The analysis of single nucleotide polymorphisms (SNPs), located within the non recombining region of the Y chromosome (NRY), has been widely accepted in molecular anthropology as a unique tool for evolutionary studies. The low mutation rate and specific distribution of Y-haplogroups in populations, allow for the reconstruction of origin, evolution, and history of groups of humans by tracing male patterns of migration backwards from modern human populations [1]. Y-single nucleotide polymorphisms also constitute forensic tools because they can significantly contribute to forensic analysis by providing information on the ethnic origin of a male DNA sample [2]. Combined with conventional markers, they could be a powerful tool in mass disasters where people from various geographical areas are involved. Recently, Y-SNP typing has been applied in the study of possible association of Y-haplogroups with male-specific (spermatogenic failure, testes and prostate cancer) and prevalently male-associated (hypertension, autism) diseases [3].

The Y Chromosome Consortium has published a single most parsimonious phylogeny of 153 binary haplogroups based on 243 binary markers and developed a simple set of rules to label unambiguously the different clades nested within this tree [4]. An extensively revised Y chromosome tree containing 311 distinct haplogroups, incorporating approximately 600 binary markers has also been published [5] and a web-based document with a regularly updated version of the Y chromosome tree has also become available [6].

In recent years, many different SNP typing techniques have been developed on the basis of various methods of allelic discrimination and detection platforms [7]. Most of these are based on allele specific hybridization, primer extension, oligonucleotide ligation or invasive cleavage. Detection methods for the products of each type of reaction, include fluorescence, luminescence and mass measurement. We selected the SNaPshot minisequencing approach which consists of single base extension of an unlabeled primer that anneals one base upstream to the relevant SNP. A multiplex minisequencing assay has already been validated for genotyping of the Y chromosome [8,9]. These studies have shown this SNP typing methodology to be robust, reliable and extremely sensitive. We have used a rapid, simple