A comparison of five DNA extraction methods from degraded human skeletal remains

• Published in: Forensic science international 2023-07, Vol.348, p.111730-111730, Article 111730
• Main Authors: Haarkötter, Christian, Gálvez, Xiomara, Vinueza-Espinosa, Diana C., Medina-Lozano, María Isabel, Saiz, María, Lorente, José Antonio, Álvarez, Juan Carlos
• Format: Article
• Language: English
• Subjects: Acids; Adsorption; Alcohol; Automation; Body Remains; Bones; Chloroform; Degradation; Degraded DNA; Deoxyribonucleic acid; DNA; DNA extraction; DNA Fingerprinting - methods; Ethanol; Femur; Fluorescence; Forensic science; Forensic sciences; Genetics; Human remains; Humans; Humerus; Isopentyl alcohol; Laboratories; Male; Methods; Microsatellite Repeats; Nucleic acids; Parameters; Phenol; Phenols; Protocol; Silica; Silicon Dioxide; Skeletal remains; Stochasticity; STR typing; Tibia; Ulna; War
• ISSN: 0379-0738; 1872-6283
• DOI: 10.1016/j.forsciint.2023.111730

Extracting DNA from degraded human remains poses a challenge for any forensic genetics laboratory, as it requires efficient high-throughput methods. While little research has compared different techniques, silica in suspension has been identified in the literature as the best method for recovering small fragments, which are often present in these types of samples. In this study, we tested five DNA extraction protocols on 25 different degraded skeletal remains. Including the humerus, ulna, tibia, femur, and petrous bone. The five protocols were organic extraction by phenol/chloroform/isoamyl alcohol, silica in suspension, High Pure Nucleic Acid Large Volume silica columns (Roche), InnoXtract™ Bone (InnoGenomics), and PrepFiler™ BTA with AutoMate™ Express robot (ThermoFisher). We analysed five DNA quantification parameters (small human target quantity, large human target quantity, human male target quantity, degradation index, and internal PCR control threshold), and five DNA profile parameters (number of alleles with peak height higher than analytic and stochastic threshold, average relative fluorescence units (RFU), heterozygous balance, and number of reportable loci) were analysed. Our results suggest that organic extraction by phenol/chloroform/isoamyl alcohol was the best performing method in terms of both quantification and DNA profile results. However, Roche silica columns were found to be the most efficient method. [Display omitted] •Five DNA extraction methods are tested each of them with 25 critical skeletal remain samples.•Organic extraction achieved the highest DNA quantification values and the most informative profiles.•After data normalization, InnoXtract™ Bone (DNA yield) and silica in column (profiles) outperformed the other protocols.•Our in-house automated DNA extraction protocol achieved good results.