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Theses

IDADIGE : Procédé de traitement des images de gels d'électrophorèse bidimensionnelle différentielle dans le contexte de la recherche de marqueurs protéiques.

Abstract : This thesis is part of the NODDICCAP project that was initiated by bioMérieux (France) with the aim of developing new tools for screening, diagnosis and evaluation of colorectal cancer prognosis using proteomic tools. The development of these new tools requires the identification of biomarkers that are discriminatory and specific for colorectal cancer. The aim of this work was to optimise images and datas analyses methods, for the identification of colorectal cancer biomarkers by the use of Differential In-Gel Electrophoresis, a variant of bi-dimensional gel electrophoresis. Initially areas for improvement in the traditional methods of 2-D gel electrophoresis image treatment were identified. This led us to reconsider the strategy, and to seek innovative methods for image and data treatment, or to adapt methods issued from closely related research areas. Method selection was guided by the constraints linked to the biological and technological context, as well as the evaluation of their effectiveness when compared to the methods usually used. The main advances gained from this work are the definition of the experimental set up, the strategic approach for image analysis, and the statistical interpretation of data. The choice of a standard cell line allowed better comparison of data between experiments. The strategic analysis of image analysis was improved by the use of a unique detection template. The creation of this template was performed by using a novel method of image merging that enabled accurate representation of each single spot for every image analysed. Finally, methods for statistical analysis of data were proposed that improved ratios studies by considering the range of each spot intensity. Moreover, the specification of an at-risk profile by a biologist allows, for example, to focus more attention on highly expressed spots. Together, all these methods put in place, from image acquisition to discovery and visualisation of potential protein markers, form the Image and Data Analysis for Differential In Gel Electrophoresis (IDADIGE) workflow. This workflow exploits different software and many functions put in place in Matlab and regrouped under the name of ProDIGE. The proteomics laboratory at bioMérieux currently uses the IDADIGE workflow, which has allowed the discovery of new colorectal biomarkers that now must be validated in a biological context.
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Submitted on : Tuesday, March 12, 2013 - 4:43:11 PM
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  • HAL Id : tel-00799838, version 1

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Bernard Fabien. IDADIGE : Procédé de traitement des images de gels d'électrophorèse bidimensionnelle différentielle dans le contexte de la recherche de marqueurs protéiques.. Traitement du signal et de l'image [eess.SP]. Ecole Nationale Supérieure des Mines de Saint-Etienne, 2008. Français. ⟨NNT : 490 IVS⟩. ⟨tel-00799838⟩

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