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.
References
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
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
Athey WT (2005) Haplogroup prediction from Y-STR values using an allele-frequency approach. J Genet Geneal 1:1–7
Athey WT (2006) Haplogroup prediction from Y-STR values using a Bayesian-allele-frequency approach. J Genet Geneal 2:34–39
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
Mertens G (2007) Y-Haplogroup frequencies in the Flemish population. J Genet Geneal 3(2):19–25
Goff PG, Athey TW (2006) Diagnostic STR values for haplogroup G. J Genet Geneal 2(1):12–17
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
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
YCC (The Y Chromosome Consortium) (2002) A nomenclature system for the tree of Y chromosomal binary haplogroups. Genome Res 12:339–348
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
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
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
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
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
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
Cinnioglu C, King R, Kivisild T, Kalfoglu E et al (2004) Excavating y-chromosome haplotype strata in Anatolia. Hum Genet 114:127–148
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
Greenhalgh T (1997) How to read a paper: Papers that report diagnostic or screening tests. BMJ 315:540–543
Press WH, Teukolsky SA, Vetterling WT, Flannery BP (1994) Numerical recipes in FORTRAN. The art of scientific computing, 2nd edn. Cambridge University Press
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
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
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
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
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
Corresponding author
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
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
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00414-009-0404-1