Open Access Research

Multiplex single-nucleotide polymorphism typing of the human Y chromosome using TaqMan probes

Begoña Martínez-Cruz1, Janet Ziegle2, Paula Sanz1, Graciela Sotelo1, Roger Anglada3, Stéphanie Plaza3, David Comas1* and the Genographic Consortium

Author Affiliations

1 Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Doctor Aiguader 88, E-08003 Barcelona, Spain

2 Applied Biosystems, Inc., 850 Lincoln Centre Drive, Foster City, CA 94404, USA

3 Genome Facility Core Service, Universitat Pompeu Fabra (UPF), Doctor Aiguader 88, E-08003 Barcelona, Spain

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Investigative Genetics 2011, 2:13  doi:10.1186/2041-2223-2-13

Published: 31 May 2011



The analysis of human Y-chromosome variation in the context of population genetics and forensics requires the genotyping of dozens to hundreds of selected single-nucleotide polymorphisms (SNPs). In the present study, we developed a 121-plex (121 SNPs in a single array) TaqMan array capable of distinguishing most haplogroups and subhaplogroups on the Y-chromosome human phylogeny in Europe.


We present data from 264 samples from several European areas and ethnic groups. The array developed in this study shows >99% accuracy of assignation to the Y human phylogeny (with an average call rate of genotypes >96%).


We have created and evaluated a robust and accurate Y-chromosome multiplex which minimises the possible errors due to mixup when typing the same sample in several independent reactions.