Structural genomic variation has only recently come into focus as a major source of genetic diversity in humans, and in biology in general. Despite its critical importance, we still have a very limited understanding of the processes that cause the structure of genomes to change over time, and of the consequences of these large-scale changes to living organisms. I propose to use two parallel and integrated approaches to study this problem, taking advantage of the unique research tools available in the budding yeast model system. (1) I will investigate the forces that cause chromosomes to break, and the cellular mechanisms that are responsible for preventing, surveying, and repairing this damage. To do so, I will use a custom and highly sensitive assay to measure the rate of gene copy number variation (CNV), and genomic analysis tools to characterize the associated structural changes. The CNV assay has two uniquely innovative features that will allow the study of problems that have never been properly addressed by conventional experimental systems. First, the assay uses diploid cells, making the results much more germane to the processes that occur in humans; and Second, this assay can detect chromosomal rearrangements stemming from DNA breaks anywhere in the genome, allowing a more comprehensive sampling of genomic variants. (2) I will also investigate the phenotypic consequences associated with chromosomal rearrangements in a diploid yeast strain that shares many of the properties that characterize the complex human genome. These include a high degree of heterozygosity, structural chromosomal polymorphisms between homologs, gene redundancy, and CNVs; all the while retaining the small (and manageable) genome of S. cerevisiae. I will use this strain to conduct a systematic functional genomics study of structural variation. This strain (JAY270) will be manipulated to generate targeted chromosomal rearrangements in all chromosomes. This collection of chromosomal mutants will then be taken through a series of phenotypic tests to establish structure-function relationships for the entire genome. I strongly believe that by opening these new and integrated avenues of investigation, my studies will contribute much needed insight into how structural genomic variation arises and how it affects all aspects of life, from the evolution of species to human health.