Bovine and equine forensic DNA analysis

Abstract

Animal forensic DNA analysis is being used for human criminal investigations (e.g traces from cats and dogs), wildlife management, breeding and food safety. The most common DNA markers used for such forensic casework are short tandem repeats (STR). Rules and guidelines concerning quality assurance (QA) and quality control (QC) have been well established for human forensic STR DNA testing, which is most crucial in order to be able to defend the results from forensic DNA analysis in court. However, for several animal species the current laboratory practices do not meet those rules and guidelines. Consequently, QA and QC in animal genetic forensic analysis are important for laboratories, authorities, suspects, victims, the legal justice system and also for public health. In this thesis forensic STR-based DNA analysis in cattle and horse is further improved and harmonized by standardizing the commonly used STR assays for forensic purposes. The conversion tables of the ISAG to the repeat-based nomenclature system, published in this thesis, allow an unambiguous nomenclature, thereby increasing the forensic usefulness of existing datasets. By carrying out large-scale population studies, the quality and statistical power of these marker sets have been assessed. We elaborate on the general considerations that apply to the validation of forensic analysis of human and animal STR markers and in this context, evaluate our contribution to the validation of cattle and horse forensic typing. We discuss how the same data allow a reconstruction of the phylogeny of breeds, survey the state-of-the-art of forensic analysis for other animal species and finally describe the future prospects of DNA forensic analysis. Although STR is still the favourite type of marker for both human and animal forensic identity and parentage testing, there is an increasing interest in the forensic use of single nucleotide polymorphism (SNP) typing. The use of autosomal SNPs in forensic genetic casework has been widely discussed. Although much effort has been done to implement human SNPs for forensic parentage and identity testing further optimization is still required. In human it is not likely that forensic SNP typing will replace STRs, but used rather as an alternative for challenging samples that defy STR analysis. We envisage that in the near future STRs will remain the favourite type of marker for animal forensic DNA typing. However, other current or future non-forensic applications will require more modern approaches as high-throughput SNP genotyping and genomic sequencing. Ideally, the recommendations concerning forensic genetic investigations are identical for human and non-human DNA, respectively. Thanks to the rapid progress, as described in this thesis for cattle and horse, this is being realized.