Changes to chromatin structure, including both epigenetic modifications and structural variants, are recurrent in many cancer types and can be the primary tumor driver. These variants are difficult to detect through traditional short-read sequencing and often remain under-characterized, especially in relation to their functional impacts on the transcriptome. With recent improvements in long-read sequencing, it has become possible to detect these alterations with a single sequencing run with greater accuracy and context than before. I have developed new software methods for that identify chromatin modifications with greater accuracy from long-read DNA sequencing and applied this method to identify chromatin accessibility and transcriptomic alterations resulting from the perturbation of chromatin remodelers in Saccharomyces cerevisiae as a model system. I have also developed a software pipeline to integrate detection of gene fusions, SNVs, mid-sized insertions and deletions, and alternative splicing from long-read RNA-seq, resulting in a comprehensive characterization of functional alterations in cancer-relevant genes. I apply these methods to three patient-derived cell lines from patients with osteosarcoma, a tumor that is driven by poorly characterized and difficult to detect structural variants. I identify multiple functional alterations in these tumors with potential therapeutic implications. This work provides a more complete understanding of the many layers of gene regulation in cancer cells.

Event Host: Colette Felton, Ph.D. Candidate, Biomolecular Engineering & Bioinformatics 

Advisor: Angela Brooks