Pretreatment: Improving Endogenous Ancient DNA Yields Using a Simple Enzymatic Predigestion Step
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.
Key wordsAncient DNA Pretreatment Contamination EDTA Proteinase K
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).