Optimized DNA sampling of ancient bones using computed tomography scans

Alberti, F., Gonzalez, J., Paijmans, J.L.A., Basler, N., Preick, M., Henneberger, K., Trinks, A., Rabeder, G., Conard, N.J., Münzel, S.C., Joger, U., Fritsch, G., Hildebrandt, T., Hofreiter, M. and Barlow, A. ORCID: 0000-0002-5532-9458, 2018. Optimized DNA sampling of ancient bones using computed tomography scans. Molecular Ecology Resources, 18 (6), pp. 1196-1208. ISSN 1755-098X

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Abstract

The prevalence of contaminant microbial DNA in ancient bone samples represents the principal limiting factor for palaeogenomic studies, as it may comprise more than 99% of DNA molecules obtained. Efforts to exclude or reduce this contaminant fraction have been numerous but also variable in their success. Here, we present a simple but highly effective method to increase the relative proportion of endogenous molecules obtained from ancient bones. Using computed tomography (CT) scanning, we identify the densest region of a bone as optimal for sampling. This approach accurately identifies the densest internal regions of petrous bones, which are known to be a source of high‐purity ancient DNA. For ancient long bones, CT scans reveal a high‐density outermost layer, which has been routinely removed and discarded prior to DNA extraction. For almost all long bones investigated, we find that targeted sampling of this outermost layer provides an increase in endogenous DNA content over that obtained from softer, trabecular bone. This targeted sampling can produce as much as 50‐fold increase in the proportion of endogenous DNA, providing a directly proportional reduction in sequencing costs for shotgun sequencing experiments. The observed increases in endogenous DNA proportion are not associated with any reduction in absolute endogenous molecule recovery. Although sampling the outermost layer can result in higher levels of human contamination, some bones were found to have more contamination associated with the internal bone structures. Our method is highly consistent, reproducible and applicable across a wide range of bone types, ages and species. We predict that this discovery will greatly extend the potential to study ancient populations and species in the genomics era.

Item Type: Journal article
Publication Title: Molecular Ecology Resources
Creators: Alberti, F., Gonzalez, J., Paijmans, J.L.A., Basler, N., Preick, M., Henneberger, K., Trinks, A., Rabeder, G., Conard, N.J., Münzel, S.C., Joger, U., Fritsch, G., Hildebrandt, T., Hofreiter, M. and Barlow, A.
Publisher: Wiley-Blackwell
Date: November 2018
Volume: 18
Number: 6
ISSN: 1755-098X
Identifiers:
NumberType
10.1111/1755-0998.12911DOI
1234227Other
Divisions: Schools > School of Science and Technology
Depositing User: Jonathan Gallacher
Date Added: 14 Nov 2019 11:49
Last Modified: 14 Nov 2019 11:49
URI: http://irep.ntu.ac.uk/id/eprint/38278

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