Optimized DNA sampling of ancient bones using Computed Tomography scans

作者：Federica Alberti, Javier González, Johanna L. A. Paijmans, Nikolas Basler, Michaela Preick, Kirstin Henneberger, Alexandra Trinks, Gernot Rabeder, Nicholas J. Conard, Susanne C. Münzel, Ulrich Joger, Guido Fritsch, Thomas B. Hildebrandt, Michael Hofreiter, Axel Barlow · 发表于：Molecular Ecology Resources · 年份：2018 · DOI：10.1111/1755-0998.12911 · 被引用次数：46 · 研究领域：Forensic and Genetic Research、Molecular Biology Techniques and Applications、Forensic Anthropology and Bioarchaeology Studies

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 contaminat...