AmericaPlex26: a SNaPshot multiplex system for genotyping the main human mitochondrial founder lineages of the Americas

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dc.contributor.authorCoutinho, A.
dc.contributor.authorValverde, G.
dc.contributor.authorFehren-Schmitz, L.
dc.contributor.authorCooper, A.
dc.contributor.authorBarreto Romero, M.
dc.contributor.authorFlores Espinoza, I.
dc.contributor.authorLlamas, B.
dc.contributor.authorHaak, W.
dc.contributor.editorAchilli, A.
dc.date.issued2014
dc.description.abstractPhylogeographic studies have described a reduced genetic diversity in Native American populations, indicative of one or more bottleneck events during the peopling and prehistory of the Americas. Classical sequencing approaches targeting the mitochondrial diversity have reported the presence of five major haplogroups, namely A, B, C, D and X, whereas the advent of complete mitochondrial genome sequencing has recently refined the number of founder lineages within the given diversity to 15 sub-haplogroups. We developed and optimized a SNaPshot assay to study the mitochondrial diversity in pre-Columbian Native American populations by simultaneous typing of 26 single nucleotide polymorphisms (SNPs) characterising Native American sub-haplogroups. Our assay proved to be highly sensitive with respect to starting concentrations of target DNA and could be applied successfully to a range of ancient human skeletal material from South America from various time periods. The AmericaPlex26 is a powerful assay with enhanced phylogenetic resolution that allows time- and cost-efficient mitochondrial DNA sub-typing from valuable ancient specimens. It can be applied in addition or alternative to standard sequencing of the D-loop region in forensics, ancestry testing, and population studies, or where full-resolution mitochondrial genome sequencing is not feasible.
dc.description.statementofresponsibilityAlexandra Coutinho, Guido Valverde, Lars Fehren-Schmitz, Alan Cooper, Maria Ine, s Barreto Romero, Isabel Flores Espinoza, Bastien Llamas, Wolfgang Haak
dc.identifier.citationPLoS One, 2014; 9(3):e93292-1-e93292-11
dc.identifier.doi10.1371/journal.pone.0093292
dc.identifier.issn1932-6203
dc.identifier.issn1932-6203
dc.identifier.orcidCooper, A. [0000-0002-7738-7851]
dc.identifier.orcidLlamas, B. [0000-0002-5550-9176]
dc.identifier.orcidHaak, W. [0000-0003-2475-2007]
dc.identifier.urihttp://hdl.handle.net/2440/94800
dc.language.isoen
dc.publisherPublic Library of Science
dc.relation.granthttp://purl.org/au-research/grants/arc/DP1095782
dc.rights© 2014 Coutinho et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
dc.source.urihttps://doi.org/10.1371/journal.pone.0093292
dc.subjectHumans
dc.subjectSensitivity and Specificity
dc.subjectGenetics, Medical
dc.subjectPhylogeny
dc.subjectFounder Effect
dc.subjectHaplotypes
dc.subjectPolymorphism, Single Nucleotide
dc.subjectIndians, South American
dc.subjectGenes, Mitochondrial
dc.subjectGenome, Mitochondrial
dc.subjectGenotyping Techniques
dc.subjectMultiplex Polymerase Chain Reaction
dc.titleAmericaPlex26: a SNaPshot multiplex system for genotyping the main human mitochondrial founder lineages of the Americas
dc.typeJournal article
pubs.publication-statusPublished

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