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Genomics Approaches for Increased Resolution in Forensic Investigations
Abstract
Short tandem repeat (STR) analysis has been the standard approach in forensic genetics for decades. This strategy has been successfully applied to identify perpetrators from crime scene evidence, determine biological relationships, and assist in missing person identifications. However, STR typing can be particularly challenging when analysing low-template or degraded DNA. The advent of massively parallel sequencing (MPS) has expanded the analytical capabilities of forensic genetics by enabling the analysis of various DNA polymorphisms with increased sensitivity. MPS provides complete sequence information from STR loci and allows the examination of additional types of variants, including single nucleotide polymorphisms (SNPs) and microhaplotypes, thereby offering new opportunities for forensic applications. In this thesis, I applied a genomics-based approach using different methodological strategies to analyse challenging forensic samples to generate reliable DNA data. The aim was to evaluate the utility of MPS in forensic genetics and explore alternative analytical strategies for improved DNA recovery. In Paper I, STRs were analysed to generate a quality-assured allele frequency reference database for the Swedish population. Paper II evaluated microhaplotypes, demonstrating robust performance when analysing degraded DNA and complex mixtures. In Paper III, I applied an extended SNP panel (FORCE) in combination with unique molecular indices (UMIs), which improved genotype accuracy and increased sensitivity. Quality-assured genotypes were recovered from casework-like samples, highlighting the potential for distant kinship inference from low-template and degraded material. Paper IV demonstrated that assays targeting large SNP sets and wholegenome datasets can recover extensive and reliable genetic information when analysing DNA samples of limited quantity and challenging quality. In addition, I showed that alternative data interpretation strategies based on genotype likelihoods were highly efficient for obtaining reliable results from sparse sequencing data. Taken together, these studies show that genomics-based MPS strategies can substantially enhance the recovery, accuracy, and interpretability of forensic DNA data. The findings from this thesis provide methodological guidance for integrating MPS in casework to increase the resolution of forensic investigations.
Product Used
Genes
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