Broken and Reassembled: The Molecular Mechanisms and Clinical Consequences of Structural Genomic Variation

Background Structural variants (SVs) are a major class of genomic variation that profoundly influences human genetic diversity, evolution, and disease. Historically underappreciated due to detection challenges, SVs are now recognized as key drivers of both constitutional disorders and cancer. Understanding their origins and consequences is fundamental to modern genomics and clinical medicine. Summary SVs arise from the complex interplay between endogenous sources of DNA damage—such as reactive oxygen species, replication stress, and transcription-replication conflicts—and error-prone repair mechanisms including non-allelic homologous recombination, microhomology-mediated end joining, fork stalling and template switching, and break-induced replication. The formation and patterns of these variants are critically constrained by the three-dimensional architecture of the nucleus, particularly topologically associating domains, which determine the spatial proximity of potential translocation partners. Key insights into these processes are provided by genomic instability syndromes (e.g., Bloom syndrome, Fanconi anemia, Werner syndrome, Nijmegen breakage syndrome), where specific repair pathway defects result in characteristic SV signatures and clinical phenotypes. Similarly, cancer genomes serve as detailed molecular archives of repair failures, with distinct SV patterns now enabling prediction of underlying deficiencies such as BRCA loss. Thus, the pattern of SVs in a tumor genome can serve as a retrospective molecular archive of underlying repair failure, enabling ‘signature-based’ prediction of HR deficiency even when germline BRCA status is unknown. Emerging technologies, especially long-read sequencing, have revolutionized the field by achieving >95% sensitivity for SV detection and resolving previously intractable rearrangements. Furthermore, recent discoveries regarding biomolecular condensates in DNA repair (e.g., PARP1, MRNIP phase separation) reveal previously unrecognized regulatory layers governing repair pathway choice and SV formation. Key Messages • Structural variants are generated by specific DNA lesions and error-prone repair processes, with their patterns shaped by nuclear architecture and three-dimensional genome organization. • Genomic instability disorders and cancer genomes provide crucial mechanistic insights by linking specific repair pathway defects to characteristic SV signatures. • Technological advances, particularly long-read sequencing, now enable comprehensive and sensitive detection of SVs, including those in complex repetitive regions. • A unified framework for understanding SVs as products of DNA damage, cellular metabolism, and chromatin context has profound clinical implications for diagnostic reverse phenotyping, synthetic lethality strategies in oncology, and the development of targeted therapies.