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UBC Theses and Dissertations

Detecting DNA methylation using nanopore sequencing : from genome-wide analysis to haplotype-resolved and parent-of-origin phasing Akbari, Vahid


DNA cytosine methylation is the most common epigenetic mark of the mammalian genome. This epigenetic modification is involved in different biological processes and its aberrations are involved in various disorders. While it is a well-studied epigenetic mark, the limitations of array-based and short-read technologies to detect DNA methylation have resulted in a gap in the study of allele-specific methylation and DNA methylation at repetitive genomic regions. Nanopore sequencing offers long-read sequencing and detection of both DNA bases and modification simultaneously. Therefore, offers the potential to overcome the caveats of previous technologies. In this thesis, I aimed to investigate genome-wide DNA methylation from nanopore sequence data and develop tools and workflows for the detection of allelic methylation using this technology and study genome-wide allele-specific methylation and imprinting. Moreover, I aimed to leverage long-read data and their methylation information to develop a novel approach for improved and parent-of-origin-aware phasing. I explored DNA methylation detection using nanopore sequencing and demonstrated that nanopore DNA methylation data are highly correlated with current widely used approaches. To detect allele-specific methylation using nanopore data, I developed the NanoMethPhase tool and workflow that enables detection of allele-specific methylation genome-wide. Using NanoMethPhase and nanopore sequencing data for several normal human cell lines, I explored genome-wide allele specific methylation and detected 42 novel imprinted regions and 7 large blocks of imprinted methylation. Using a combination of nanopore sequencing and strand-seq with methylation at human imprinted regions, I developed a novel methodology that enables the assignment of genomic variants to their parental origin without any data from parents. Finally, I used nanopore sequencing to study DNA methylation in advanced tumour samples from the personalized onco-genomics program at BC Cancer. I detected several hundred genes across tumour samples with tumour-specific allelic methylation and aberrant expression. I further detected several known imprinted regions with loss of imprinted methylation across tumour samples. Through these projects and studies, I developed tools and methods that enable allele-specific methylation analysis and parent-of-origin-aware genomic phasing. Moreover, I contributed to our understanding of allele-specific methylation and imprinting in normal and cancerous cells.

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