Investigating the origin and functional impact of "hidden" structural variants in rare genetic diseases - 1. Project Summary Structural variants (SVs) in the form of copy-number variants (CNVs), inversions, translocations, and insertions often underlie the genetic etiology of genomic disorders, common disease traits and cancer. As such, SVs provide opportunities to study critical dosage sensitive genes, as well their underlying mechanism of formation. SVs result from distinct mutational mechanisms, including DNA recombination, replication, and repair-associated processes, each leaving specific genomic scars and identifiable signatures that can be accessed with appropriate sequencing methodologies. Despite its relevance, SVs still lack basic information such as somatic and germline de novo formation rate, mutational signatures associated with DNA metabolic processes and specific contribution to the expression of clinical traits. Some classes are more affected by this knowledge gap because they escape detection by routine genome sequencing. These “hidden” DNA variants include inversions, complex genomic rearrangements (CGRs), mobile elements insertions, balanced translocations. We and others have shown that DNA repair mechanisms, such as break-induced replication (BIR) and microhomology-mediated break-induced replication (MMBIR), largely contribute to the germline formation of some of those SVs. Our data indicate that BIR and MMBIR are prone to occur in genomic regions laden with large repeats, here called highly‐ similar intrachromosomal repeats (HSIRs), often leading to SVs perturbing nearby dosage sensitive genes. The general overarching goals of this research program include i) investigating the structure, molecular features and mechanism of generation of “hidden” DNA structural variants such as inversions and ii) establishing their impact to disease expression. Accumulating data from our lab provide data to support the following hypotheses: i) genetic diseases caused by “hidden” SVs present highly diverse genomic structure that contributes to variability in gene and disease expression; ii) HSIRs provide substrate for ectopic recombination and template-switching generating a relevant fraction of SVs. These hypotheses will be tested by investigating the following questions: (1) What are the relative contributions of distinct DNA repair mechanisms to the formation of inversions? (2) What is the contribution of inversions to pathogenic structural variants in unsolved rare Mendelian disorders? (3) Do HSIRs contribute to diversification of the genomic structure of disease loci with a role in gene and disease expression variability? To accomplish that, we will combine extensive genomic and transcriptomic analysis with robust phenotypic characterization. This research program will build on our current NIGMS funded projects to investigate the mechanism of origin of SVs, their impact on genomic structure, gene expression and disease phenotypes. Importantly, the methodologies developed here will enable studies of related “hidden” SV types such as insertions and CGRs (e.g., chromothripsis) and their role on disease and phenotypic expression. In summary, this application will provide understanding of human biological processes and disease mechanisms with broad implications for the diagnosis of birth defects, neurodevelopment, and cancer.
