Abstract
Ancient DNA samples generally contain a mixture of both endogenous and exogenous (contaminant) DNA. The authentic endogenous DNA content varies widely between samples and substrates but usually constitutes only a small fraction of the total DNA, while the remainder comprises contamination deriving from bacteria, fungi, and other microorganisms and in some cases also modern human DNA. Recently, several protocols have been developed to improve access to the endogenous DNA fraction by decreasing the exogenous fraction prior to extraction. The most common of these involve pretreatment with single or multiple washes with weak sodium phosphate or sodium hypochlorite (bleach) solutions, as described in Chapter 2. Here, we present an alternative, less aggressive pretreatment protocol that uses a brief predigestion step in an EDTA-based lysis buffer to increase the endogenous fraction prior to extraction.
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References
Kemp BM, Smith DG (2005) Use of bleach to eliminate contaminating DNA from the surface of bones and teeth. Forensic Sci Int 154:53–61
Malmström H, Storå J, Dalén L, Holmlund G, Götherström A (2005) Extensive human DNA contamination in extracts from ancient dog bones and teeth. Mol Biol Evol 22:2040–2047
Damgaard PB, Margaryan A, Schroeder H, Orlando L, Willerslev E, Allentoft ME (2015) Improving access to endogenous DNA in ancient bones and teeth. Sci Rep 5:11184
Korlević P, Gerber T, Gansauge M-T, Hajdinjak M, Nagel S, Aximu-Petri A et al (2015) Reducing microbial and human contamination in DNA extractions from ancient bones and teeth. BioTechniques 59:87–93
Boessenkool S, Hanghøj K, Nistelberger HM, Der Sarkissian C, Gondek AT, Orlando L et al (2017) Combining bleach and mild predigestion improves ancient DNA recovery from bones. Mol Ecol Resour 17:742–751
Campos PF, Craig OE, Turner-Walker G, Peacock E, Willerslev E, Gilbert MTP (2012) DNA in ancient bone – where is it located and how should we extract it? Ann Anat 194:7–16
Gamba C, Jones ER, Teasdale MD, McLaughlin RL, Gonzalez-Fortes G, Mattiangeli V et al (2014) Genome flux and stasis in a five millennium transect of European prehistory. Nat Commun 5:5257
Acknowledgments
Centre for GeoGenetics is supported by the Danish National Research Foundation (DNRF94) and the Lundbeck Foundation. HS is supported by the European Research Council (ERC Synergy Project “Nexus1492”; FP7/2007-2013/grant agreement no. 319209) and the HERA JRP “Citigen” through the European Union’s Horizon 2020 research and innovation program under grant agreement no. 649307. MEA is funded by The Villum Foundation (Young Investigator Programme, grant no. 10120).
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Schroeder, H., de Barros Damgaard, P., Allentoft, M.E. (2019). Pretreatment: Improving Endogenous Ancient DNA Yields Using a Simple Enzymatic Predigestion Step. In: Shapiro, B., Barlow, A., Heintzman, P., Hofreiter, M., Paijmans, J., Soares, A. (eds) Ancient DNA. Methods in Molecular Biology, vol 1963. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9176-1_3
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DOI: https://doi.org/10.1007/978-1-4939-9176-1_3
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Online ISBN: 978-1-4939-9176-1
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