Interpreting variation in pharmacogenes using multiplex assays

Abstract

With the advent of genome sequencing technologies, our ability to read DNA sequences is unprecedented. However, understanding how the variation we encounter impacts humans is a formidable challenge. Technologies like multiplex assays, in which we can measure tens of thousands of variants in a high-throughput, pooled manner, allow us to tackle this problem at scale. In particular, genes that are involved in drug response, called pharmacogenes, pose a unique opportunity to apply multiplex assays. These assays would not only help us better understand pharmacogene biology, they would also provide vital evidence for tailoring drug regimens to a patient’s genotype. To advance towards this goal, in Chapter 1, I give an introduction to multiplex assays and outline what pharmacogenes we should prioritize for this approach. In Chapter 2, I detail how I used multiplex assays to interrogate the biology of vitamin K epoxide reductase (VKOR), the target of warfarin. By applying assays for abundance and activity to VKOR, I suggest a resolution for the controversy over VKOR topology, identify residues that are functionally constrained in the protein, and interpret human variants found in genomic databases. In Chapter 3, I show how applying an abundance assay to cytochrome P450 2C9 (CYP2C9) identifies highly conserved core regions of the protein and the show that 42% of missense variants present in genome databases have decreased abundance, suggesting that drug metabolism may be affected in individuals with these variants. Finally, in chapter 4, I outline challenges in designing multiplex assays for pharmacogenes, including tackling combinatorial variation, and comment on the promising future of pharmacogenomics.