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

Date

2024-05-01

Author

Yaka, Reyhan
Maja Krzewińska, Krzewinska
Lagerholm, Vendela Kempe
Linderholm, Anna
ÖZER, FÜSUN
Somel, Mehmet
Götherström, Anders

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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.

Subject Keywords

aDNA library, ancient DNA, DNA extraction, optimization, whole genome capture

URI

https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85191615455&origin=inward
https://hdl.handle.net/11511/109658

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Department of Biology, Article