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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Date

2013

Department

Perustieteiden korkeakoulu

Major/Subject

Informaatiotekniikka

Mcode

T-61

Degree programme

Language

en

Pages

(10) + 64

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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.

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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