New forensic DNA profiling techniques for human identification

Abstract

Highly degraded biological samples are commonly encountered in missing persons cases, historical human remains, war graves, mass disasters and various forensic casework. As biological tissue degrades, DNA becomes progressively fragmented and chemical modifications can occur, complicating successful standard short tandem repeat typing. Alternative genotyping strategies such as single nucleotide polymorphism typing and the emergence of massively parallel sequencing to examine ancestry and phenotype SNPs have ushered in a new era of forensic intelligence testing for problematic samples. Despite showing promise, a number of technical concerns still exist for the use of these strategies in forensic investigation. The research presented in this thesis explores, develops and assesses alternative techniques using both traditional and new technologies for the retrieval of forensic intelligence data from highly degraded samples. I develop new techniques for the screening and genotyping of highly degraded DNA and generate a new dataset of ancestry data from an Australian population for use in analysing historical samples. Issues relating to the implementation of these technologies are discussed, including laboratory workflow, data analysis and interpretation, ethics, and the need for standard guidelines for forensic laboratories to adopt in their methodology. Specifically, in this thesis I use: • A SNP typing strategy based on conventional techniques and equipment to develop a screening tool that estimates sample degradation and presumptive broad biological profile for the triage of forensic samples – Chapter 2 • Emerging target enrichment and massively parallel sequencing technologies for the generation of ancestry and phenotype data for forensic investigation – Chapter 3 • Techniques developed and assessed in Chapter 2 and 3 to analyse a set of degraded DNA and forensic casework samples, demonstrating the utility of the methods to genotype and provide forensic intelligence data for challenging samples – Chapter 4 • mtDNA and autosomal SNP analysis to construct the first Australian reference population database for ancestry testing of historical human remains – Chapter 5. In essence, my research aimed to explore techniques to improve the genetic assessment of highly degraded and compromised forensic samples, and to build on current knowledge concerning the implementation of such techniques in forensic investigations.