Improving access to endogenous DNA in ancient bones and teeth

Peter de Barros Damgaard, Ashot Margaryan, Hannes Schroeder, Ludovic Antoine Alexandre Orlando, Eske Willerslev, Morten Erik Allentoft

    93 Citations (Scopus)
    675 Downloads (Pure)

    Abstract

    Poor DNA preservation is the most limiting factor in ancient genomic research. In the majority of ancient bones and teeth, endogenous DNA molecules represent a minor fraction of the whole DNA extract, rendering shot-gun sequencing inefficient for obtaining genomic data. Based on ancient human bone samples from temperate and tropical environments, we show that an EDTA-based enzymatic 'pre-digestion' of powdered bone increases the proportion of endogenous DNA several fold. By performing the pre-digestion step between 30 min and 6 hours on five bones, we observe an asymptotic increase in endogenous DNA content, with a 2.7-fold average increase reached at 1 hour. We repeat the experiment using a brief pre-digestion (15 or 30 mins) on 21 ancient bones and teeth from a variety of archaeological contexts and observe an improvement in 16 of these. We here advocate the implementation of a brief pre-digestion step as a standard procedure in ancient DNA extractions. Finally, we demonstrate on 14 ancient teeth that by targeting the outer layer of the roots we obtain up to 14 times more endogenous DNA than when using the inner dentine. Our presented methods are likely to increase the proportion of ancient samples that are suitable for genome-scale characterization.

    Original languageEnglish
    Article number11184
    JournalScientific Reports
    Volume5
    Number of pages12
    ISSN2045-2322
    DOIs
    Publication statusPublished - 17 Jun 2015

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