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Reducing microbial and human contamination in DNA extractions from ancient bones and teeth

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Korlević,  Petra
Advanced DNA Sequencing Techniques, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;
The Leipzig School of Human Origins (IMPRS), Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

/persons/resource/persons181053

Gerber,  Tobias       
Single Cell Genomics, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;
The Leipzig School of Human Origins (IMPRS), Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

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Gansauge,  Marie-Theres       
Advanced DNA Sequencing Techniques, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;
The Leipzig School of Human Origins (IMPRS), Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

/persons/resource/persons181056

Hajdinjak,  Mateja       
Advanced DNA Sequencing Techniques, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;
The Leipzig School of Human Origins (IMPRS), Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

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Nagel,  Sarah
Advanced DNA Sequencing Techniques, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

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Ayinuer-Petri,  Aximu
Advanced DNA Sequencing Techniques, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

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Meyer,  Matthias
Advanced DNA Sequencing Techniques, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

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Korlevic_Reducing_Biotechniques_2015.pdf
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Citation

Korlević, P., Gerber, T., Gansauge, M.-T., Hajdinjak, M., Nagel, S., Ayinuer-Petri, A., et al. (2015). Reducing microbial and human contamination in DNA extractions from ancient bones and teeth. BioTechniques, 59(2), 87-93. doi:10.2144/000114320.


Cite as: https://hdl.handle.net/21.11116/0000-0009-4A49-3
Abstract
Although great progress has been made in improving methods for generating DNA sequences from ancient biological samples, many, if not most, samples are still not amenable for analyses due to overwhelming contamination with microbial or modern human DNA. Here we explore different DNA decontamination procedures for ancient bones and teeth for use prior to DNA library preparation and high-throughput sequencing. Two procedures showed promising results: (i) the release of surface-bound DNA by phosphate buffer and (ii) the removal of DNA contamination by sodium hypochlorite treatment. Exposure to phosphate removes on average 64% of the microbial DNA from bone powder but only 37% of the endogenous DNA (from the organism under study), increasing the percentage of informative sequences by a factor of two on average. An average 4.6-fold increase, in one case reaching 24-fold, is achieved by sodium hypochlorite treatment, albeit at the expense of destroying 63% of the endogenous DNA preserved in the bone. While both pretreatment methods described here greatly reduce the cost of genome sequencing from ancient material due to efficient depletion of microbial DNA, we find that the removal of human DNA contamination remains a challenging problem.