Human Genomics of Complex Trait Severity

Genetics account for a large, mostly unexplained proportion of human disease. Though the role of genetics in simple, Mendelian traits has long been established, it is more difficult to disambiguate the role of various human genetic factors in complex disease traits. However, as genetics technology and methodology has advanced, from genome-wide association studies (GWAS) to next-generation sequencing (NGS), our ability to detect the role of both rare and common human genetic variation in complex disease traits has greatly improved, allowing us to demonstrate robust genetic factors involved in a variety of disease from metabolic to viral. However, despite the outstanding progress in human genetics, many complex disease traits lack robustly associated genetic variants, the existing variation only accounts for a small proportion of the estimated heritability, or the trait lacks comprehensive genetic investigation all together.

In this thesis I conducted a common variant study using GWAS and a comprehensive NGS analysis - both standards in the field - to investigate the role of human genetics in the severity of complex disease traits ranging from viral disease to metabolic: herpes simplex virus type 2 (HSV-2) and non-alcoholic fatty liver disease (NAFLD). Chapter 1 provides a broad overview of current human genetics methodologies and the advantages and caveats to each technology for complex disease traits, as well as the background and current state of genetics research for the two complex traits investigated: HSV-2 and NAFLD.

Chapter 2 utilizes a GWAS to investigate the role of common human genetic variation in HSV-2 severity, which has previously only been investigated through a small handful of candidate gene studies. We were unable to replicate previous candidate gene associations, though we did detect several variants in or near biologically plausible genes (including ABCA1 and KIF1B) that approached, though did not reach, genome-wide statistical significance with HSV-2 severity as measured by the quantitative viral shedding rate. This is the first genome-wide investigation of human genetics in HSV-2.

Chapter 3 utilizes whole-exome sequencing at both the single-variant and gene levels to further elucidate the role of human genetics in gold standard liver biopsy confirmed NAFLD fibrosis extreme phenotypes: protective and progressor. We were able to replicate known associations with PNPLA3 and TM6SF2 and advanced fibrosis, despite the limited available sample size. We also observed enrichment of variation in distinct genes for progressor or protective NAFLD phenotypes, though these genes did not reach statistical significance. This is the first NGS study of NAFLD, and thus the first investigation of the role of rare variation in NAFLD.

Overall, this thesis applied genome-wide techniques to interrogate gaps in the genetics of complex trait severity, from viral to liver disease, using unique, well-phenotyped cohorts. Human genetics remains a complicated field that will require the continued use of well-phenotyped cohorts in larger numbers, as well as both complementary and confirmatory sequencing and bioinformatics methods to fully detangle. While the research in this thesis is primarily hypothesis generating, and potentially associated variants will have to be replicated and investigated on a functional level to be confirmed as causal, the exploration of genetic associations with complex disease traits can prove highly informative for both understanding the underlying biology of these traits and for identifying genes and pathways that may act as biomarkers or treatment targets. Thus, this thesis has acted as a primer to expand knowledge of the role of human genetics in two highly complex and varied traits, HSV-2 and NAFLD, paving the way for further studies, ultimately with the goal of improving human health.