Dissection of mitochondrial superhaplogroup H using coding region SNPs

Haplogroup H (hg H) includes about 40-50% of the West Eurasian mitochondrial DNA (mtDNA) samples investigated so far. In order to enhance discrimination within this haplogroup we selected 45 coding region SNPs that allow to ascribe samples to the main phylogenetic branches of super hg HV (that embraces hg H) and, in particular, to H sublineages with a much finer resolution than previous studies. SNP selection was carried out using the most up-to-date available literature on population and forensic genetics and extended by means of phylogenetic analysis of complete or coding region genomes (> 430) and control region sequences. A meticulous inspection of the H phylogeny led us to the observation of various but uncharacterized subclades of hg H. The selected SNPs were amplified in two PCR-multiplex reactions and subsequently targeted in three single-base extension multiplex reactions. A total of 2214 West Eurasian samples were screened for hg H specific loci 2706 and 7028, of which 859 fell in hg H and were further subjected to subhaplogroup typing. We observed 35 different subhaplogroups in total, 33 of which were found at frequencies below 5%. This assay can be used as a prescreening tool in forensic casework for rapid discrimination between divergent lineages (very effective for high-volume crime cases) or as discriminatory assay, when identical hg H haplotypes were obtained by control region sequencing.