DNA Recovery Using Different Extraction Kits and Cotton Swabs in Forensic DNA Analysis

Background: It is essential to recover as much DNA as possible from evidence samples to ensure optimal DNA analysis in forensic casework. However, both DNA collection and purification procedures cause a substantial loss of genetic material. Thus, a large loss of DNA through the pre-PCR procedures, including swabbing and extraction, may significantly affect downstream analysis results. In this study, different cotton swabs and extraction kits used for forensic samples were compared separately. Methods: The recovery of cell-free DNA (control DNA) and cell-bound DNA (blood and saliva) was evaluated using five different extraction kits: Chelex^® 100 Resin, Wizard^® Genomic DNA Purification Kit, QIAamp^® DNA Micro Kit, QIAamp^® DNA Investigator Kit and DNeasy^® Blood & Tissue Kit. The DNA recovery efficiency of the different extraction kits was assessed using real-time quantitative PCR targeting nuclear and mitochondrial DNA targets. In addition, nine cotton swabs from four manufacturers (Selefa^®, Puritan^®, Texwipe^®, and Heinz Herenz) with different production lots were evaluated for DNA quantity and quality using real-time PCR and short tandem repeat (STR) analysis. Results: Overall, large differences in DNA recovery were observed between the different extraction kits. The QIAInvestigator kit demonstrated the highest recovery at low DNA amounts, which is particularly beneficial for minute forensic samples. The swab comparison revealed variations not only in DNA recovery between swab manufacturers but also between lots of the same swab brand, and the DNA quantity was not clearly correlated with downstream DNA profile quality. Conclusions: Our findings emphasise the importance of considering the choice of extraction kit, swab brand and batch-to-batch variation in forensic laboratory procedures, as they may influence DNA recoveries and affect the success rate in forensic casework.