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International Journal of Legal Medicine

, Volume 119, Issue 1, pp 10–15 | Cite as

Hierarchical analysis of 30 Y-chromosome SNPs in European populations

  • M. Brion
  • B. Sobrino
  • A. Blanco-Verea
  • M. V. Lareu
  • A. Carracedo
Original Article

Abstract

Analysis of Y-chromosome haplogroups defined by binary polymorphisms, has became a standard approach for studying the origin of modern human populations and for measuring the variability between them. Furthermore, the simplicity and population specificity of binary polymorphisms allows inferences to be drawn about the population origin of any male sample of interest for forensic purposes. From the 245 binary polymorphisms that can be analysed by PCR described in the Y Chromosome Consortium tree, we have selected 30 markers. The set of 30 has been grouped into 4 multiplexes in order to determine the most frequent haplogroups in Europe, using only 1 or 2 multiplexes. In this way, we avoid typing unnecessary SNPs to define the final haplogroup saving effort and cost, since we only need to type 9 SNPs in the best case and in the worst case, no more than 17 SNPs to define the haplogroup. The selected method for allele discrimination was a single base extension reaction using the SNaPshot multiplex kit. A total of 292 samples from 8 different districts of Galicia (northwest Spain) were analysed with this strategy. No significant differences were detected among the different districts, except for the population from Mariña Lucense, which showed a distant haplogroup frequency but not higher Φst values.

Keywords

Y chromosome Single nucleotide polymorphisms SNPs Single base extension SNaPshot reaction Europe 

Notes

Acknowledgements

The technical assistance of Meli Rodriguez and Raquel Calvo is highly appreciated. This work was supported by the grant from the “Ministerio de Ciencia y Tecnologia” (DGCYT.P4.BIO2000-09822).

References

  1. Borsting C, Sanchez JJ, Morling N (2004) Multiplex PCR, amplicon size and hybridization efficiency on the NanoChip electronic microarray. Int J Legal Med (in press)Google Scholar
  2. Brion M, Salas A, González-Neira A, Lareu MV, Carracedo A (2003) Insights over the Iberian population origin through the construction of highly informative Y-chromosome haplotypes using biallelic markers, STRs and the MSY1 minisatellite. Am J Phys Anthropol 122:147–161CrossRefPubMedGoogle Scholar
  3. Chen X, Sullivan PF (2003) Single nucleotide polymorphism genotyping: biochemistry, protocol, cost and throughput. Pharmacogenom J 3:77–96CrossRefGoogle Scholar
  4. Gill P (2001) An assessment of the utility of single nucleotide polymorphisms (SNPs) for forensic purposes. Int J Legal Med 114:204–210CrossRefPubMedGoogle Scholar
  5. Henegariu O, Heerema NA, Dlouhy SR, Vance GH, Vogt PH (1997) Multiplex PCR: critical paremeters and step-by-step protocol. Biotechniques 23:504–511PubMedGoogle Scholar
  6. Jobling MA, Tyler-Smith C (2003) The human Y chromosome: an evolutionary marker comes of age. Nat Rev Genet 4:598–612CrossRefPubMedGoogle Scholar
  7. Jorde LB, Watkins WS, Bamshad MJ (2001) Population genomics: a bridge from evolutionary history to genetic medicine. Hum Mol Genet 10:2199–2207CrossRefPubMedGoogle Scholar
  8. Karafet TM, Zegura SL, Posukh O et al. (1999) Ancestral Asian source(s) of New World Y-chromosome founder haplotypes. Am J Hum Genet 64:817–831PubMedGoogle Scholar
  9. Rosser Z, Zerjal T, Hurles MH et al. (2000) Y chromosomal diversity within Europe is clinal and influenced primarily by geography, rather than language. Am J Hum Genet 67:1526–1543PubMedGoogle Scholar
  10. Sanchez JJ, Borsting C, Hallenberg C, Buchard A, Hernandez A, Morling N (2003) Multiplex PCR and minisequencing of SNPs—a model with 35 Y chromosome SNPs. Forensic Sci Int 137:74–84CrossRefPubMedGoogle Scholar
  11. Sanchez JJ, Brion M, Parson W et al. (2004) Duplications of the Y-chromosome specific loci P25 and 92R7 and forensic implications. Forensic Sci Int 140:241–250CrossRefPubMedGoogle Scholar
  12. Schneider S, Roessli D, Excoffier L (2000) Arlequin ver. 2.000: a software for population genetics data analysis. Genetics and Biometry Laboratory, University of Geneva, SwitzerlandGoogle Scholar
  13. Seielstad MT, Minch E, Cavalli-Sforza LL (1998) Genetic evidence for a higher female migration rate in humans. Nat Genet 20:278–280CrossRefPubMedGoogle Scholar
  14. Semino O, Passarino G, Oefner PJ et al. (2000) The genetic legacy of paleolithic Homo sapiens sapiens in extant Europeans: a Y chromosome perspective. Science 290:1155–1159PubMedGoogle Scholar
  15. Weale ME, Shah T, Jones AL et al. (2003) Rare deep-rooting Y chromosome lineages in humans: lessons of phylogeography. Genetics 165:229–234PubMedGoogle Scholar
  16. Y Chromosome Consortium (2002) A nomenclature system for the tree of human Y-chromosomal binary haplogroups. Genome Res 12:339–348PubMedGoogle Scholar
  17. Zhao Z, Fu YX, Hewett-Emmett D, Boerwinkle E (2003) Investigating single nucleotide polymorphism (SNP) density in the human genome and its implications for molecular evolution. Gene 312:207–213CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  • M. Brion
    • 1
  • B. Sobrino
    • 1
  • A. Blanco-Verea
    • 1
  • M. V. Lareu
    • 1
  • A. Carracedo
    • 1
  1. 1.Institute of Legal MedicineUniversity of Santiago de CompostelaSantiago de CompostelaSpain

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