International Journal of Legal Medicine

, Volume 123, Issue 4, pp 357–360 | Cite as

Subtyping of Y-chromosomal haplogroup E-M78 (E1b1b1a) by SNP assay and its forensic application

  • S. Caratti
  • S. Gino
  • C. Torre
  • C. RobinoEmail author
Short Communication


The continual discovery of new single-nucleotide polymorphisms (SNPs) has led to an increased resolution of the Y chromosome phylogeny. Some of these Y-SNPs have shown to be restricted to small geographical regions and therefore may prove useful in the forensic field as tools for the prediction of population of origin of unknown casework samples. Here, we describe a system for the molecular dissection of haplogroup E-M78 (E1b1b1a), consisting of multiplex polymerase chain reaction and minisequencing of M78 and nine population-informative Y-SNPs (M148, M224, V12, V13, V19, V22, V27, V32, V65) in a single reaction. Sensitivity and admixture studies demonstrated that the SNP protocol allows robust genotyping from as little as 50 pg of male DNA, even in the presence of 500-fold amounts of female DNA. In order to evaluate the suitability of E1b1b1a, subhaplogrouping for population-of-origin prediction, the distribution of E-M78 and its derived variants was determined in an Italian population sample (n = 326).


Forensic genetics Y chromosome Single-nucleotide polymorphism Haplogroup Minisequencing 



The continuing support of the Compagnia di San Paolo to C. Torre’s laboratory is gratefully acknowledged.

Supplementary material

414_2009_350_MOESM1_ESM.pdf (81 kb)
Table S1 Characteristics of multiplex PCR primers used in this study (PDF 81 kb)
414_2009_350_MOESM2_ESM.pdf (31 kb)
Table S2 Characteristics of SBE primers (PDF 30 kb)
414_2009_350_MOESM3_ESM.pdf (19 kb)
Table S3 Amplicon size and mean peak height ratio of SBE products in wild-type and mutated individuals (PDF 19 kb)
414_2009_350_MOESM4_ESM.pdf (16 kb)
Table S4 Frequency distribution of E-M78 and its subhaplogroups in the Italian population sample (PDF 16 kb)
414_2009_350_MOESM5_ESM.pdf (46 kb)
Table S5 List of Y-STR minimal haplotypes observed in Italians carrying E-M78 subhaplogroups (PDF 46 kb)
414_2009_350_MOESM6_ESM.pdf (54 kb)
Fig. S1 Phylogenetic tree of Y-chromosomal haplogroup E (PDF 54 kb)
414_2009_350_MOESM7_ESM.pdf (525 kb)
Fig. S2 Frequency contour maps of E-M78 and its subhaplogroups (PDF 525 kb)
414_2009_350_MOESM8_ESM.pdf (157 kb)
Fig. S3 Representative electropherograms of haplogroups observed in the Italian population sample (PDF 156 kb)
414_2009_350_MOESM9_ESM.pdf (221 kb)
Fig. S4 Y-SNP profiles in admixture and sensitivity studies (PDF 220 kb)


  1. 1.
    Prinz M, Boll K, Baum H, Shaler B (1997) Multiplexing of Y chromosome specific STRs and performance for mixed samples. Forensic Sci Int 85:209–218PubMedCrossRefGoogle Scholar
  2. 2.
    Jobling MA, Tyler-Smith C (2003) The human Y chromosome: an evolutionary marker comes of age. Nat Rev Genet 4:598–612PubMedCrossRefGoogle Scholar
  3. 3.
    Jobling MA (2001) Y-chromosomal SNP haplotype diversity in forensic analysis. Forensic Sci Int 118:158–162PubMedCrossRefGoogle Scholar
  4. 4.
    Amigo J, Phillips C, Lareu M, Carracedo A (2008) The SNPforID browser: an online tool for query and display of frequency data from the SNPforID project. Int J Legal Med 122:435–440PubMedCrossRefGoogle Scholar
  5. 5.
    Szibor R, Plate I, Schmitter H, Wittig H, Krause D (2006) Forensic mass screening using mtDNA. Int J Legal Med 120:372–376PubMedCrossRefGoogle Scholar
  6. 6.
    Köhnemann S, Sibbing U, Pfeiffer H, Hohoff C (2008) A rapid mtDNA assay of 22 SNPs in one multiplex reaction increases the power of forensic testing in European Caucasians. Int J Legal Med 122:517–523PubMedCrossRefGoogle Scholar
  7. 7.
    Dixon LA, Murray CM, Archer EJ, Dobbins AE, Koumi P, Gill P (2005) Validation of a 21-locus autosomal SNP multiplex for forensic identification purposes. Forensic Sci Int 154:62–77PubMedCrossRefGoogle Scholar
  8. 8.
    Sobrino B, Brión M, Carracedo A (2005) SNPs in forensic genetics: a review on SNP typing methodologies. Forensic Sci Int 154:181–194PubMedCrossRefGoogle Scholar
  9. 9.
    Sanchez JJ, Børsting 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 137:74–84PubMedCrossRefGoogle Scholar
  10. 10.
    Brión 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 geographical origin of male lineages. Electrophoresis 26:4411–4420PubMedCrossRefGoogle Scholar
  11. 11.
    Onofri V, Alessandrini F, Turchi C, Pesaresi M, Buscemi L, Tagliabracci A (2006) Development of multiplex PCRs for evolutionary and forensic applications of 37 human Y chromosome SNPs. Forensic Sci Int 157:23–35PubMedCrossRefGoogle Scholar
  12. 12.
    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
  13. 13.
    King TE, Parkin EJ, Swinfield G et al (2007) Africans in Yorkshire? The deepest-rooting clade of the Y phylogeny within an English genealogy. Eur J Hum Genet 15:288–293PubMedCrossRefGoogle Scholar
  14. 14.
    Karafet TM, Mendez FL, Meilerman MB, Underhill PA, Zegura SL, Hammer MF (2008) New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree. Genome Res 18:830–838PubMedCrossRefGoogle Scholar
  15. 15.
    Cruciani F, La Fratta R, Torroni A, Underhill PA, Scozzari R (2006) Molecular dissection of the Y chromosome haplogroup E-M78 (E3b1a): a posteriori evaluation of a microsatellite-network-based approach through six new biallelic markers. Hum Mutat 27:831–832PubMedCrossRefGoogle Scholar
  16. 16.
    Cruciani F, La Fratta R, Trombetta B et al (2007) Tracing past human male movements in northern/eastern Africa and western Eurasia: new clues from Y-chromosomal haplogroups E-M78 and J-M12. Mol Biol Evol 24:1300–1311PubMedCrossRefGoogle Scholar
  17. 17.
    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
  18. 18.
    Underhill PA, Passarino G, Lin AA et al (2001) The phylogeography of Y chromosome binary haplotypes and the origins of modern human populations. Ann Hum Genet 65:43–62PubMedCrossRefGoogle Scholar
  19. 19.
    Lindblad-Toh K, Winchester E, Daly MJ et al (2000) Large-scale discovery and genotyping of single-nucleotide polymorphisms in the mouse. Nat Genet 24:381–386PubMedCrossRefGoogle Scholar
  20. 20.
    Anslinger K, Keil W, Weichhold G, Eisenmenger W (2000) Y-chromosomal STR haplotypes in a population sample from Bavaria. Int J Legal Med 113:189–192PubMedCrossRefGoogle Scholar
  21. 21.
    Konrad KD, Pentoney SL Jr (1993) Contribution of secondary structure to DNA mobility in capillary gels. Electrophoresis 14:502–508PubMedCrossRefGoogle Scholar
  22. 22.
    Vallone PM, Just RS, Coble MD, Butler JM, Parsons TJ (2004) A multiplex allele-specific primer extension assay for forensically informative SNPs distributed throughout the mitochondrial genome. Int J Legal Med 118:147–157PubMedCrossRefGoogle Scholar
  23. 23.
    Gill P, Whitaker J, Flaxman C, Brown N, Buckleton J (2000) An investigation of the rigor of interpretation rules for STRs derived from less than 100 pg of DNA. Forensic Sci Int 112:17–40PubMedCrossRefGoogle Scholar
  24. 24.
    Di Gaetano C, Cerutti N, Crobu F et al (2008) Differential Greek and northern African migrations to Sicily are supported by genetic evidence from the Y chromosome. Eur J Hum Genet . doi: 10.1038/ejhg.2008.120 PubMedGoogle Scholar
  25. 25.
    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
  26. 26.
    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
  27. 27.
    Forster P, Röhl A, Lünnemann P, Brinkmann C, Zerjal T, Tyler-Smith C, Brinkmann B (2000) A short tandem repeat-based phylogeny for the human Y chromosome. Am J Hum Genet 67:182–196PubMedCrossRefGoogle Scholar
  28. 28.
    Robino C, Crobu F, Di Gaetano C et al (2008) Analysis of Y-chromosomal SNP haplogroups and STR haplotypes in an Algerian population sample. Int J Leg Med 122:251–255CrossRefGoogle Scholar
  29. 29.
    De Knijff P (2000) Messages through bottlenecks: on the combined use of slow and fast evolving polymorphic markers on the human Y chromosome. Am J Hum Genet 67:1055–1061PubMedCrossRefGoogle Scholar
  30. 30.
    Schlecht J, Kaplan ME, Barnard K, Karafet T, Hammer MF, Merchant NC (2008) Machine-learning approaches for classifying haplogroup from Y chromosome STR data. PLoS Comput Biol 4:e1000093PubMedCrossRefGoogle Scholar
  31. 31.
    Bouakaze C, Keyser C, Amory S, Crubézy E, Ludes B (2007) First successful assay of Y-SNP typing by SnaPshot minisequencing on ancient DNA. Int J Legal Med 121:493–499PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  1. 1.Department of Anatomy, Pharmacology, and Legal MedicineUniversity of TurinTurinItaly

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