Nanopore Sequencing for Investigation of the Human Epigenome

The invention of next generation sequencing (NGS) revolutionized the field of human genetics, providing a practical way to study genetics in a genome-wide fashion. With the ability to sequence the whole genome came the ability to observe the epigenome, the patterns and interactions of epigenetic signatures across the whole genome. Over the years, existing epigenetic methods have been adapted to NGS, and new approaches of using NGS to study the epigenome have been demonstrated. Now NGS-based studies are gold standards in studying the human epigenome. Despite the advances in our understanding of the human epigenome, many gaps still remain. The epigenome is composed of numerous chemical components, and the observed phenotype is a result of complex interactions of these epigenetic features. The epigenome is also highly heterogeneous, further complicating the analysis of epigenetic interactions. In addition, limitations of our understanding of the genome, e.g. repetitive elements, centromeric regions, and large-scale genomic rearrangements, is translated directly to the lack of understanding of their epigenome. The emergence of nanopore sequencing has opened new doors for studying the human genome and epigenome. Here I describe how I adapted NGS epigenomic methods to nanopore sequencing, and how this furthers our knowledge of the epigenome. I first present the application of nanopore sequencing in observing multiple layers of epigenetic information and uncovering epigenetic patterns across the genome. Then I show the utility of the long read in studying the epigenome, observing allele-specific epigenetic patterns on single-molecules. Lastly, I implemented targeted sequencing on nanopore to generate deep sequencing coverage in select genomic regions and its usage in variant detection