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UBC Theses and Dissertations

Computational methods for systems biology data of cancer Ding, Jiarui


High-throughput genome sequencing and other techniques provide a cost-effective way to study cancer biology and seek precision treatment options. In this dissertation I address three challenges in cancer systems biology research: 1) predicting somatic mutations, 2) interpreting mutation functions, and 3) stratifying patients into biologically meaningful groups. Somatic single nucleotide variants are frequent therapeutically actionable mutations in cancer, e.g., the ‘hotspot’ mutations in known cancer driver genes such as EGFR, KRAS, and BRAF. However, only a small proportion of cancer patients harbour these known driver mutations. Therefore, there is a great need to systematically profile a cancer genome to identify all the somatic single nucleotide variants. I develop methods to discover these somatic mutations from cancer genomic sequencing data, taking into account the noise in high-throughput sequencing data and valuable validated genuine somatic mutations and non-somatic mutations. Of the somatic alterations acquired for each cancer patient, only a few mutations ‘drive’ the initialization and progression of cancer. To better understand the evolution of cancer, as well as to apply precision treatments, we need to assess the functions of these mutations to pinpoint the driver mutations. I address this challenge by predicting the mutations correlated with gene expression dysregulation. The method is based on hierarchical Bayes modelling of the influence of mutations on gene expression, and can predict the mutations that impact gene expression in individual patients. Although probably no two cancer genomes share exactly the same set of somatic mutations because of the stochastic nature of acquired mutations across the three billion base pairs, some cancer patients share common driver mutations or disrupted pathways. These patients may have similar prognoses and potentially benefit from the same kind of treatment options. I develop an efficient clustering algorithm to cluster high-throughput and high-dimensional bio- logical datasets, with the potential to put cancer patients into biologically meaningful groups for treatment selection.

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Attribution-NonCommercial 4.0 International