ena-STUDY-UNIVERSITY OF POTSDAM-09-03-2018-10:21:12:471-212
Optimized DNA sampling of ancient bones using Computed Tomography (CT) scans
The prevalence of contaminant microbial DNA in ancient bone samples represents the principal limiting factor for paleogenomic studies. Contaminant DNA may comprise more than 99% of DNA molecules obtained from ancient samples, and 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, internal bone regions. This targeted sampling can produce as much as fifty-fold greater endogenous DNA recovery, providing a directly proportional reduction in sequencing costs. The observed increases in endogenous DNA proportion are not associated with any consistent increase in human contamination, nor any reduction in absolute endogenous molecule recovery. 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.
The prevalence of contaminant microbial DNA in ancient bone samples represents the principal limiting factor for paleogenomic studies. Contaminant DNA may comprise more than 99% of DNA molecules obtained from ancient samples, and 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, internal bone regions. This targeted sampling can produce as much as fifty-fold greater endogenous DNA recovery, providing a directly proportional reduction in sequencing costs. The observed increases in endogenous DNA proportion are not associated with any consistent increase in human contamination, nor any reduction in absolute endogenous molecule recovery. 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.