Evaluation of bone preparation approaches using length-based analysis and targeted sequencing for forensic human identification of historic skeletal remains.

Abstract

Advances in DNA technology have significantly enhanced the forensic community's ability to develop genetic profiles from unidentified human skeletal remains. However, sampling requires mechanical grinding of hard tissues before DNA isolation. This processing can compromise genetic profiles, particularly in aged bones. We compared the industry-standard pulverization method with an alternative powder-free preparation involving prolonged demineralization and subsequent slicing of 19th-century cortical bone. Data from DNA quantification, STR genotyping, and targeted SNP sequencing were used to evaluate powdered samples versus demineralized slices from paired human bones. Average human DNA yields for pulverized samples and demineralized slices were 0.032&#x2009;ng and 0.692&#x2009;ng, respectively. Demineralized slices recovered more amplifiable DNA than traditional homogenization methods (p&#x2009;<&#x2009;0.05). No pulverized samples produced STR profiles, whereas demineralized slices from the same bone samples yielded partial profiles. Samples underwent DNA repair, library preparation, and hybridization capture using the FORensic Capture Enrichment (FORCE) panel. Applying low-coverage (1X) analysis of high-throughput sequencing (HTS) data, demineralized slices outperformed those prepared by traditional pulverization methods (p&#x2009;<&#x2009;0.05) and substantially increased the information recovered compared with conventional STR analysis methods. Based on HTS data from pulverized samples, DNA fragment length ranged from 27 to 95&#x2009;bp, and FORCE SNP recovery was 33.23%. In contrast, for demineralized slices, DNA fragment length ranged from 85 to 114&#x2009;bp, and FORCE SNP recovery was 83.24%. The required reagents and equipment are typically available in forensic labs, and the workflow outlined herein significantly increases the success of DNA recovery from challenging skeletal samples.