Dissection of mitochondrial superhaplogroup H using coding region SNPs

Authors

  • Anita Brandstätter,

    1. Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
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  • Antonio Salas,

    1. Unidad de Genética, Instituto de Medicina Legal, Facultad de Medicina, Santiago de Compostela, and Centro Nacional de Genotipado (CeGen), Hospital Clínico Universitario, Galicia, Spain
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  • Harald Niederstätter,

    1. Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
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  • Christoph Gassner,

    1. Central Institute for Blood Transfusion and Immunological Department, General Hospital and University Clinics, Innsbruck, Austria
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  • Angel Carracedo,

    1. Unidad de Genética, Instituto de Medicina Legal, Facultad de Medicina, Santiago de Compostela, and Centro Nacional de Genotipado (CeGen), Hospital Clínico Universitario, Galicia, Spain
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  • Walther Parson Professor

    Corresponding author
    1. Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
    • Institute of Legal Medicine, Innsbruck Medical University, Muellerstrasse 44, A-6020, Innsbruck, Austria Fax: +43-5125072764
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Abstract

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.

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