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Comparison and optimization of protocols and whole-genome capture conditions for ancient DNA samples
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Comparison and optimization of protocols and whole-genome capture conditions for ancient DNA samples.pdf
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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Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License
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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
Journal
BioTechniques
DOI
https://doi.org/10.2144/btn-2023-0107
Collections
Department of Biology, Article
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ACM
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BibTeX
R. Yaka et al., “Comparison and optimization of protocols and whole-genome capture conditions for ancient DNA samples,”
BioTechniques
, vol. 76, no. 5, pp. 216–223, 2024, Accessed: 00, 2024. [Online]. Available: https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85191615455&origin=inward.