Crime scene samples often contain low-quantity and low-quality nuclear DNA that limit the applicability of traditional STR based techniques. Some sample types can be suitable for whole genome sequencing though an excess of sensitive personal data may be generated and its use connected to a comparably high cost. Instead, smaller SNP panels may be used for shorter turnaround time, simpler data processing and to a lower cost. Previous studies have demonstrated the successful use of the QIAseq FORCE kit (5 500 SNPs, Qiagen) when analyzing challenging forensic samples, such as degraded bone samples and rootless hair.

Here we compare results obtained with the use of the QIAseq FORCE kit with STR results for two challenging forensic sample types: hair shafts and fired cartridge cases. In order to mimic a true scenario, volunteers were instructed to first handle the cartridges, load and fire a gun whereafter the cases were collected and swabbed for DNA (Jansson et al. 2020). From each volunteer, hair shafts were collected. DNA was extracted from 10 cm hairs with four methods: Loreille et al. 2022 (modified), PrepFiler Express BTA Forensic DNA extraction kit, EZ1 DNA Investigator Kit, and a Chelex-based method. Samples were quantified with qPCR and analyzed with a standard STR kit (PowerPlex Fusion 6C). A subset of the hair and cartridge case samples, displaying low but detectable DNA amounts, was analyzed using the QIAseq FORCE kit, and comparisons were done between the SNP results from the mock crime scene samples and reference samples.
Results show that FORCE analysis, with subsequent bioinformatic processing and probabilistic genotype analysis, gave successful trace vs donor comparisons with high LR values in some cases where STR analyzing failed to provide a useful result. Out of eleven hair shaft samples, two gave a usable STR result (LRs 108-109 to donor). In comparison, FORCE analysis showed association with the donor in nine samples, with LRs ranging from 10^4 to 10^660. For ten cartridge case samples analyzed, no usable STR results were obtained. In contrast, FORCE analysis provided support for association with the donor in four samples (LRs 10^3-10^18).

A few results displayed possible contamination detected with the more sensitive SNP analysis provided with the QIAseq FORCE kit. This raises awareness that DNA results obtained with sequencing must be interpreted with caution.

In summary, our study shows the promising application of SNP analysis using the QIAseq FORCE kit on challenging forensic samples.

Authors

• Arvid H Gynnå (National Forensic Centre, Swedish Police Authority, Sweden)
• Adam Staadig (Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Sweden)
• Ricky Ansell (National Forensic Centre, Swedish Police Authority and Department of Physics, Chemistry and Biology, Linköping University, Sweden)
• Andreas Tillmar (Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine and Department of Biomedical and Clinical Sciences, Faculty of Health Sciences, Linköping University, Sweden)
• Siri Aili Fagerholm (National Forensic Centre, Swedish Police Authority, Sweden)