title: Human mtDNA site-specific variability values can act as haplogroup markers.
abstract: Sequencing of entire human mtDNA genomes has become rapid and efficient, leading to the production of a great number of complete mtDNA sequences from a wide range of human populations. We introduce here a new statistical approach for classifying mtDNA nucleotide sites, simply by comparing the mean simple deviation (MSD) of their specific variability values estimated on continent-specific dataset sequences, without the need for any reference sequence. Excellent correspondence was observed between sites with the highest MSD values and those marking known mtDNA haplogroups. This in turn supports the classification of 81 sites (23 in Africa, eight in Asia, eight in Europe, 34 in Oceania, and eight in America) as novel markers of 47 mtDNA haplogroups not yet identified by phylogeographic studies. Not only does this approach allow refinement of mtDNA phylogeny, an essential requirement also for mitochondrial disease studies, but may greatly facilitate the discrimination of candidate disease-causing mutations from haplogroup-specific polymorphisms in mtDNA sequences of patients affected by mitochondrial disorders.
authors.affiliation: Dipartimento di Biochimica e Biologia Molecolare, Università degli Studi di Bari, Bari, Italy.
authors.forename: Matteo
authors.initials: M
authors.lastname: Accetturo
authors.forename: Monica
authors.initials: M
authors.lastname: Santamaria
authors.forename: Daniela
authors.initials: D
authors.lastname: Lascaro
authors.forename: Francesco
authors.initials: F
authors.lastname: Rubino
authors.forename: Alessandro
authors.initials: A
authors.lastname: Achilli
authors.forename: Antonio
authors.initials: A
authors.lastname: Torroni
authors.forename: Mila
authors.initials: M
authors.lastname: Tommaseo-Ponzetta
authors.forename: Marcella
authors.initials: M
authors.lastname: Attimonelli
mesh_terms: D004252:DNA Mutational Analysis / Q000379:methods*; D004272:DNA, Mitochondrial / Q000737:chemistry* / Q000145:classification; D005819:Genetic Markers; D006239:Haplotypes; D006801:Humans; D010802:Phylogeny; D011110:Polymorphism, Genetic; D044469:Racial Groups / Q000235:genetics
chemical_list: D004272:DNA, Mitochondrial; D005819:Genetic Markers