Effect of X-ray irradiation on ancient DNA in sub-fossil bones – Guidelines for safe X-ray imaging

Abstract

Sub-fossilised remains may still contain highly degraded ancient DNA (aDNA) useful for palaeogenetic investigations. Whether X-ray computed [micro-] tomography ([µ]CT) imaging of these fossils may further damage aDNA remains debated. Although the effect of X-ray on DNA in living organisms is well documented, its impact on aDNA molecules is unexplored. Here we investigate the effects of synchrotron X-ray irradiation on aDNA from Pleistocene bones. A clear correlation appears between decreasing aDNA quantities and accumulating X-ray dose-levels above 2000 Gray (Gy). We further find that strong X-ray irradiation reduces the amount of nucleotide misincorporations at the aDNA molecule ends. No representative effect can be detected for doses below 200 Gy. Dosimetry shows that conventional μ CT usually does not reach the risky dose level, while classical synchrotron imaging can degrade aDNA significantly. Optimised synchrotron protocols and simple rules introduced here are sufficient to ensure that fossils can be scanned without impairing future aDNA studies.

Quantifying the impact of µCT‐scanning of human fossil teeth on ESR age results

“…This may actually be the main source of difference between the two studies, as our results show that the dose absorbed by the enamel is about eight times lower when using a metallic filter (Table ). This is consistent with previous observations by Immel et al () (see Figure 8 of their work): these authors indicate that for a given device and configuration the use of a filter may divide the dose absorbed by the enamel by a factor of >6.…”

“…The experimental results illustrate the variability of dose that may be given to tooth enamel during μCT‐scan analyses. As expected, dose values are clearly parameter dependent, which makes comparisons with previous studies by Grün, Athreya, et al (), Grün, Mahat, et al () and Immel et al () not so straightforward. Following a somewhat similar methodology to that of the present work, Grün, Athreya, et al () nevertheless estimated the dose values given by CT‐scanning to be between 250 and 420 Gy, that is, more than 10 times higher than our estimates.…”

“…The average X‐ray dose absorbed by the volume of each fragment is thus expressed in terms of gamma equivalent dose ( D E ). This methodology is similar to that employed by Grün, Athreya, et al (), while the dosimetry evaluation in Immel et al () was obtained with a dosimeter equipped with a ionization chamber producing water surface equivalent X‐ray dose estimates.…”

“…However, although noninvasive, X‐ray irradiation may nevertheless impact the fossil remains at different levels. For example, Immel et al () recently assessed whether µCT‐scan analysis could damage ancient DNA remains in fossil bones. Their results showed that no significant effect could be detected for doses below 200 Gy, a level that most conventional μCT instruments usually do not reach.…”

“…If confirmed, such values may simply preclude any further ESR dating of remains that have been previously µCT‐scanned. However, it is also known that many sources of uncertainties may impact, to a greater or lesser extent, the magnitude of this laboratory dose: it may strongly vary (by a factor of >300 according to Figures 7 and 8 from Immel et al, ) depending on the device used, the characteristic of the X‐ray source or the acquisition parameters, such as the scanning time, the position of the tooth with respect to the X‐ray source, or even the nature of the sample holder (e. g., Grün, Mahat, & Joannes‐Boyau, ).…”