Date of Graduation
8-2015
Document Type
Dissertation (PhD)
Program Affiliation
Human and Molecular Genetics
Degree Name
Doctor of Philosophy (PhD)
Advisor/Committee Chair
Eric Boerwinkle
Committee Member
Paul Scheet
Committee Member
Hope Northrup
Committee Member
Laura Mitchell
Committee Member
Wenyi Wang
Abstract
A typical human exome harbors dozens of loss-of-function (LOF) variants predicted to severely disrupt or abolish gene function. These variants are enriched at the extremely rare end of the allele frequency spectrum (< 0.1%), suggesting purifying selection against these sites. However, most previous population-based sequencing studies have not included analysis of genotype-phenotype relationships with LOF variants. Thus, the contribution of LOF variation to health and disease within the general population remains largely uncharacterized.
Using whole exome sequence from 8,554 participants in the Atherosclerosis Risk in Communities (ARIC) study, we explored the impact of LOF variation on a broad spectrum of human phenotypes. First, we selected 20 common chronic disease risk factor phenotypes and performed gene-based association tests. Analysis of this sample verified two relationships in well-studied genes (PCSK9 and APOC3) and identified eight new loci. Novel relationships included elevated fasting glucose in heterozygous carriers of LOF variation in TXNDC5, which encodes a biomarker for type 1 diabetes progression, and apparent recessive effects of C1QTNF8 on serum magnesium levels. Next, we explored the effect of LOF variation on 308 small molecular metabolites, observing 8 significant genotype-phenotype associations. We highlight the relationship between serum histidine and HAL, a gene essential to histidine catabolism, demonstrating the biologically interpretability of associations with molecular metabolite targets. Finally, we explore the impact of LOF variation on a rare birth defect by comparing sequence from 342 unrelated left ventricular outflow tract obstruction (LVOTO) cases to ARIC sequence, identifying genes harboring case-exclusive LOF mutations. Comparison to an a priori list of cardiac candidate genes revealed 28 genes potentially related to LVOTO, including 22 not previously associated with a human disorder. Genotype validation in these samples revealed diverse inheritance patterns, including 9 confirmed de novo variants (ACVR1, JARID2, KMT2D, NF1, NR2F2, PLRG1, SMURF1, TBX20, and ZEB2).
The analytical strategy presented here highlights the role of biologically-informed annotation on large-scale human genetic studies. The genes identified by these methods may have applications in disease prediction and drug development, and future genome studies will continue to refine our understanding of the scope of genetic variation affecting human health and disease.
Keywords
genome, exome, loss-of-function, rare variation, gene, disease