AmericaPlex26: A SNaPshot Multiplex System for Genotyping the Main Human Mitochondrial Founder Lineages of the Americas

Alexandra Coutinho, Guido Valverde, Lars Fehren-Schmitz, Alan Cooper, Maria Barreto Romero, Isabel Flores Espinoza, Bastien Llamas, Wolfgang Haak

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    Abstract

    Phylogeographic 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.

    Original languageEnglish
    Article numbere93292
    Number of pages11
    JournalPLoS One
    Volume9
    Issue number3
    DOIs
    Publication statusPublished - 26 Mar 2014

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    Coutinho, A., Valverde, G., Fehren-Schmitz, L., Cooper, A., Barreto Romero, M., Flores Espinoza, I., Llamas, B., & Haak, W. (2014). AmericaPlex26: A SNaPshot Multiplex System for Genotyping the Main Human Mitochondrial Founder Lineages of the Americas. PLoS One, 9(3), [e93292]. https://doi.org/10.1371/journal.pone.0093292