DNA damage omics: concepts, genome-wide mapping technologies, and research perspectives

DNA damage threatens genome integrity and contributes to cancer, ageing, and other diseases. Conventional assays have established the foundations of DNA damage research, but many provide low-throughput, qualitative, or indirect measurements and cannot localize lesions across the genome. DNA damage omics addresses these limitations by coupling lesion-specific enrichment or enzymatic labeling with next-generation sequencing to profile damage at genome-wide, and in some cases single-base or single-cell, resolution. This review first summarizes the major sources and types of DNA damage and the capabilities of classical detection methods. It then organizes sequencing strategies for double-strand breaks, single-strand breaks, DNA cross-links, and base lesions according to their capture principles, resolution, and biological readouts. For each lesion class, we relate the molecular event captured by an assay to its experimental requirements, principal sources of bias, and most appropriate applications, thereby distinguishing direct lesion mapping from measurements of repair intermediates or downstream genomic consequences. Across these approaches, integration with chromatin, epigenomic, transcriptomic, single-cell, and spatial data indicates that DNA damage is distributed non-randomly and is shaped by sequence context, chromatin state, and three-dimensional genome organization. The review also compares major technical constraints, including enrichment bias, limited sensitivity in low-input samples, incomplete coverage of repetitive or GC-extreme regions, and the lack of standardized analytical pipelines. Emerging long-read, spatiotemporal, and single-cell approaches may improve lesion-to-mutation mapping and support biomarker discovery and therapeutic stratification. By linking detection principles to appropriate biological questions and explicitly defining current limitations, this review provides a practical framework for selecting DNA damage sequencing methods and for advancing their mechanistic and translational use.