Comparison and optimization of protocols and whole-genome capture conditions for ancient DNA samples.

Yaka R, Lagerholm VK, Linderholm A, Özer F, Somel M, Götherström A

BioTechniques - (-) - [2024-03-26; online 2024-03-26]

Ancient DNA (aDNA) obtained from human remains is typically fragmented and present in relatively low amounts. Here we investigate a set of optimal methods for producing aDNA data by comparing silica-based DNA extraction and aDNA library preparation protocols. We also test the efficiency of whole-genome enrichment (WGC) on ancient human samples by modifying a number of parameter combinations. We find that the Dabney extraction protocol performs significantly better than alternatives. We further observed a positive trend with the BEST library protocol indicating lower clonality. Notably, our results suggest that WGC is effective at retrieving endogenous DNA, particularly from poorly-preserved human samples, by increasing human endogenous proportions by 5x. Thus, aDNA studies will be most likely to benefit from our results.

NGI Short read [Service]

NGI Stockholm (Genomics Production) [Service]

National Genomics Infrastructure [Service]

PubMed 38530148

DOI 10.2144/btn-2023-0107

Crossref 10.2144/btn-2023-0107

Publications 9.5.0