Comparison and optimization of protocols and whole-genome capture conditions for ancient DNA samples.
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Yaka R, Lagerholm VK, Linderholm A, Özer F, Somel M, Götherström A
BioTechniques 76 (5) 216-223 [2024-05-00; 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.
Bioinformatics Support for Computational Resources [Service]
NGI Stockholm (Genomics Production) [Service]
National Genomics Infrastructure [Service]
PubMed 38530148
DOI 10.2144/btn-2023-0107
Crossref 10.2144/btn-2023-0107