All ETDs from UAB

Advisory Committee Chair

Richard M Myers

Advisory Committee Members

Gregory Barsh

Gregory Cooper

Robin Lorenz

Eric Mendenhall

Document Type

Dissertation

Date of Award

2018

Degree Name by School

Doctor of Philosophy (PhD) Heersink School of Medicine

Abstract

The development of next-generation sequencing (NGS) technologies has led to unparalleled advances in our understanding of the genetic basis of disease, evolution, and genetic and genomic regulation. Building on the advances made in the Human Genome Project and more recent efforts such as the Encylopedia of DNA Elements (ENCODE) and the Roadmap Epigenomics Project, whole-genome and whole-exome sequencing (WGS/WES) and a wide variety of NGS-enabled functional assays are bridging the gap between scientific discovery and clinical medicine. This trend towards genomically informed “bench-to-bedside” translational medicine is driven in large part by the sharply decreasing costs for NGS in both clinical and research settings, experimental ingenuity, and increased technological advancements in NGS quantitative metrics. NGS and functional genomics are enabling greater diagnostic and prognostic power as well as more sophisticated and precise therapeutic targeting in a diseases ranging from pediatric intellectual disability to pancreatic cancer. In this work, we have employed NGS and functional genomics to address significant clinical and scientific challenges in multiple areas of translational medicine. In an international collaboration, we employ WES and integration of assays such as chromatin immunoprecipitation sequencing (ChIP-seq) and RNA-seq to to discover and characterize a novel cause of de novo syndromic developmental delay and intellectual disability. Next, we addressed methodological challenges in the application of small RNA-sequencing for blood-based biomarker discovery by repurposing CRISPR/Cas9 as a programmable restriction enzyme to remove highly abundant technical artifacts during library construction. Finally, in order to identify genetic mechanisms conferring chemotherapeutic resistance in pancreatic ductal adenocarcinoma (PDAC), a nearly uniformal lethal cancer, we integrated PDAC tumor transcriptomics with genome-wide CRISPR/Cas9 knockout and activation screens to identify genes whose perturbation drives multi-drug resistance to FOLFIRINOX (folinic acid, 5-fluoruracil, Oxaliplatin, irinotecan) and gemcitabine. Taken together, these studies demonstrate the significant potential of NGS and functional genomics to advance biomedical knowledge and meaningful improve the lives of patients.

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