Skip to main content
SpringerLink
Log in

Software for Y-haplogroup predictions: a word of caution

  • SHORT COMMUNICATION
  • Published:
International Journal of Legal Medicine Aims and scope Submit manuscript

Abstract

The development of online software designed for genetic studies has been exponentially growing, providing numerous benefits to the scientific community. However, they should be used with care, since some require adjustments. The efficiency of two programs for haplogroup prediction was tested with 119 samples of known haplotypes and haplogroups from Argentine populations. Quantitative estimates of the predictive quality of both software systems were computed with the uncertainty coefficient; and sensitivity, specificity, positive, and negative likelihood ratios were also calculated to assert the reliability of both programs, showing high probabilities of assigning an incorrect haplogroup.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

References

  1. Bosch E, Calafell F, Santos F et al (1999) Variation in short tandem repeats is deeply structured by genetic background on the human Y chromosome. Am J Hum Genet 65:1623–1638

    Article  CAS  PubMed  Google Scholar 

  2. Behar DM, Garrigan D, Kaplan M et al (2004) Contrasting patterns of the Y chromosome variation in Ashkenazi Jewish and host non-Jewish European populations. Hum Genet 114:354–365

    Article  CAS  PubMed  Google Scholar 

  3. Athey WT (2005) Haplogroup prediction from Y-STR values using an allele-frequency approach. J Genet Geneal 1:1–7

    Google Scholar 

  4. Athey WT (2006) Haplogroup prediction from Y-STR values using a Bayesian-allele-frequency approach. J Genet Geneal 2:34–39

    Google Scholar 

  5. Salas A, Jaime JC, Álvarez-Iglesias V, Carracedo Á (2008) Gender bias in the multiethnic genetic composition of central Argentina. J Hum Genet 53:662–674

    Article  CAS  PubMed  Google Scholar 

  6. Mertens G (2007) Y-Haplogroup frequencies in the Flemish population. J Genet Geneal 3(2):19–25

    Google Scholar 

  7. Goff PG, Athey TW (2006) Diagnostic STR values for haplogroup G. J Genet Geneal 2(1):12–17

    Google Scholar 

  8. 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(6):e1000093. doi:10.1371/journal.pcbi1000093

    Article  PubMed  Google Scholar 

  9. Ramallo V, Alfaro EL, Dipierri JE, Bianchi NO, Bailliet G (2005) Caracterización de linajes paternos en muestras provenientes de tres provincias del NOA. Revista de la Sociedad Argentina de Genética. Journal or Basic & Applied Genetics Actas XXXIV Congreso Argentino de Genética XVII(Suplement):181, Septiembre

    Google Scholar 

  10. YCC (The Y Chromosome Consortium) (2002) A nomenclature system for the tree of Y chromosomal binary haplogroups. Genome Res 12:339–348

    Article  Google Scholar 

  11. de Knijff P, Kayser M, Caglia A, Corach D, Fretwell N, Gehrig C, Graziosi G et al (1997) Chromosome Y microsatellites: population genetic and evolutionary aspects. Int J Legal Med 110:134–140

    Article  PubMed  Google Scholar 

  12. Kayser M, Caglia A, Corach D, Fretwell N, Gehrig C, Graziosi G, Heidorn F (1997) Evaluation of Y-chromosomal STRs: a multicenter study. Int J Legal Med 110:125–133

    Article  CAS  PubMed  Google Scholar 

  13. Bravi CM, Sans M, Bailliet G, Martinez-Marignac VL, Bianchi NO (1997) Characterization of mitochondrial and Y-chromosome haplotypes in an Uruguayan population of African ancestry. Hum Biol 69(5):641–652

    CAS  PubMed  Google Scholar 

  14. Bianchi NO, Catanesi CI, Bailliet G, Martinez-Marignac VL, Bravi CM, Vidal-Rioja LB, Herrera RJ, Lopez Camelo JS (1998) Characterization of ancestral and derived Y-chromosome haplotypes of New World native populations. Am J Hum Genet 63:1862–1871

    Article  CAS  PubMed  Google Scholar 

  15. Bailliet G, Castilla EE, Adams JP, Orioli IM, Martínez-Marignac VL, Richard SM, Bianchi NO (2001) Correlation between molecular and conventional genealogies in Aicuña: a rural population from Northwestern Argentina. Hum Hered 51:150–159

    Article  CAS  PubMed  Google Scholar 

  16. Sengupta S, Zhivotovsky LA, King R, Mehdi SQ et al (2006) Polarity and temporality of high-resolution ychromosome distributions in India identify both indigenous and exogenous expansions and reveal minor genetic influence of Central Asian pastoralists. Am J Hum Genet 78:202–221

    Article  CAS  PubMed  Google Scholar 

  17. Cinnioglu C, King R, Kivisild T, Kalfoglu E et al (2004) Excavating y-chromosome haplotype strata in Anatolia. Hum Genet 114:127–148

    Article  PubMed  Google Scholar 

  18. McAlister FA, Straus SE, Sackett DL (1999) Why we need large, simple studies of the clinical examination: the problem and a proposed solution. Lancet 354:1721–24

    Article  CAS  PubMed  Google Scholar 

  19. Greenhalgh T (1997) How to read a paper: Papers that report diagnostic or screening tests. BMJ 315:540–543

    CAS  PubMed  Google Scholar 

  20. Press WH, Teukolsky SA, Vetterling WT, Flannery BP (1994) Numerical recipes in FORTRAN. The art of scientific computing, 2nd edn. Cambridge University Press

  21. Karafet TM, Mendez FL, Meilerman MB, Underhill PA, Zegura SL, Hammer MF (2008) New binary polimorphisms reshape and increase the resolution of the Human Y chromosomal haplogroup tree. Genome Res 18:830–838

    Article  CAS  PubMed  Google Scholar 

  22. Underhill P, Passarino G, Lin AA, Shen P, Mirazón Lahr M, Foley RA, Oefner PJ, Cavalli-Sforza L (2001) The phylogeography of Y chromosome binary haplotypes and the origins of modern human populations. Anal Hum Genet 65:43–62

    Article  CAS  Google Scholar 

  23. Zalloua PA, Xue Y, Khalife J, Makhoul N, Debiane L, Platt DE, Royyuru AK, Herrera RJ, Soria Hernanz DF, Blue-Smith J, Spencer Wells R, Comas D, Bertranpetit J, Tyler-Smith C, The Genographic Consortium. 2008. Am J Hum Genet. April 2008. Supplementary Data

  24. Di Gaetano C, Cerutti N, Crobu F, Robino C, Inturri S, Gino S, Guarrera S, Underhill PA, King RJ, Romano V, Cali F, Gasparini N, Matullo G, Salerno A, Torre C, Piazza A (2009) Differential Greek and northen African migrations to Sicily are supported by genetic evidence from the Y chromosome. Eur J Hum Gen 17(1):91–99

    Article  Google Scholar 

Download references

Acknowledgments

The authors thank Dr. J.E. Dipierri and E.L. Alfaro for their valuable contribution, Dr. J.C. Muzzio for his help with the uncertainty coefficient calculations, and Dr. A.N. Califano and C.M. Bravi for their suggestions.

Grant sponsorship: CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas), CICPBA (Comisión de Investigaciones Científicas de la Provincia de Buenos Aires), ANPCyT (Agencia Nacional de Promoción Científica y Tecnológica), and Antorchas Foundation of Argentina.

G. Bailliet and J.S. López Camelo are members of the CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas), Argentina.

Author information

Authors and Affiliations

  1. Laboratorio de Genética Molecular Poblacional, Instituto Multidisciplinario de Biología Celular (IMBICE), CICPBA, CCT, La Plata–CONICET, Argentina

    Marina Muzzio, Virginia Ramallo, Josefina M. B. Motti, Maria R. Santos, Jorge S. López Camelo & Graciela Bailliet

  2. Instituto Multidisciplinario de Biología Celular (IMBICE), 526 e/10 y 11, P.O. Box C.C. 403, 1900, La Plata, Argentina

    Marina Muzzio

Authors
  1. Marina Muzzio
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Virginia Ramallo
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Josefina M. B. Motti
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Maria R. Santos
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Jorge S. López Camelo
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Graciela Bailliet
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Marina Muzzio.

Electronic supplementary material

Below is the link to the electronic supplementary material.

ESM Table 3

Profiles with haplotypes and haplogroups used for validation (DOC 259 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Muzzio, M., Ramallo, V., Motti, J.M.B. et al. Software for Y-haplogroup predictions: a word of caution. Int J Legal Med 125, 143–147 (2011). https://doi.org/10.1007/s00414-009-0404-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00414-009-0404-1

Keywords

Search

Navigation