Abstract 7734: The gap score: A functional biomarker of drug sensitivity

Abstract Accurate identification of tumors most likely to benefit from DNA damage response (DDR)-targeted therapies remains a major clinical challenge. Current biomarkers, including genomic instability assays and multi-gene HRD panels, rely on “genomic scarring” to infer homologous recombination repair (HRR) defects. While informative, these static measurements capture historical DNA repair events and fail to provide a real-time functional assessment of DDR pathway activity. RAD51 foci assays offer dynamic evaluation but remain intrinsically tied to HDR capacity, thereby overlooking non-HR mechanisms that drive therapeutic vulnerability.Here, we present single-stranded DNA (ssDNA) gaps as a mechanistically grounded and clinically actionable biomarker that reflects the common denominator of DDR dysfunction across tumor types. We developed a robust, scalable ssDNA gap detection assay optimized for clinical specimens, enabling real-time quantification of endogenous replication-associated gaps without prior drug exposure. Using this platform, we demonstrate that ssDNA gaps are intrinsically elevated in BRCA-deficient cancers, independent of genotoxic stress, revealing a native replication vulnerability not captured by HRD scores.AI-assisted imaging analysis enabled fully automated and unbiased quantification of gap burden across tumor sections and xenograft samples. ssDNA gap levels strongly correlated with sensitivity to PARP inhibitors and other replication-perturbing agents, outperforming HRD-score and RAD51-based assays in predicting therapeutic response. Mechanistically, gap formation in BRCA-deficient tumors arises during replication through combined contributions of abasic site accumulation, PrimPol-mediated repriming, and aberrant nuclease processing. These findings establish ssDNA gaps as the functional consequence of impaired genome maintenance, integrating multiple upstream DDR alterations into a single measurable phenotype.Collectively, our data position ssDNA gap burden as a rapid, reliable, and more biologically faithful biomarker than traditional HRD metrics for stratifying patients likely to benefit from DDR-targeted therapies. By shifting biomarker development from HR deficiency to replication gap biology, this approach enables improved patient selection in clinical trials and supports the implementation of precision medicine strategies that directly measure tumor vulnerability rather than relying on genomic proxies. Citation Format: Sharon B. Cantor, Jenna Whalen, Tokio Sano. The gap score: A functional biomarker of drug sensitivity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 7734.