Multiplex PCR for the assignment of some major branches of the Y chromosome tree.

Abstract

In this paper we describe a multiplex PCR useful to as-sign some major Y chromosome tree branches (DE, G2, I, J and J2) (for the nomenclature of the Y chromosome tree branches, see YCC 2002). These are prev alent in all Southern European populations, accoun ting between 51% and 77% of the total male population (Di Giacomo et al. 2003 and personal data). The identification of the allelic state at every locus in the study is done either directly (presence/a bsenc e of the specific PCR fragment), or can be simply obtained with further sequential steps of dot-blot hybrid ization with specific probes. In the last years a large number of single nucleotide polymorphic (SNP) binary markers have been identified in the non-recombining portion of the human Y chrom o-some (NRY) (YCC 2002). SNPs are ideal genetic mar k-ers for med ical and population genetic studie s, since they are widespread in the human genome and are easily de-tected by PCR based methods. In general, the SNPs ex-hibit only two, evolutionarily stable, alleles. This ad van t-age is often counterbalanced by the necessity of typing large numbers of them in many individuals. Genotyping for these markers is of great importance in forensics and in association studies. Moreover, since the NRY lacks genetic recombination during meioses, it is a pow erful tool in phylogenetic studies. In order to increase the pro-ductivity of such studies, the first choice will be to study simultaneously more SNPs in a single multiplex PCR reaction. Two papers concerning the use of mult iplex PCR in the study of the human Y chromosome SNP variation have been published recently. One of them uses a mini-sequencing/capillary electrophoresis method for Y chro-mosome typing in forensic studies (Sanchez et al. 2003); the other one uses a primer extension/mass spectroscopy method for high throughput SNP genotyping of the Y chromosome (Paracchini et al. 2002). The method pre-sented here provides a reliable effort-effective, time-effec -tive and cost-effective method for the early stages of human Y chromosome genotyping, being particularly useful when little information or no information at all is available about the genetic structure of the population under study.