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International Journal of Legal Medicine

, Volume 122, Issue 3, pp 251–255 | Cite as

Analysis of Y-chromosomal SNP haplogroups and STR haplotypes in an Algerian population sample

  • C. Robino
  • F. Crobu
  • C. Di Gaetano
  • A. Bekada
  • S. Benhamamouch
  • N. Cerutti
  • A. Piazza
  • S. Inturri
  • C. Torre
Short Communication

Abstract

The distribution of Y-chromosomal single nucleotide polymorphism (SNP) haplogroups and short tandem repeat (STR) haplotypes was determined in a sample of 102 unrelated men of Arab origin from northwestern Algeria (Oran area). A total of nine different haplogroups were identified by a panel of 22 binary markers. The most common haplogroups observed in the Algerian population were E3b2 (45.1%) and J1 (22.5%). Y-STR typing by a 17-loci multiplex system allowed 93 haplotypes to be defined (88 were unique). Striking differences in the allele distribution and gene diversity of Y-STR markers between haplogroups could be found. In particular, intermediate alleles at locus DYS458 specifically characterized the haplotypes of individuals carrying haplogroup J1. All the intermediate alleles shared a common repeat sequence structure, supporting the hypothesis that the variant originated from a single mutational event.

Keywords

Y chromosome Single nucleotide polymorphism Short tandem repeat Algeria DYS458 

Notes

Acknowledgements

The continuing support of the Compagnia di San Paolo to C. Torre’s laboratory is gratefully acknowledged. We also thank Dr Boudjema A, Medienne Benchekor S and Meghoufel N for assistance in the collection of the samples.

Supplementary material

414_2007_203_MOESM1_ESM.pdf (15 kb)
Fig. S1 NJ tree forAlgerian Arabs “A-AR”(n = 102) and 11 reference populations: Algerian Berbers “A-B”(n = 16), northern “E-N”(n = 47) and southern Egyptians “E-S”(n = 50) [14]; Moroccan Arabs “M-AR”(n = 60), Moroccan Berbers “M-B”(n = 49) [18]; Andalusians“T-AN”(n = 132) and cosmopolitan (Tunisi) “T-T”Tunisians (n = 54) [19]; Tunisian Berbers “T-B”(n = 66) [20]; Portuguese “POR”(n = 250) [21]; Sicilians “SIC”(n = 255) [22]; Spaniards from Andalusia “SPA”(n = 56) [23] (PDF 14 KB)
414_2007_203_MOESM2_ESM.xls (28 kb)
Table S1 Complete Y-SNP typing results and haplogroups observed in the Algerian population sample (XLS 28 KB)
414_2007_203_MOESM3_ESM.xls (32 kb)
Table S2 Complete list of Y-chromosomal haplotypes observed in the Algerian population sample (XLS 32 KB)
414_2007_203_MOESM4_ESM.pdf (29 kb)
Table S3 Pairwise distance (RST) between Algerian Arabs (A-AR) and eleven reference populations: Algerian Berbers “A-B” (n = 16), northern “E-N” (n = 47) and southern Egyptians “E-S” (n = 50) [14]; Moroccan Arabs “M-AR” (n = 60), Moroccan Berbers “M-B” (n = 49) [18]; Andalusians “T-AN” (n = 132) and cosmopolitan (Tunisi) “T-T” Tunisians (n = 54) [19]; Tunisian Berbers “T-B” (n = 66) [20]; Portuguese “POR” (n = 250) [21]; Sicilians “SIC” (n = 255) [22]; Spaniards from Andalusia “SPA” (n = 56) [23]. RST and p values are shown below and above the diagonal, respectively. Significant comparisons are shown in bold (PDF 30 KB)
414_2007_203_MOESM5_ESM.pdf (24 kb)
Table S4 Most frequent Y-STR alleles within major haplogroups found in the Algerian population sample (unique alleles are underlined) (PDF 24 KB)

References

  1. 1.
    Gusmao L, Butler JM, Carracedo A et al (2006) DNA Commission of the International Society of Forensic Genetics (ISFG): an update of the recommendations on the use of Y-STRs in forensic analysis. Int J Legal Med 120:191–200PubMedCrossRefGoogle Scholar
  2. 2.
    Willuweit S, Roewer L (2007) Y chromosome haplotype reference database (YHRD): Update. FSI: Genetics 1:83–87Google Scholar
  3. 3.
    Jobling MA (2001) Y-chromosomal SNP haplotype diversity in forensic analysis. Forensic Sci Int 118:158–162PubMedCrossRefGoogle Scholar
  4. 4.
    Wetton JH, Tsang KW, Khan H (2005) Inferring the population of origin of DNA evidence within the UK by allele-specific hybridization of Y-SNPs. Forensic Sci Int 152:45–53PubMedCrossRefGoogle Scholar
  5. 5.
    Brion M, Sanchez JJ, Balogh K et al (2005) Introduction of an single nucleodite polymorphism-based “Major Y-chromosome haplogroup typing kit” suitable for predicting the geographic origin of male lineages. Electrophoresis 26:4411–4420PubMedCrossRefGoogle Scholar
  6. 6.
    Miller SA, Dykes DD, Polesky HF (1988) A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res 16:1215PubMedCrossRefGoogle Scholar
  7. 7.
    Cinnioglu C, King R, Kivisild T et al (2004) Excavating Y-chromosome haplotype strata in Anatolia. Hum Genet 114:127–148PubMedCrossRefGoogle Scholar
  8. 8.
    Oefner PJ, Underhill PA (1998) DNA mutation detection using denaturing high performance liquid chromatography (DHPLC). In: Dracopoli NC et al (eds) Current protocols in human genetics, Suppl 19. Wiley, NewYork, pp 7.10.1–7.10.12Google Scholar
  9. 9.
    Jobling MA, Tyler-Smith C (2003) The human Y chromosome: an evolutionary marker comes of age. Nat Rev Genet 4:598–612PubMedCrossRefGoogle Scholar
  10. 10.
    Schoske R, Vallone PM, Kline MC, Redman JW, Butler JM (2004) High-throughput Y-STR typing of U.S. populations with 27 regions of the Y chromosome using two multiplex PCR assays. Forensic Sci Int 139:107–121PubMedCrossRefGoogle Scholar
  11. 11.
    Schneider S, Roessli D, Excoffier L (2000) Arlequin Version 2.000: A Software for Population Genetics Data Analysis, Genetics and Biometry Laboratory, University of Geneva, SwitzerlandGoogle Scholar
  12. 12.
    Felsenstein J (1989) PHYLIP: phylogeny inference package (version 3.2). Cladistics 5:164–166Google Scholar
  13. 13.
    Delfiner P (1976) Linear estimation of non-stationary spatial phenomena. In: Guarasio M, David M, Haijbegts C (eds) Advanced geostatistics in the mining industry. Reidel, Dordrecht, pp 49–68Google Scholar
  14. 14.
    Arredi B, Poloni ES, Paracchini S et al (2004) A predominantly neolithic origin for Y-chromosomal DNA variation in North Africa. Am J Hum Genet 75:338–345PubMedCrossRefGoogle Scholar
  15. 15.
    Cruciani F, La Fratta R, Santolamazza P et al (2004) Phylogeographic analysis of haplogroup E3b (E-M215) Y chromosomes reveals multiple migratory events within and out of Africa. Am J Hum Genet 74:1014–1022PubMedCrossRefGoogle Scholar
  16. 16.
    Semino O, Magri C, Benuzzi G et al (2004) Origin, diffusion, and differentiation of Y-chromosome haplogroups E and J: inferences on the neolithization of Europe and later migratory events in the Mediterranean area. Am J Hum Genet 74:1023–1034PubMedCrossRefGoogle Scholar
  17. 17.
    Di Giacomo F, Luca F, Popa LO et al (2004) Y chromosomal haplogroup J as a signature of the post-neolithic colonization of Europe. Hum Genet 115:357–371PubMedCrossRefGoogle Scholar
  18. 18.
    Quintana-Murci L, Bigham A, Rouba H, Barakat A, McElreavey K, Hammer M (2004) Y-chromosomal STR haplotypes in Berber and Arabic-speaking populations from Morocco. Forensic Sci Int 140:113–115PubMedCrossRefGoogle Scholar
  19. 19.
    Cherni L, Pereira L, Goios A et al (2005) Y-chromosomal STR haplotypes in three ethnic groups and one cosmopolitan population from Tunisia. Forensic Sci Int 152:95–99PubMedCrossRefGoogle Scholar
  20. 20.
    Frigi S, Pereira F, Pereira L et al (2006) Data for Y-chromosome haplotypes defined by 17 STRs (AmpFLSTR Yfiler) in two Tunisian Berber communities. Forensic Sci Int 160:80–83PubMedCrossRefGoogle Scholar
  21. 21.
    Alves C, Gomes V, Prata MJ, Amorim A, Gusmao L (2007) Population data for Y-chromosome haplotypes defined by 17 STRs (AmpFlSTR YFiler) in Portugal. Forensic Sci Int DOI  10.1016/j.forsciint.2006.10.002
  22. 22.
    Robino C, Inturri S, Gino S et al (2006) Y-chromosomal STR haplotypes in Sicily. Forensic Sci Int 159:235–240PubMedCrossRefGoogle Scholar
  23. 23.
    Gonzalez-Neira A, Gusmao L, Brion M, Lareu MV, Amorim A, Carracedo A (2000) Distribution of Y-chromosome STR defined haplotypes in Iberia. Forensic Sci Int 110:117–126PubMedCrossRefGoogle Scholar
  24. 24.
    Bosch E, Calafell F, Santos FR et al (1999) Variation in short tandem repeats is deeply structured by genetic background on the human Y chromosome. Am J Hum Genet 65:1623–1638PubMedCrossRefGoogle Scholar
  25. 25.
    Mulero JJ, Chang CW, Calandro LM, Green RL, Li Y, Johnson CL, Hennessy LK (2006) Development and validation of the AmpFlSTR Yfiler PCR amplification kit: a male specific, single amplification 17 Y-STR multiplex system. J Forensic Sci 51:64–75PubMedCrossRefGoogle Scholar
  26. 26.
    Onofri V, Alessandrini F, Turchi C, Fraternale B, Buscemi L, Pesaresi M, Tagliabracci A (2007) Y-chromosome genetic structure in sub-Apennine populations of Central Italy by SNP and STR analysis. Int J Legal Med 121:234–237PubMedCrossRefGoogle Scholar
  27. 27.
    Sobrino B, Brion M, Carracedo A (2005) SNPs in forensic genetics: a review on SNP typing methodologies. Forensic Sci Int 154:181–194PubMedCrossRefGoogle Scholar
  28. 28.
    Nebel A, Filon D, Brinkmann B, Majumder PP, Faerman M, Oppenheim A (2001) The Y chromosome pool of Jews as part of the genetic landscape of the Middle East. Am J Hum Genet 69:1095–1112PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2007

Authors and Affiliations

  • C. Robino
    • 1
  • F. Crobu
    • 2
  • C. Di Gaetano
    • 2
  • A. Bekada
    • 3
  • S. Benhamamouch
    • 3
  • N. Cerutti
    • 2
  • A. Piazza
    • 2
  • S. Inturri
    • 1
  • C. Torre
    • 1
  1. 1.Department of Anatomy, Pharmacology and Legal MedicineUniversity of TurinTurinItaly
  2. 2.Department of Genetics, Biology and BiochemistryUniversity of TurinTurinItaly
  3. 3.Département de Biotechnologie, Faculté des SciencesUniversité d’OranOranAlgeria

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