Comparative Assessment of Automated and Manual DNA Extraction Methods for the Genetic Analysis of Degraded Bone Samples

Background: Efficient DNA extraction from degraded skeletal remains is essential for forensic and ancient DNA analysis. The main aim of this study was to compare the performance of an automated DNA extraction system with a manual DNA extraction protocol when applied to challenging skeletal samples. Specifically, the automated Maxwell Forensic Sample Concentrator system was evaluated against a modified manual Dabney extraction protocol. Methods: DNA was extracted from skeletal material originating from twelve human individuals. Maxwell extractions using 50 mg and/or 100 mg of starting material were compared with Dabney extractions using 50 mg. DNA extracts were quantified using SD quants targeting nuclear DNA and two mitochondrial DNA fragments. Selected extracts were further analysed by mitochondrial DNA sequencing. Results: Both extraction approaches generated comparable DNA yields and sequencing results for moderately degraded samples. In the highly degraded samples analysed in this study, the Dabney protocol generally yielded higher nuclear and mitochondrial DNA quantities and was often associated with a higher sequencing performance. The Maxwell system nevertheless performed well for less degraded material and, in some cases, produced sequencing results comparable to Dabney. Maxwell extraction with 100 mg input was effective for better-preserved samples but was less consistent for highly degraded material. Conclusions: The efficiency of the extraction methods depended largely on the degree of DNA degradation. The findings of this study suggest that the Dabney protocol may be more suitable for heavily degraded skeletal remains, whereas the automated Maxwell system represents a practical and efficient option for less degraded samples. The choice of method therefore depends on the sample condition and the analytical objectives.