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

Yaka R., Maja Krzewińska K., Lagerholm V. K., Linderholm A., ÖZER F., SOMEL M., ...More

BioTechniques, vol.76, no.5, pp.216-223, 2024 (SCI-Expanded) identifier identifier identifier

  • Publication Type: Article / Article
  • Volume: 76 Issue: 5
  • Publication Date: 2024
  • Doi Number: 10.2144/btn-2023-0107
  • Journal Name: BioTechniques
  • Journal Indexes: Science Citation Index Expanded (SCI-EXPANDED), Scopus, Aerospace Database, Aquatic Science & Fisheries Abstracts (ASFA), BIOSIS, Biotechnology Research Abstracts, CAB Abstracts, Chemical Abstracts Core, Communication Abstracts, EMBASE, MEDLINE, Metadex, Veterinary Science Database, Directory of Open Access Journals, DIALNET, Civil Engineering Abstracts
  • Page Numbers: pp.216-223
  • Keywords: aDNA library, ancient DNA, DNA extraction, optimization, whole genome capture
  • Middle East Technical University Affiliated: Yes

Abstract

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.