A Spatio-Temporal Analysis Framework for Characterizing Radiation-Induced Genomic Instability

Chronic low-dose ionizing radiation induces complex genomic instability encompassing both structural variants and point mutations, yet these alterations are typically analyzed as independent events--limiting detection of mechanistic coupling between rearrangement formation and localized mutagenesis at breakpoint junctions. This gap is particularly consequential given the widespread occupational and environmental exposure contexts--nuclear energy, medical imaging, and environmental contamination-- where coupled genomic alterations may contribute to cancer risk through mechanisms invisible to type-agnostic analyses. We developed an integrated analytical framework combining temporal pattern tracking, breakpoint-proximal mutation enrichment analysis, and systematic testing across all structural variant types to resolve these coupled dynamics across dose and time. Applying this framework to whole-genome sequencing data from primary human endothelial cells (HUVEC) exposed to chronic low-dose gamma radiation (0.001-2 mGy/hr) over three weeks, we discovered 7.13-fold enrichment of doublet base substitutions (DBS) within 10bp of inversion breakpoints--a signal absent from other structural variant types. This enrichment decayed sharply with distance (to [~] 1.9 x at 100bp), indicating localized mutagenesis at these junctions. Temporal analysis revealed divergent fates: inversions appeared transiently (100% single-timepoint) while DBS showed greater persistence (9.0% multi-timepoint). Among the INV-DBS events identified, affected genes include 16 high-constraint loci (pLI [≥] 0.9) involved in DNA damage response, signal transduction, and chromatin regulation--pathways critical for maintaining genomic stability. Our framework provides a generalizable approach for investigating structural variant-mutation relationships, with applications to radiation biology, cancer genomics, and mechanistic studies of DNA repair fidelity.