Deep mutation modelling in cancer driver mutation and cancer driver gene detection

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http://urn.fi/URN:NBN:fi:hulib-202106072531
Julkaisun nimi: Deep mutation modelling in cancer driver mutation and cancer driver gene detection
Tekijä: Maljanen, Katri
Muu tekijä: Helsingin yliopisto, Matemaattis-luonnontieteellinen tiedekunta
University of Helsinki, Faculty of Science
Helsingfors universitet, Matematisk-naturvetenskapliga fakulteten
Julkaisija: Helsingin yliopisto
Päiväys: 2021
Kieli: eng
URI: http://urn.fi/URN:NBN:fi:hulib-202106072531
http://hdl.handle.net/10138/330695
Opinnäytteen taso: pro gradu -tutkielmat
Koulutusohjelma: Life Science Informatics -maisteriohjelma
Master's Programme in Life Science Informatics
Magisterprogrammet i Life Science Informatics
Opintosuunta: Algoritminen bioinformatiikka
Algorithmic Bioinformatics
Algoritmisk bioinformatik
Tiivistelmä: Cancer is a leading cause of death worldwide. Unlike its name would suggest, cancer is not a single disease. It is a group of diseases that arises from the expansion of a somatic cell clone. This expansion is thought to be a result of mutations that confer a selective advantage to the cell clone. These mutations that are advantageous to cells that result in their proliferation and escape of normal cell constraints are called driver mutations. The genes that contain driver mutations are known as driver genes. Studying these mutations and genes is important for understanding how cancer forms and evolves. Various methods have been developed that can discover these mutations and genes. This thesis focuses on a method called Deep Mutation Modelling, a deep learning based approach to predicting the probability of mutations. Deep Mutation Modelling’s output probabilities offer the possibility of creating sample and cancer type specific probability scores for mutations that reflect the pathogenicity of the mutations. Most methods in the past have made scores that are the same for all cancer types. Deep Mutation Modelling offers the opportunity to make a more personalised score. The main objectives of this thesis were to examine the Deep Mutation Modelling output as it was unknown what kind of features it has, see how the output compares against other scoring methods and how the probabilities work in mutation hotspots. Lastly, could the probabilities be used in a common driver gene discovery method. Overall, the goal was to see if Deep Mutation Modelling works and if it is competitive with other known methods. The findings indicate that Deep Mutation Modelling works in predicting driver mutations, but that it does not have sufficient power to do this reliably and requires further improvements.
Avainsanat: cancer
driver mutations
driver genes
deep learning


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