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dc.contributor.advisorPoterlowicz, Krzysztof
dc.contributor.authorMurat, Katarzyna
dc.date.accessioned2019-08-22T15:13:13Z
dc.date.available2019-08-22T15:13:13Z
dc.date.issued2018
dc.identifier.urihttp://hdl.handle.net/10454/17220
dc.description.abstractThe field of cancer genomics is currently being enhanced by the power of Epigenome-wide association studies (EWAS). Over the last couple of years comprehensive sequence data sets have been generated, allowing analysis of genome-wide activity in cohorts of different individuals to be increasingly available. Finding associations between epigenetic variation and phenotype is one of the biggest challenges in biomedical research. Laboratories lacking dedicated resources and programming experience require bioinformatics expertise which can be prohibitively costly and time-consuming. To address this, we have developed a collection of freely available Galaxy tools (Poterlowicz, 2018a), combining analytical methods into a range of convenient analysis pipelines with graphical user-friendly interface.The tool suite includes methods for data preprocessing, quality assessment and differentially methylated region and position discovery. The aim of this project was to make EWAS analysis flexible and accessible to everyone and compatible with routine clinical and biological use. This is exemplified by my work undertaken by integrating DNA methylation profiles of melanoma patients (at baseline and mitogen-activated protein kinase inhibitor MAPKi treatment) to identify novel epigenetic switches responsible for tumour resistance to therapy (Hugo et al., 2015). Configuration files are publicly published on our GitHub repository (Poterlowicz, 2018b) with scripts and dependency settings also available to download and install via Galaxy test toolshed (Poterlowicz, 2018a). Results and experiences using this framework demonstrate the potential for Galaxy to be a bioinformatics solution for multi-omics cancer biomarker discovery tool.en_US
dc.language.isoenen_US
dc.rights<a rel="license" href="http://creativecommons.org/licenses/by-nc-nd/3.0/"><img alt="Creative Commons License" style="border-width:0" src="http://i.creativecommons.org/l/by-nc-nd/3.0/88x31.png" /></a><br />The University of Bradford theses are licenced under a <a rel="license" href="http://creativecommons.org/licenses/by-nc-nd/3.0/">Creative Commons Licence</a>.eng
dc.subjectMelanomaen_US
dc.subjectCancer genomicsen_US
dc.subjectEpigenome-wide association studies (EWAS)en_US
dc.subjectGalaxy toolsen_US
dc.subjectCancer biomarkersen_US
dc.subjectBioinformatics analysisen_US
dc.titleBioinformatics analysis of epigenetic variants associated with melanomaen_US
dc.type.qualificationlevelresearch mastersen_US
dc.publisher.institutionUniversity of Bradfordeng
dc.publisher.departmentDepartment of Chemistry and Biosciencesen_US
dc.typeThesiseng
dc.type.qualificationnameMPhilen_US
dc.date.awarded2018
refterms.dateFOA2019-08-22T15:13:13Z


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