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Improving access to endogenous DNA in ancient bone and teeth

Peter B. Damgaard, Ashot Margaryan, Hannes Schroeder, Ludovic Orlando, Eske Willerslev, Morten E. Allentoft
doi: https://doi.org/10.1101/014985
Peter B. Damgaard
1Centre for GeoGenetics, Natural History Museum, University of Copenhagen
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Ashot Margaryan
1Centre for GeoGenetics, Natural History Museum, University of Copenhagen
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Hannes Schroeder
1Centre for GeoGenetics, Natural History Museum, University of Copenhagen
2Faculty of Archaeology, Leiden University, PO Box 9515, 2300 Leiden, The Netherlands
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Ludovic Orlando
1Centre for GeoGenetics, Natural History Museum, University of Copenhagen
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Eske Willerslev
1Centre for GeoGenetics, Natural History Museum, University of Copenhagen
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Morten E. Allentoft
1Centre for GeoGenetics, Natural History Museum, University of Copenhagen
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  • For correspondence: morten.allentoft@gmail.com
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Abstract

Poor DNA preservation is the most limiting factor in ancient genomic research. In the vast majority of ancient bones and teeth, endogenous DNA molecules only represent a minor fraction of the whole DNA extract, rendering traditional shot-gun sequencing approaches cost-ineffective for whole-genome characterization. Based on ancient human bone samples from temperate and tropical environments, we show that an initial 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 identify the optimal pre-digestion time and document an average increase of 2.7 times in the endogenous DNA fraction after 1 hour of pre-digestion. With longer pre-digestion times, the increase is asymptotic while molecular complexity decreases. We repeated the experiment with n=21 and t=15-30’, and document a significant increase in endogenous DNA content (one-sided paired t-test: p=0.009). We advocate the implementation of a short pre-digestion step as a standard procedure in ancient DNA extractions from bone material. Finally, we demonstrate on 14 ancient teeth that crushed cementum of the roots contains up to 14 times more endogenous DNA than the dentine. Our presented methodological guidelines considerably advance the ability to characterize ancient genomes.

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Posted February 06, 2015.
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Improving access to endogenous DNA in ancient bone and teeth
Peter B. Damgaard, Ashot Margaryan, Hannes Schroeder, Ludovic Orlando, Eske Willerslev, Morten E. Allentoft
bioRxiv 014985; doi: https://doi.org/10.1101/014985
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Improving access to endogenous DNA in ancient bone and teeth
Peter B. Damgaard, Ashot Margaryan, Hannes Schroeder, Ludovic Orlando, Eske Willerslev, Morten E. Allentoft
bioRxiv 014985; doi: https://doi.org/10.1101/014985

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