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

Autor: Yaka R; Centre for Palaeogenetics, Stockholm, Sweden.; Department of Archaeology & Classical Studies, Stockholm University, Stockholm, Sweden.; Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey., Maja Krzewińska; Centre for Palaeogenetics, Stockholm, Sweden.; Department of Archaeology & Classical Studies, Stockholm University, Stockholm, Sweden., Lagerholm VK; Centre for Palaeogenetics, Stockholm, Sweden.; Department of Archaeology & Classical Studies, Stockholm University, Stockholm, Sweden., Linderholm A; Centre for Palaeogenetics, Stockholm, Sweden.; Department of Geological Sciences, Stockholm University, Stockholm, Sweden., Özer F; Department of Anthropology, Hacettepe University, Ankara, Turkey., Somel M; Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey., Götherström A; Centre for Palaeogenetics, Stockholm, Sweden.; Department of Archaeology & Classical Studies, Stockholm University, Stockholm, Sweden.
Jazyk: angličtina
Zdroj: BioTechniques [Biotechniques] 2024 May; Vol. 76 (5), pp. 216-223. Date of Electronic Publication: 2024 Mar 26.
DOI: 10.2144/btn-2023-0107
Abstrakt: 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.
Databáze: MEDLINE
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