Improving the analysis of Y-SNP haplogroups by a single highly informative 16 SNP multiplex PCR-minisequencing assay.

The SNP haplogroups of the Y-chromosome are nonrandomly distributed among human populations. They are used for tracing the phylogeographical history of paternal lineages of male individuals and can be a useful tool for approaching the patrilineal bio-geographic ancestry of unknown forensic evidences. With the aim of facilitating the inference of the principal informative worldwide Y-SNP haplogroups, we have selected the minimum possible number of key Y-SNPs to be amplified in a sensitive single multiplex PCR and detected by minisequencing. This assay, that includes 16 Y-SNPs, was tested for male human specificity, sensitivity, and reproducibility. Its effectiveness was assessed in a set of degraded DNA samples and in a panel of male individuals from different worldwide populations. All these tests demonstrated the convenience of this assay for assigning the major Y haplogroups to forensic evidences by one single PCR-minisequencing reaction.