Laboratory Methods

Recovering palaeogenomic data from bones that are thousands of years old can be challenging because the DNA surviving within them may be present in only trace amounts, have advanced degradation, and is typically overwhelmed by high levels of contaminating DNA from the deposition environment. An important part of our work is the development and optimisation of laboratory methods for recovering palaeogenomic data from these challenging samples. This includes the optimisation of hybridisation capture methodologies for ancient DNA (see Paijmans et al. 2016), publication of library protocols (see e.g. Henneberger et al. 2019), and optimisation of ancient DNA sequencing protocols for Illumina platforms (see Paijmans et al. 2018).

CT scan guided bone sampling

One recent project investigated the use of computed tomography (CT) scanning to guide DNA sampling of ancient bones (see Alberti et al 2018). The CT scans revealed that the densest region of ancient long bones is typically the outermost surface layer of the bone. Palaeogenomics researchers (including ourselves) have typically removed this outermost layer since it is assumed to contain excessive contamination relative to internal parts. Working with Prof. Michi Hofreiter’s Group in Potsdam, we decided to investigate the properties of DNA sampled from this dense outermost layer. We found that, for many bones, the outermost in fact contains a higher percentage of endogenous DNA (that is the original DNA from the nuclei of the bone cells, and not from external contaminants) compared to internal bone regions, and may therefore provide the optimal sampling location for many palaeogenomics studies.

CT scan of the cross-section of an ancient longbone (top left) showing the dense outermost layer. We developed a method of sampling this layer (bottom left) by drilling multiple shallow holes and collecting the resulting bone powder. The graph on the right shows that the percentage of endogenous DNA obtained from the outermost layer (blue bars) is generally higher than for internal bone regions (orange and cyan bars). The greatest increase we achieved was a massive 52-fold increase in endogenous DNA! See Alberti et al. 2018

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