MethylFlow - A Novel Pipeline for Preprocessing and Analysis of Bisulfite Sequencing DNA ethylation Data

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School of Science | Master's thesis
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Author
Date
2013
Department
Perustieteiden korkeakoulu
Major/Subject
Informaatiotekniikka
Mcode
T-61
Degree programme
Language
en
Pages
(10) + 64
Series
Abstract
DNA methylation is one of the key epigenetic mechanisms through which gene expression is regulated. This epigenetic mark typically occurs when a methyl group is added to cytosine nucleotides in DNA, which leads to modification of the 3-dimensional structure of the DNA molecule without changes in the underlying DNA sequence. Alterations of DNA methylation patterns have been linked to several diseases including cancer. Next-generation sequencing technology combined with bisulfite treatment, called Bisulfite Sequencing, and has become the most promising tools in the field. This thesis focuses on development and implementation of a novel pipeline, MethylFlow, for pre-processing and methylation analysis of Whole-Genome and Reduced Representation Bisulfite Sequencing data. Raw data are first filtered based on their quality in order to discard unreliable information, and then further analysed in order to identify differences and similarities among methylomes. MethylFlow combines several existing software, as well as self-made scripts, and links them together through an open source component-based workflow framework called Anduril. MethylFlow was used in the analysis of RRBS data obtained from four patients affected by Diffuse Large B-Cell Lymphoma, an aggressive type of blood cancer. All four patients, after an initial positive response to treatment, underwent relapse. DNA methylation samples were obtained from both primary and relapse tumors and then compared in order to link DNA methylation changes to differential gene expression.
Description
Supervisor
Lähdesmäki, Harri
Thesis advisor
Hautaniemi, Sampsa
Ovaska, Kristian
Keywords
DNA methylation, bisulfite sequencing, cancer, pipeline, bioinformatics, systems biology
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https://urn.fi/URN:NBN:fi:aalto-2020122859910
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[dipl] Perustieteiden korkeakoulu / SCI