A thesis submitted to the Faculty of Medicine, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of Doctor of Philosophy / Two classes of hypervariable loci, VNTRs and (CA)n repeats, represent a rich source of highly polymorphic markers in the human genome. The main objective of this study was to assess their usefulness in elucidating the relationships between 17 southern African populations and to assess the feasibility of paternity testing using these hypervariable markers in the local context. / WHSLYP2017

Thesis (Ph. D.)--Ohio State University, 2002. / Title from first page of PDF file. Document formatted into pages; contains xi, 115 p.: ill. Includes abstract and vita. Advisor: Shili Lin, Dept. of Statistics. Includes bibliographical references (p. 106-115).

Diss. (sammanfattning) Uppsala : Uppsala universitet, 2005. / Härtill 4 uppsatser.

Thesis (Ph.D.). / Written for the Dept. of Anatomy and Cell biology. Title from title page of PDF (viewed 2008/05/09). Includes bibliographical references.

Thesis (doctoral)--Lund University, 1998. / Added t.p. with thesis statement inserted.

Thesis (doctoral)--Lund University, 1998. / Added t.p. with thesis statement inserted.

This document only includes an excerpt of the corresponding thesis or dissertation. To request a digital scan of the full text, please contact the Ruth Lilly Medical Library's Interlibrary Loan Department (rlmlill@iu.edu).

Single nucleotide polymorphisms (SNPs) have great potential to serve as important biomarkers in the clinic to identify those at increased risk for developing cancer, progressing more rapidly, and not responding to therapies. However, the clinical application of cancer-associated SNPs has proven to be more complicated than expected. One of the necessary steps will certainly be the description of the molecular and cellular mechanisms behind the observed associations. The p53 tumour suppressor pathway harbours well-described SNPs that affect p53 signalling and cancer. The aim of the work presented in this thesis was to utilise this knowledge to more efficiently characterise cancer-associated SNPs. Firstly, cancer-associated SNPs in a p53 network gene, CD44, were studied. Specifically, based on CD44’s known roles in both p53-dependent and independent signalling, it was predicted that the cancer-associated SNPs could function as biomarkers for chronic lymphocytic leukaemia progression, and for the response to anti-EGFR therapy for colorectal cancer. Indeed, supportive data is presented. Next, a methodology is presented that aims to identify cancer-associated SNPs in functional p53 binding sites using genome-wide datasets. Interestingly, a SNP is identified that dramatically influences the ability of p53 to regulate transcription of the KITLG oncogene and that associates with one of the largest risks of cancer identified to date. Intriguingly, the SNP is also shown to have undergone positive selection throughout human evolution, signifying a selective advantage, but similar SNPs are demonstrated to be rare in the genome due to negative selection, indicating that polymorphisms in p53 binding sites have been primarily detrimental to humans. Lastly, and in order to begin to explore if other polymorphic transcription factor binding motifs could be found in cancer-associated SNPs, a methodology was designed to identify SNPs in E-box transcription factor binding motifs, as they are sensitive to single base pair changes and affect cancer. Taken together, the work presented in this thesis shows how the study of how SNPs associate with, and impact upon, cancer has great potential to improve both biological knowledge and clinical outcomes.

The chromosome constitution of human cleavage stage embryos has been extensively investi-gated using a variety of techniques, revealing high levels of aneuploidy and mosaicism. However, the final phase of preimplantation development, the blastocyst stage has received relatively little attention mostly because it is only recently that embryo culture has become sufficiently well optimised to reliabley generate blastocysts. One of the aims of this study was to examine blastocyst cytogenetics, characterising the extent and variety of aneuploidy and, where possible, determining the origin of the abnormalities detected. Both the frequency of aneuploidy and the incidence of mosaicism were significantly lower in the 52 embryos generated by 20 patients that had successfully undergone the first cellular differentiation, producing trophectoderm (TE) and inner cell mass (ICM). Valuable tools for the detailed chromosomal analysis of blastocysts, used in both research and clinical contexts, were comparative genomic hybridization (CGH) and array CGH (aCGH). However, validation of these methods, especially aCGH, was required in order to verify accuracy. A low error rate and a low misdiagnosis risk were demonstrated. The morphology of 1397 embryos at the cleavage and blastocyst stages from 229 patients was evaluated in relation to their chromosomal complement. The results obtained during this part of the project showed that, in general, there is little correlation between cleavage stage morphology and chromosome status. A weak link between morphology and aneuploidy, however, was found for embryos at the blastocyst stage. Chromosomally normal female embryos had a tendency to grow faster than male embryos at the cleavage stage and therefore tended to achieve superior morphological scores, whereas the trend was reversed at the blastocyst stage. Abnormal embryos carrying types of aneuploidy compatible with formation of a clinically recognised pregnancy had morphologies indistinguishable from those of euploid embryos. This study also aimed to utilise aCGH for the preimplantation genetic diagnosis (PGD) of imbal-ances due to structural chromosome rearrangements (e.g. translocations) in 39 carriers, a total of 139 embryos were assessed. The data obtained revealed that carriers of Robertsonian translocations are at increased risk of aneuploidy affecting additional chromosomes not involved the translocation, a phenomenon known as an interchromosomal effect (ICE). Finally, the clinical outcomes of 300 patients undergoing preimplantation genetic screening (PGS) using aCGH, for various different indications, were evaluated at both the cleavage (795 embryos) and blastocyst stages (1097 embryos). The pregnancy rate following cleavage stage biopsy was significantly lower than following blastocyst stage biopsy. The miscarriage rate was significantly reduced following PGS for patients with recurrent miscarriages. This work provided promising data supporting the clinical use of comprehensive chromosome analysis for the screening or diagnosis of preimplantation embryos and also yielded scientifically useful information concerning the frequency and nature of aneuploidy at the final stage of development before implantation.

Neurological diseases are devastating illnesses that affect over one billion people worldwide. Drosophila melanogaster provides a genetically tractable system in which to study gene function and the mechanisms of pathogenesis of neurological diseases. In this study I have investigated the function of survival motor neuron (SMN), the causative gene in the neuromuscular disease spinal muscular atrophy (SMA), in growth and differentiation in Drosophila. In addition, I have used the fruit fly to investigate a putative modifier of a previously characterised Drosophila model of Parkinson's disease. Spinal muscular atrophy is an autosomal recessive neurological disease that is characterised by motor neuron loss resulting in muscle weakness. The disease is caused by the deletion or mutation of the survival motor neuron (SMN) gene. In Drosophila, SMN was found to be highly expressed in dividing tissues and a reduction in SMN levels resulted in growth defects, stem cell defects and developmental delay. SMN was also shown to regulate chromosome morphology of the endocycling nurse cells of the female germline. Therefore it appears that SMN has a role in growth control and development in Drosophila. Parkinson's disease is a common disorder that results in widespread neurodegeneration with a predilection for dopaminergic neuron loss resulting in movement defects. A defining neuropathological feature of the disease is the presence of alpha-synuclein containing inclusions. Using a Drosophila model of PD, I have shown that specific alpha-synuclein-induced phenotypes in the fly can be suppressed by the overexpression of the E3 ubiquitin ligase, Nedd4.