in Afghan individuals from five populations located at a major continental crossroad in the history of human migrations. A total of 456 blood samples from unrelated male individuals donors aged from 20 to 55 years old with ancestry traced back at least two generations and originating from five tribes: Hazara, Ouzbek, Tadjik, Turkmen and Pachtoun were collected and analyzed (see Results in Supplementary data).

In order to assess the genetic diversity of these microsatellites in Afghanistan and in an extended regional context, we compared our data to a set of populations taken from the literature. These data were collected from populations located in a proximate area surrounding Afghanistan (India [1], [2], [3], Kuwait [4], Iran [5], Iraq [6], Syria, Lebanon, Jordan, Palestine, Yemen, Oman, Saudi Arabia, Pakistan, Bangladesh, Dubai [7] and Egypt [8]).

After Bonferroni's correction, no deviations from the Hardy–Weinberg equilibrium were observed at any of the 15 STR loci in the five samples. The exclusion probability and discrimination probability were high in every case. All loci show a high degree of intra-population genetic diversity. The polymorphic information content (PIC) values indicate good informativeness for all STR markers [9], [10], [11], [12]. The most polymorphic loci are D2S1338, FGA and D18S51 and they also are the most discriminating; TPOX shows the lowest number of alleles with 5 both in Ouzbeks and Turkmen (see Supplementary data).

These results strongly support the use of this set of genetic markers for forensic personal identification and paternity testing in the Afghans, thereby further confirming its efficiency for forensic practice. No new variant was found although some of the known alleles were hardly described. Alleles with low frequencies were confirmed by reamplification and reanalysis (vWA (15.2) [5]; D3S1358 (12); D19S433 (17.2 and 18.2); D2S1338 (27 and 28) [13]; and D21S11 (33) [1]).

Genetic diversity among populations is only accounting for 0.5–2% of the total genetic variation, with most of the variability being detected within each of the 29 populations used for comparisons (all indices are highly significant, P-value <0.001, see Supplementary data Fig. 1). Yet, 11 of the 15 STR exhibit a strong and highly significant correlation between genetic and geographic distances (CSF1PO, P-value=0.0184; D13S317, P-value=0; D18S51, P-value=0; D19S433, P-value=0.0024; D2S1338, P-value=0.0006; D3S1358, P-value=0; D7S820, P-value=0; D8S1179, P-value=0; FGA, P-value=0.0066; TPOX, P-value=0.0301; vWA, P-value=0.0047, see Supplementary data Fig. 2). The importance of geography as a factor shaping the genetic profiles depicted for these microsatellites is also confirmed when genetic distances between pairs of populations are plotted using multidimensional scaling analyses. Fig. 3 (see Supplementary data) shows the MDS representations for loci D13S317 and D7S820. The five Afghan populations exhibit an intermediate genetic profile to Middle-eastern and Indian–Pakistanis’ populations, which are pooled in two distinct clusters.

To conclude, our data indicate that standardized multiloci STR panels may be a useful forensic tool, which can be applied for identification purposes in the Afghan population. The genetic comparison of five different Afghan ethnic groups with other populations located in the same regional area showed a significant differentiation according to geographic criteria, thus stressing the use of proper databases for forensic genetics calculations. However, it is important to keep in mind that the intra-population genetic diversity of these microsatellites is several times higher (more than an order of magnitude) than the inter-population genetic variation, like many other polymorphic genetic systems studied in anthropology (e.g. HLA, mtDNA, GM immunoglobulin, and Y chromosome).

This study is following ISFG guidelines [14] and this letter is following the FSI Genetics guidelines for this type of publication [15].

Back to Article Outline

Conflict of interest statement 

The authors declare no conflicts of interest.

Back to Article Outline

Acknowledgements 

We are grateful to all donors who made this study possible. This work was supported by ANR Program AFGHAPOP No BLAN07-3_222301.

Back to Article Outline

Appendix A. Supplementary data 

Back to Article Outline

References 

  1. Mastana SS, Murry B, Sachdeva MP, Das K, Young D, Das MK, et al. Genetic variation of 13 STR loci in the four endogamous tribal populations of Eastern India. Forensic Sci. Int. 2007;169:266–273
  2. Roy S, Eaaswarkhanth M, Dubey B, Haque I. Autosomal STR variations in three endogamous populations of West Bengal, India. Leg. Med. (Tokyo). 2008;10:326–332
  3. Bindu GH, Trivedi R, Kashyap VK. Allele frequency distribution based on 17 STR markers in three major Dravidian linguistic populations of Andhra Pradesh, India. Forensic Sci. Int. 2007;170:76–85
  4. Alenizi M, Goodwin W, Ismael S, Hadi S. STR data for the AmpFlSTR® Identifiler® loci in Kuwaiti population. Leg. Med. (Tokyo). 2008;10:321–325
  5. Shepard EM, Herrera RJ. Iranian STR variation at the fringes of biogeographical demarcation. Forensic Sci. Int. 2006;158:140–148
  6. Barni F, Berti A, Pianese A, Boccellino A, Miller MP, Caperna A, et al. Allele frequencies of 15 autosomal STR loci in the Iraq population with comparisons to other populations from the middle-eastern region. Forensic Sci. Int. 2007;167:87–92
  7. Alshamali F, Alkhayat AQ, Budowle B, Watson ND. STR population diversity in nine ethnic populations living in Dubai. Forensic Sci. Int. 2005;152:267–279
  8. Coudray C, Guitard E, el-Chennawi F, Larrouy G, Dugoujon JM. Allele frequencies of 15 short tandem repeats (STRs) in three Egyptian populations of different ethnic groups. Forensic Sci. Int. 2007;169:260–265
  9. Excoffier L, Laval G, Schneider S. Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol. Bioinform. Online. 2005;1:47–50
  10. Reynolds J, Weir BS, Cockerham CC. Estimation of the coancestry coefficient: basis for a short-term genetic distance. Genetics. 1983;105:767–779
  11. Mantel N. The detection of disease clustering and a generalized regression approach. Cancer Res. 1967;27:209–220
  12. Rohlf FS. NTSYSpc: Numerical Taxonomy and Multivariate Analysis System. Ver 2.10m. New York: Applied Biostatistics, Inc.; 2000;
  13. Stanciu F, Stoian IM, Popescu OR. Comprehensive STR data for the AmpFlSTR Identifiler from Transylvania (NW Romania). Leg. Med. (Tokyo). 2009;11:48–50
  14. Olaisen B, Bär W, Brinkmann B, Budowle B, Carracedo A, Gill P, et al. DNA recommendations 1997 of the International Society for Forensic Genetics. Vox Sang. 1998;74(1):61–63
  15. Carracedo A, Butler JM, Gusmão L, Parson W, Roewer L, Schneider PM. Publication of population data for forensic purposes. Forensic Sci. Int. Genet. 2010;4(April (3)):145–147

PII: S1872-4973(11)00049-4

doi:10.1016/j.fsigen.2011.03.004

Forensic Science International: Genetics
Volume 6, Issue 1 , Pages e44-e45, January 2012

Article Tools