Methods Development for Targeted Nanopore Sequencing

This dissertation focuses on methods development for "third-generation" (long-read) sequencing technologies. With a focus on nanopore sequencing, this work discusses methods development and applications for targeted sequencing of select genomic loci. The methods described here make extensive use of the CRISPR/Cas9 system for target enrichment, adapting these tools to ligate sequencing adaptors at desired loci. We apply this strategy to look at numerous features salient to human neoplasia: DNA methylation, structural variation, point mutations, and chromatin accessibility. The methods are then applied to cell lines and primary patient tissue; and these genomic features are evaluated and compared