title: The Genographic Project public participation mitochondrial DNA database.
abstract: The Genographic Project is studying the genetic signatures of ancient human migrations and creating an open-source research database. It allows members of the public to participate in a real-time anthropological genetics study by submitting personal samples for analysis and donating the genetic results to the database. We report our experience from the first 18 months of public participation in the Genographic Project, during which we have created the largest standardized human mitochondrial DNA (mtDNA) database ever collected, comprising 78,590 genotypes. Here, we detail our genotyping and quality assurance protocols including direct sequencing of the mtDNA HVS-I, genotyping of 22 coding-region SNPs, and a series of computational quality checks based on phylogenetic principles. This database is very informative with respect to mtDNA phylogeny and mutational dynamics, and its size allows us to develop a nearest neighbor-based methodology for mtDNA haplogroup prediction based on HVS-I motifs that is superior to classic rule-based approaches. We make available to the scientific community and general public two new resources: a periodically updated database comprising all data donated by participants, and the nearest neighbor haplogroup prediction tool.
authors.forename: Doron M
authors.initials: DM
authors.lastname: Behar
authors.forename: Saharon
authors.initials: S
authors.lastname: Rosset
authors.forename: Jason
authors.initials: J
authors.lastname: Blue-Smith
authors.forename: Oleg
authors.initials: O
authors.lastname: Balanovsky
authors.forename: Shay
authors.initials: S
authors.lastname: Tzur
authors.forename: David
authors.initials: D
authors.lastname: Comas
authors.forename: R John
authors.initials: RJ
authors.lastname: Mitchell
authors.forename: Lluis
authors.initials: L
authors.lastname: Quintana-Murci
authors.forename: Chris
authors.initials: C
authors.lastname: Tyler-Smith
authors.forename: R Spencer
authors.initials: RS
authors.lastname: Wells
mesh_terms: D004272:DNA, Mitochondrial / Q000235:genetics*; D030561:Databases, Nucleic Acid; D005260:Female; D006801:Humans; D008297:Male; D008928:Mitochondria / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
chemical_list: D004272:DNA, Mitochondrial