Rat genome variation and complex traits

Exploring the relation between genotype and phenotype is essential in understanding the mechanisms underlying human complex diseases such as hypertension and diabetes. Studying these type of diseases in human is difficult due to fluctuations in environmental influences and their heterozygous genomes. Therefore we here use inbred rat as an animal model for human complex diseases to study the role of genomic variation in disease phenotypes. Technical advances in next-generation sequencing (NGS) make it now possible to produce large-scale datasets of genomes, transcriptomes, chromatin status and many more other applications. In this thesis work is described that assesses the use of NGS-based applications in rat functional genomic research as a tool to identify and molecularly characterize genomic variants in complex traits. First (Chapter 2) we collect and catalogue the genomic variation present in 40 widely used rat inbred strains and we use this inventory to characterize the presence and properties of genomic substrain variation. Next (Chapter 3) we use this inventory in an outbred breeding of 1600+ rats to map Quantitative Trait Loci (QTLs) of 160 phenotypes with high resolution, providing starting points to directly investigate the relation of candidate genomic variants with a given phenotype. Since most candidate variants reside outside protein coding regions, we set out to explore (Chapter 4) the effect of these noncoding variants on molecular phenotypes. We found that the genomic variants can act in a multi-level fashion and over large distance. Besides studying the relation of genomic variants in complex traits, we also molecularly characterize part of a complex trait: cancer; by investigating tumors in a Tp53 knockout rat model (Chapter 5). Interestingly we found, in contrast with the current p53 dogma, that the tumors of homozygous Tp53 -/- rats were genomically stable and we thus conclude that the mere loss of functional p53 is not sufficient to induce large-scale genomic instability. In this thesis multiple NGS techniques were used to dissect the intricate relationship between genomic variants and their role in complex traits in rat. The research described in this thesis is a basis for further fundamental research and reports multiple genome-wide resources, which have the potential to change current healthcare. The current knowledge needed for the interpretation of all this data is not yet sufficient, but the contribution of this work is an important step in the dissection of complex disease in man.