TY - JOUR

T1 - Optimized DNA sampling of ancient bones using Computed Tomography scans

AU - Alberti, Federica

AU - Gonzalez, Javier

AU - Paijmans, Johanna L. A.

AU - Basler, Nikolas

AU - Preick, Michaela

AU - Henneberger, Kirstin

AU - Trinks, Alexandra

AU - Rabeder, Gernot

AU - Conard, Nicholas J.

AU - Münzel, Susanne C.

AU - Joger, Ulrich

AU - Fritsch, Guido

AU - Hildebrandt, Thomas

AU - Hofreiter, Michael

AU - Barlow, Axel

PY - 2018/11/1

Y1 - 2018/11/1

N2 - 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 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.

AB - 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 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.

KW - paleogenetics

KW - ancient DNA

KW - computer tomography

KW - palaeogenomics

KW - petrous bone

U2 - 10.1111/1755-0998.12911

DO - 10.1111/1755-0998.12911

M3 - Erthygl

VL - 18

SP - 1196

EP - 1208

JO - Molecular Ecology Resources

JF - Molecular Ecology Resources

SN - 1755-098X

IS - 6

ER -