Methods and discoveries from fine-mapping disease-associated variants in complex traits

During the last two decades, genome-wide association studies (GWAS) have cataloged an ever-increasing set of disease-relevant variants. The majority of these variants (~90%) lie in non-coding regions of the human genome. Although not directly coding for protein sequence and structure, these variants are able to modulate the level of protein expression via regulatory mechanisms, such as interacting with transcription factors and histone binding proteins. Unlike variants in the coding region, we cannot directly infer the target protein of non-coding variants or the direction of regulation from genetic sequences alone. Because of this, our understanding of the mechanisms through which non-coding variants contribute to disease is limited, despite potential causal relationships provided by GWA studies. Further, unlike coding variants, where a deterministic relationship exists between genetic variation and the resultant protein sequence, the regulatory functions of non-coding variants are largely contextualized on tissue/cell type as well as the extra-cellular environment. For this reason, disease-relevant cell types and culture conditions must be used in order to maximize power to detect causal relationship while minimizing false discoveries. This thesis develops methods to discover shared and unique properties of disease-relevant cell lines, and to extract potential disease causal relationships from several cell lines that have been traditionally challenging to collect. Chapter 1 provides a broad introduction of our current understanding of the regulatory role of non-coding variants, and discusses challenges in interpreting their functional impact to motivate the remainder of the thesis. Chapter 2 introduces a cost-effective method to screen individuals based on their ethnic background to maximize power and reduce ancestry confounding for genetic linkage studies. Chapter 3, 4 and 5 present pipelines to analyze specialized cell type and to augment limited their limited sample size by referencing large databases such as the Genotype-Tissue Expression, the ENCODE project, and other publicly available datasets on Gene Expression Omnibus (GEO). Chapter 3 discusses annotating coronary artery disease (CAD) risk variants with human coronary artery smooth muscle cells (HCASMC); chapter 4 discusses annotating age-related macular degeneration (AMD) risk variants with retinal pigmented epithelial cells (RPE); and chapter 5 discusses the discovery of recurrent somatic mutations in leptomeningeal carcinomatosis with tumor cells circulating in the cerebral spinal fluid. Chapter 6 presents a web-based visualization tool called LocusCompare, which is used extensively in chapter 3 and 4. Similarly, chapter 7 extends a method used in chapter 3 and 4 into an R package called sinib to approximate sum of non-independent binomial random variables. Chapter 8 presents a foray into predictive modeling of the regulatory role of non-coding variants in the context of extra-cellular environment in the model organism S. cerevisiae. This chapter demonstrates the feasibility of predicting the regulatory functions of non-coding variants. We anticipate that the model can also be applied to disease-relevant human cell lines. Together, this thesis demonstrates that appropriate cell lines and extra-cellular environments are critical for the interpretation of potential disease causal variants.

Keywords: Biology.
Advisor: Montgomery Stephen
Quertermous Thomas 
Li Jin (Billy) 
Pritchard Jonathan (Jonathan K.)