<p>There is a continuous development of different crop varieties in the crop trade. The cultivated crops tend to be more and more alike which require an effective method for crop identification. Crop type and crop type purity has become a quality measure in crop trade both nationally and internationally. A number of well known quality attributes of interest in the crop trade can be correlated to the specific crop type and therefore it is of great importance to reliably be able to identify different crop varieties. It is well known from the literature that there exist genomic variations at the nucleotide level between different crop varieties and these variations might potentially be useful for automated variety identification.</p><p>This project deals with the crop variety identification area where the possibilities of distinguishing between different wheat varieties are investigated. Experience from performing wheat variety identification at protein level has shown unsatisfactory results and therefore DNA-based techniques are proposed instead. DNA-based techniques are dependent upon the availability of sequence data from the wheat genome and some work has concerned examining the availability of sequence data from wheat. But the focus of the work has been on defining a method for computational detection of single nucleotide variations in ESTs from wheat and to experimentally test that method. Results from these experiments show that the method defined in this project detects polymorphic variations that can be correlated to variety variations</p>

In this dissertation we propose methodology for testing SNP-sets for genetic associations, both for sequencing and genome-wide association studies. Due to the large scale of this kind of data, there is an emphasis on producing methodology that is not only accurate and powerful, but also computationally efficient.

Epithelial sodium channels (ENaC) are located throughout the epithelial lining of the respiratory tract and play a crucial role in ion and fluid homeostasis of the lungs. Increasing ENaC activity through stimulation of β₂-adrenergic receptors has been shown to increase sodium and fluid reabsorption from the airspace to the interstitial space. In cystic fibrosis lung disease there is a hyperabsorption of sodium through ENaC which results in dehydration of the airway surface liquid. Previous work has identified a common functional genetic variant of SCNN1A, the gene encoding the ENaC alpha-subunit. This variant manifests as an alanine to threonine substitution at amino acid 663 (T663), with the T663 variant resulting in a more active channel due to a greater number of channels in the membrane. We sought to determine the influence of the T663 variant on exhaled ions, pulmonary function, and the diffusing capacity of the lungs in healthy subjects as well as in patients with cystic fibrosis. We used exercise, which can increase endogenous epinephrine by up to 1000 fold at peak exercise, and albuterol, an exogenous β₂-adrenergic agonist, to stimulate ENaC activity. In healthy individuals we hypothesized that the T663 variant would be beneficial for lung function due to a greater fluid removal, which could improve gas transfer in a healthy lung. In the CF patients we predicted that the T663 variant would be detrimental to lung function due to an exaggerated absorption of sodium and drying/thickening of the mucus layer in the airways. Measurements of exhaled sodium were made in the healthy subjects at baseline, 30, 60, and 90 minutes post-albuterol administration. Subjects with the A663 variant had higher baseline exhaled sodium and a significant decrease in exhaled sodium by 90 minutes after β₂-adrenergic stimulation with albuterol, suggesting a removal of sodium from the airways. No changes in exhaled sodium were seen in the T663 variant in response to albuterol. In response to exercise the A663 variant had a greater increase in the diffusing capacity of the lung than the T663 variant, possibly due to differences in alveolar sodium and therefore fluid handling. Taken together, these results suggest that healthy humans with the A663 variant can increase ENaC activity in response to β₂-adrenergic stimulation, whereas individuals with the T663 variant have a diminished capacity for increasing ENaC activity in response to β₂-adrenergic stimulation. In CF patients, the T663 variant had significantly lower baseline pulmonary function, weight, and body mass index. In response to exercise, patients with the T663 variant had a greater increase in the diffusing capacity of the lungs, possibly due to purinergic inhibition of ENaC. Finally, we recruited additional CF patients to confirm our pulmonary function findings. Individuals with at least one allele resulting in the T663 variant had significantly lower body mass index, and tended to have lower exhaled chloride and pulmonary function. These results suggest greater dehydration of the lung in CF patients with the T663 variant. Overall, these results may suggest that the T663 variant modifies disease severity in CF, although more work is certainly warranted to confirm this result.

Dysregulation of cellular metabolism is associated with multiple diseases including cancer. Polyamines are organic cations shown to control gene expression at the transcriptional, post-transcriptional, and translational level. The activity of ornithine decarboxylase (ODC), the first enzyme in polyamine synthesis, is associated with normal and neoplastic growth. A single nucleotide polymorphism (SNP, rs2302615, SNP +316 nucleotides 3' of the transcriptional start site) in the ODC1 gene has been found to be both functional and prognostic for risk of colorectal carcinogenesis. A comprehensive investigation of genetic variability in ODC1 gene was performed. We confirmed frequencies of 12 SNPs occurring in participants of a clinical cancer prevention trial. We identified haplotypes accounting for over 90% of the genetic diversity in the ODC1 gene. Mechanistically, we addressed two of them, which account for more than half of the participants in the clinical trial. Two ODC1 intron 1 SNPs, rs2302616 (SNP +263 nucleotides 3' of the transcriptional start site) and rs2302615, were found to be associated with disease processes. Both of them predicted metachronous adenoma and response to agents targeting the polyamine pathway in participants of the clinical trial. The rs2302616 functionally modulate a DNA G-quadruplex structure and predicted the ODC1 rate-limiting product putrescine by genotype. Both SNPs cooperate to modulate ODC1 transcriptional activity involving both a G-quadruplex structure and Sp1 binding site at rs2302616, and rs2302615 flanked MYC-binding E-boxes. Haplotype analysis, using both these SNPs, might provide better discrimination of both disease prognosis and treatment prediction in cancer chemoprevention clinical trials.

Les technologies actuelles permettent d'explorer le génome entier pour identifier des variants génétiques associés à des phénotypes particuliers, notamment de maladies. C'est le rôle de la bioinformatique de répondre à cette problématique. Dans le cadre de cette thèse, un nouvel outil logiciel a été développé qui permet de mesurer avec une bonne précision le nombre de marqueurs génétiques effectivement indépendants correspondant à un ensemble de marqueurs génotypés dans une population donnée. Cet algorithme repose sur la mesure de l'entropie de Shannon contenue au sein de ces marqueurs, ainsi que des niveaux d'information mutuelle calculés sur les paires de SNPs choisis au sein d'une fenêtre de SNPs consécutifs, dont la taille est un paramètre du programme. Il a été montré que ce nombre de marqueurs indépendants devient constant dès que la population est homogène avec une taille suffisante (N > 60 individus) et que l'on utilise une fenêtre assez grande (taille > 100 SNPs). Ce calcul peut avoir de nombreuses applications pour l'exploitation des données.Une analyse génome-entier a été réalisée sur le photo-vieillissement. Elle a porté sur 502 femmes caucasiennes pour lesquelles un grade de photo-vieillissement a été évalué selon une technologie bien établie. Les femmes ont été génotypées sur des puces Illumina OmniOne (1M SNPs), et deux gènes ont été identifiés (STXBP5L et FBX040) associés à un SNP passant le seuil de Bonferroni, dont l'implication dans le photo-vieillissement était jusqu'alors inconnue. De plus, cette association a aussi été retrouvé dans deux autres phénotypes suggérant un mécanisme moléculaire commun possible entre le relâchement cutané et les rides. On n'observe pas de réplication au niveau du critère lentigines, la troisième composante étudiée du photo-vieillissement.Ces travaux sont en cours de publication dans des revues scientifiques internationales à comité de lecture.

Après 25 ans de recherche intensive, aucun vaccin ou traitement définitif contre le SIDA n'existe, et les mécanismes moléculaires de pathogenèse de l'infection VIH-1 ne sont pas clairement élucidés. Les avancées technologiques permettent de comparer des sujets malades avec des sujets contrôles sur tout le génome. Il est ainsi possible d'identifier sans a priori des gènes potentiellement impliqués dans le développement de la maladie avec pour conséquence le développement rationnel de nouvelles stratégies diagnostiques ou thérapeutiques. Durant ma thèse, j'ai réalisé deux études d'association 'génome entier' dans le SIDA, en comparant les 275 non-progresseurs à long terme ou les 85 progresseurs rapides de la cohorte GRIV avec une cohorte de contrôles séronégatifs. J'ai réalisé une troisième analyse en exploitant les données issues de trois études 'génome entier' internationales dont la nôtre (France, Pays-Bas, USA), ciblant plus particulièrement les SNPs de fréquence faible (fréquence de l'allèle mineur, MAF<5%). Ces approches 'génome entier' ont réaffirmé le rôle central du HLA dans la progression vers le SIDA, mais aussi dévoilé de nouveaux gènes candidats très pertinents donnant une nouvelle lumière sur les mécanismes moléculaires de la maladie.

The recent decade has witnessed great advances in microarray and genotyping technologies which allow genome-wide single nucleotide polymorphism (SNP) data to be captured on a single chip. As a consequence, genome-wide association studies require the development of algorithms capable of manipulating ultra-large-scale SNP datasets. Towards this goal, this thesis proposes two SNP selection methods; the first using Independent Component Analysis (ICA) and the second based on a modified version of Fast Orthogonal Search. The first proposed technique, based on ICA, is a filtering technique; it reduces the number of SNPs in a dataset, without the need for any class labels. The second proposed technique, orthogonal search based SNP selection, is a multivariate regression approach; it selects the most informative features in SNP data to accurately model the entire dataset. The proposed methods are evaluated by applying them to publicly available gene SNP datasets, and comparing the accuracies of each method in reconstructing the datasets. In addition, the selection results are compared with those of another SNP selection method based on Principal Component Analysis (PCA), which was also applied to the same datasets. The results demonstrate the ability of orthogonal search to capture a higher amount of information than ICA SNP selection approach, all while using a smaller number of SNPs. Furthermore, SNP reconstruction accuracies using the proposed ICA methodology demonstrated the ability to summarize a greater or equivalent amount of information in comparison with the amount of information captured by the PCA-based technique reported in the literature. The execution time of the second developed methodology, mFOS, has paved the way for its application to large-scale genome wide datasets. / Thesis (Master, Computing) -- Queen's University, 2010-12-15 18:03:00.208

No description available.

<p>Initially, a pilot study was carried out in order to reconstruct the major paternal and maternal lineages of the Muslim population living in the Cape metropolitan area. The Study has shown the ability of molecular genetic tools to give insight into the origins and history of local communities. The study was also used as a point of reference for the Strand Muslim Community project. Genetic variations of the Y-chromosome and mitochondrial DNA for the pilot study were analyzed using the RFLP technique. The SNaPshot mini-sequencing technique was used to genotype single nucleotide polymorphisms (SNP) on the Y-chromosome and mitochondrial DNA in 115 males from the Strand Muslim community.</p>

Le neuroblastome (NB) représente 8% de tous les cancers pédiatriques et est caractérisé par sa grande hétérogénéité clinique. Afin d’évaluer son pronostic, plusieurs facteurs génétiques sont utilisés : amplification de MYCN, délétion 1p, gain 11q et gain 17q. Les buts de notre travail étaient d’abord de vérifier si l’hybridation in situ en fluorescence (FISH) permet une analyse complète de ces anomalies et ensuite, en utilisant une analyse globale du génome telle le polymorphisme nucléotidique simple (SNP), de vérifier la concordance avec les résultats de la FISH et le pronostic potentiel des anomalies du 14q, en particulier du gène AKT. Nous avons donc établi un panel de sondes pour la FISH qui a été appliqué sur 16 tumeurs non-fixées. Après isolation de l’ADN de 36 tumeurs, nous avons effectué une analyse génotypique par SNP utilisant les puces « Affymetrix Genome-Wide Human SNP Array 6.0 » contenant 945,826 sondes non polymorphiques et 906,000 sondes polymorphiques. Nos résultats ont démontré que la FISH permet l’évaluation complète des anomalies génétiques importantes du NB et que les anomalies déséquilibrées sont détectées très précisément par SNP. Les anomalies du 14q tendent à être associées avec des facteurs cliniques comme le grade et l’évolution, contrairement aux anomalies d’AKT. L’analyse du 14q a révélé trois gènes d’intérêt, MAX, BCL11B et GPHN, qui devraient être analysés sur un plus grand échantillon. Ainsi, l’étude par FISH semble adaptée pour détecter les anomalies génétiques classiques du NB, alors que celles retrouvées en 14q représentent de potentielles cibles thérapeutiques pour cette tumeur. / Neuroblastoma (NB) accounts for 8% of all childhood cancers and is characterized by its clinical heterogeneity. To evaluate its prognostic, many genetic markers are used: MYCN amplification, 1p deletion, 11q gain and 17q gain. Our goals were first to verify if fluorescence in situ hybridization (FISH) allows a complete analysis of these abnormalities and, second, using a global genomic analysis as single nucleotide polymorphism (SNP), to verify the concordance with FISH results and the prognostic potential of 14q abnormalities, especially these of AKT gene. We then established a FISH panel that has been applied on 16 unfixed tumors. After DNA isolation of 36 tumors, we made a genotypic analysis by SNP using « Affymetrix Genome-Wide Human SNP Array 6.0 » containing 945,826 nonpolymorphic probes and 906,000 polymorphic probes. Our results have demonstrated that FISH allows a complete evaluation of the NB’s important genetic abnormalities and that unbalanced abnormalities are detected very precisely by SNP. 14q abnormalities seem to be associated with clinical factors such as tumor grading and evolution, unlike AKT abnormalities. Analysis of 14q abnormalities revealed three genes of interest, MAX, BCL11B and GPHN, which should be analyzed on a larger sample. Thereby, FISH study seems appropriate to detect the NB’s classic genetic abnormalities, while those found in 14q represent potential therapeutic targets for this tumor.