Investigating the use of the MiSeq FGxTM platform for highly degraded DNA samples for the identification of human remains

Abstract

Forensic mortuaries in South Africa and worldwide are faced with the ever-increasing challenge of managing unidentified bodies. Unidentified human remains pose a serious burden on society and governing bodies. The state’s Forensic Pathology Services are straining under an ever-increasing caseload, which includes bodies that are decomposed, burnt, or skeletonised. The loss of physical features and fingerprints makes identifying these individuals particularly difficult. The financial burden on government is also felt since the storage and subsequent disposal takes up space and incurs costs. Therefore, better methods in identifying these individuals is required to ensure unknown bodies are restored to their families, to improve service delivery, and to reduce financial burdens felt by the Western Cape Government. This multi-phased project aims to improve methods of identification human identification using DNA analysis in the context of bodies which are no longer physically recognisable (Ethics approval ref: 222/2019). Consequently, the project focused on samples such as teeth and nails, which are more resistant to decomposition than soft tissues. However, due to these properties, obtaining usable DNA from hard tissue is particularly challenging. This CHEC-funded project focused on the first phase of this larger study, which aimed to optimise DNA extraction methods from control teeth (n=52) and nails (n=25). The standard DNA extraction method (QIAamp DNA Investigator kit), currently used by the South African Police Service, was initially tested to generate baseline results. Adjustments were made to this baseline method which significantly improved DNA recovery and integrity for both sample types. Additionally, the phenol chloroform method was assessed on teeth, which improved DNA recovery but not DNA profiling success. The respective modified QIAamp DNA Investigator methods were partially successful on forensic casework teeth and consistently successful on nails from deceased individuals. These protocols have been translated into standard operating procedures which will be included in the internal validation study scheduled for 2020. Further work is required to optimise DNA extraction from bone, as well as to investigate next generation sequencing methods to generate DNA profiles on highly degraded forensic samples (e.g. bone and teeth) which are typically encountered in skeletonised human remains. The outcomes of this ongoing project have the potential to addresses capacity and quality aspects of service delivery of the Forensic Pathology Services in the local Cape Town by improving methods of identification. This will, in turn, help address the burden communities feel when loved ones go missing and their bodies remain unidentified and never returned to them. This project was aligned with the outcomes stipulated in PSG3.