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Thesis (M.Sc.(Med.) (Bioethics and Health Law))--University of the Witwatersrand, Faculty of Health Sciences, 2014. / With the completion of the Human Genome project, advances in bioinformatics, computational biology and scientific techniques, human genetic research has established itself as a leading focus of study for many involved in the biological research world. However with all forms of research comes the relevant ethical procedure to guide these studies. Human genetic studies are especially intricate in their ethics evaluations as not only do they require biological material to be obtained from an individual or group of individuals but it in turns gives a researcher access to one’s own personal genetic code, i.e. DNA sequence. Such information has become extremely useful in identifying predispositions and causative factors for certain diseases, identifying possible phenotypic traits, clues into one’s ancestry as well as the overall potential for commercial gain by pharmaceutical companies in drug and gene therapy research and development through acts of gene patenting. Thus with the biological world completely open to exploitation, the need for various control regulations and guidelines to be further developed to address these issues persists. The main questions addressed in studies such as these are those of ownership - who does the sample belong to - access and benefit sharing should any product be developed from information gathered from these samples, consent for use of these samples outside its intended purpose as well as protection of vulnerable groups for unique genetics studies. There are four main sections in this report. First the concepts of Genomic Sovereignty and Common heritage are discussed. Following this, some philosophical theories of ownership are investigated to provide justification toward the concept of ownership with regard to the human body and international bioethical guidelines are then discussed with regard to research involving samples of human genetic material from population groups. The third section is an analysis of the law with regard to ownership, patenting and benefit sharing from research using human genetic material. The fourth section synthesizes the information of the previous 3 sections to produce an alternate approach in dealing with research involving human genetic material from population groups.

The potential phenotypic effects of synonymous SNPs (sSNPs) have long been overlooked. Although several sSNPs are no longer thought to be silent, no one has identified which sSNPs may contribute to phenotypic variation on a genome-wide scale. sSNPs that cause a change in codon-usage frequency or mRNA secondary structures may alter translational and protein folding kinetics. In addition, sSNPs that alter splice-site consensus sequences may cause aberrant slicing, which could change the protein product. A sSNP that contributes to any of these molecular mechanisms may thus alter protein structure and function. To computationally identify sSNPs with a potential impact, SynSNP was created. SynSNP is a text-based tool written in Python. All sSNPs published within dbSNP are first identified. SynSNP uses established bioinformatics tools to determine which of the sSNPs may potentially result in a molecular effect. The potentially functional sSNPs are then assessed to determine whether any have previously been associated with a trait or disease in genome-wide association studies (GWAS) and/or occur within genes known to be associated with disease in OMIM (Online Mendelian Inheritance in Man). Of the 90,102 identified sSNPs, 21,086 (23.4%) were predicted to potentially have a functional impact, through one or more of the three molecular mechanisms investigated. Of the sSNPs predicted to potentially have a functional impact, 14 (0.07%) had previously been associated with a trait or disease in GWAS. A subset of 4,057 (19.2%) of the potentially functional sSNPs were within genes known to be associated with disease in OMIM. Only six (0.03%) of the potentially functional sSNPs had previously been associated with a trait or disease in GWAS and occurred within genes known to be associated with disease in OMIM. SynSNP could be developed further to aid the discovery of more sSNPs with a potential functional impact. A significant proportion of sSNPs may have a functional impact and their potential role in disease should therefore not be underestimated or neglected.