The studies in this thesis describe the development of a microarray based minisequencing system and its application to highly parallel genotyping of single nucleotide polymorphisms. The technical developments included identification of a three-dimensional microarray surface coating with high binding capacity for oligonucleotides modified with amino groups as the most optimal one for the system. The system was also established for multiplexed, reproducible quantitative analysis of SNP alleles both on the level of DNA and RNA. The sensitivity of the system to distinguish SNP alleles present as a minority in a mixed sample was found to be 1-6%. The microarray based minisequencing system was applied in a pharmacogenetic study on antihypertensive drug response. A panel of 74 SNPs located in candidate genes related to blood pressure regulation were genotyped in DNA samples from hypertensive patients that had been treated with the antihypertensive drugs irbesartan or atenolol. Multiple regression analysis of the genotype data against the reduction in blood pressure identified genotype combinations of four to five SNPs that explain 44-56% of the reduction in blood pressure in the two treatment groups. The genotypes of two individual SNPs in the angiotensinogen (AGT) gene and a SNP in the low density lipoprotein receptor (LDLR) gene appeared to be associated to reduced blood pressure after treatment with atenolol, while a SNP in the apolipoprotein B (APOB) gene was associated to blood pressure reduction after irbesartan treatment. The genotype of one SNP in the adrenergic alpha-2A-receptor gene (ADRA2A) was related to the reduction in left ventricular mass following atenolol treatment while the genotypes of two SNPs, one in the APOB gene and one in the AGT gene were related to the reduction in left ventricular mass in the patients treated with irbesartan.

<p>The studies in this thesis describe the development of a microarray based minisequencing system and its application to highly parallel genotyping of single nucleotide polymorphisms. The technical developments included identification of a three-dimensional microarray surface coating with high binding capacity for oligonucleotides modified with amino groups as the most optimal one for the system. The system was also established for multiplexed, reproducible quantitative analysis of SNP alleles both on the level of DNA and RNA. The sensitivity of the system to distinguish SNP alleles present as a minority in a mixed sample was found to be 1-6%. </p><p>The microarray based minisequencing system was applied in a pharmacogenetic study on antihypertensive drug response. A panel of 74 SNPs located in candidate genes related to blood pressure regulation were genotyped in DNA samples from hypertensive patients that had been treated with the antihypertensive drugs irbesartan or atenolol. Multiple regression analysis of the genotype data against the reduction in blood pressure identified genotype combinations of four to five SNPs that explain 44-56% of the reduction in blood pressure in the two treatment groups. The genotypes of two individual SNPs in the angiotensinogen (AGT) gene and a SNP in the low density lipoprotein receptor (LDLR) gene appeared to be associated to reduced blood pressure after treatment with atenolol, while a SNP in the apolipoprotein B (APOB) gene was associated to blood pressure reduction after irbesartan treatment. The genotype of one SNP in the adrenergic alpha-2A-receptor gene (ADRA2A) was related to the reduction in left ventricular mass following atenolol treatment while the genotypes of two SNPs, one in the APOB gene and one in the AGT gene were related to the reduction in left ventricular mass in the patients treated with irbesartan.</p>

Duchenne muscular dystrophy is an inherited, X-linked recessive skeletal muscle disorder that is characterized by mutations in the dystrophin gene [1]. Therefore, the disease affects primarily males and women are typically carriers. 1 in 3500 males in the United States are affected [1]. Dystrophin is a critical, large scaffolding protein in the dystrophin-glycoprotein complex found at the sarcolemma of skeletal muscle [1]. The complex helps maintain sarcolemma integrity and stability during muscle contractions by coupling the extracellular matrix proteins to the intracellular cytoskeleton in skeletal muscle [1]. Loss-of-function mutations in the dystrophin protein affect all skeletal muscle found throughout the human body. The 427 kD protein is also present in cardiac muscle, the brain, and peripheral nerves, thus affecting these tissues over time, as well [1]. One theory suggests the weakened stability of the dystrophin-glycoprotein complex when dystrophin is not expressed results in transient membrane tears during contraction, which permit pathological calcium influx [1]. Damaged skeletal muscle results in repair and regeneration of the tissue however, continual damage over time (referred to as muscle wasting) results in extensive fibrosis and loss of muscle fibers. The purpose of this thesis is to provide a comprehensive review on several molecular mechanisms that underlie Duchenne muscular dystrophy and to investigate current treatments and propose potential therapeutic targets for future research.

Chromosomal Instability (CIN) occurs in over 90% of all sporadic tumors and manifests as whole chromosome loss or gain, gene deletions, amplifications, inversion, and translocations. CIN is not only a hallmark of cancer but promotes tumorigenesis. CIN is caused by errors during mitosis and one major CIN-promoting mechanism is centrosome over-duplication (amplification); another cancer hallmark. Centrosome amplification causes abnormal mitotic spindle assembly, directly promoting chromosome mis-segration with consequent aneuploidy and other forms of CIN. Central to controlling centrosome numbers and function are the Polo kinases, including Polo-like kinase 4 (Plk4). Plk4 is a component of centrosomes and recognized as the master-regulator of centrosome function and duplication. Plk4 is a mitotic kinase whose levels increase throughout S-phase and G2 to peak in mitosis. During late mitosis, Plk4 localizes to a spot on parent centrioles, licensing this single site for future daughter centriole assembly. Plk4 activity initiates the hierarchial recruiment of two conserved essential centriole proteins: Ana2, followed by the cartwheel protein Sas6. By analysis in a yeast-2-hybrid screen, we identified several novel interactions of centriole proteins, including the interaction of Ana2 and Plk4. Plk4 phosphorylates Ana2 to both positively and negatively regulate centriole duplication. Our preliminary data suggests that Plk4 recruits Ana2 by phosphorylating a protein on the outer centriole surface, generating a phospho-landing platform, and that this Plk4 target is Sas4 (CPAP in humans). Notably, the Sas4 pattern on centrioles is complex, forming both a ring and an asymmetric spot during mitotic progression. Like Sas4, Ana2 is a Plk4 substrate, and when mixed with purified Ana2, Sas4 stimulates Ana2 hyperphosphorylation in vitro. Thus, Plk4 influences centriole assembly on multiple platforms.

A dissertation submitted to the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, in fulfdment of the requirements for the degree of Doctor of Philosophy / Asthma is a complex syndrome which has a significant inflammatory basis which results from the complex interactions between heterogenous genetic and environmental factors. Although the environmental allergens are fairly well known, little information concerning the genetic differences between atopic and non-atopic individuals is available. Alpha-1 antitrypsin is the archetypal member of the serine proteinase inhibitor or serpin superfamily and the most important proteinase inhibitor in the lung with specificity to neutrophil elastase. Genetic deficiency of the protein is classically associated with early onset emphysema, bronchiecstasis, panniculitis, rheumatoid arthritis and glomerulonephritis. The S(E264V), Z(E342K), Ml (213 Ala) and M2 (R101H) variants of alpha-1 antitrypsin have been implicated in the pathogenesis of asthma. A novel finding was the identification of 2 new variants, the M1E(JOhannesburg) and the M IN(johannesburg) associated with asthma in individuals from South Africa / IT2018

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<p>In Molecular Medicine a wide range of methods are applied to analyze the genome to find genetic predictors of human disease. Apart from predisposing disease, genetic variations may also serve as genetic markers in the search for factors underlying complex diseases. Additionally, they provide a means to distinguish between species, analyze evolutionary relationships and subdivide species into strains. </p><p>The development and improvement of laboratory techniques and computational methods was a spin-off effect of the Human Genome Project. The same techniques for analyzing genomic sequence variations may be used independent of organism or source of DNA or RNA. In this thesis, methods for high-throughput analysis of sequence variations were developed, evaluated and applied. </p><p>The performance of several genotyping assays were investigated prior to genotyping 4000 samples in a co-operative genetic epidemiological study. Sequence variations in the estrogen receptor alpha gene were found to be associated with an increased risk of breast and endometrial cancer in Swedish women.</p><p>Whole genome amplification (WGA) enables large scale genetic analysis of sparse amounts of biobanked DNA samples. The performance of two WGA methods was evaluated using four-color minisequencing on tag-arrays. Our in-house developed assay and “array of arrays” format allow up to 80 samples to be analyzed in parallel on a single microscope slide. Multiple displacement amplification by the Φ29 DNA polymerase gave essentially identical genotyping results as genomic DNA. To facilitate accurate method comparisons, a cluster quality assessment approach was established and applied to assess the performance of four commercially available DNA polymerases in the tag-array minisequencing assay. </p><p>A microarray method for genotyping human group A rotavirus (HRV) was developed and applied to an epidemiological survey of infectious HRV strains in Nicaragua. The method combines specific capture of amplified viral sequences on microarrays with genotype-specific DNA-polymerase mediated extension of capture oligonucleotides with fluorescent dNTPs.</p>