Homologous recombination deficiency (HRD) can arise from germline or somatic pathogenic variants as well as other genomic damage and epigenetic alterations in the HR repair pathway. Patients with tumors presenting with an HRD phenotype can show sensitivity to Poly (ADP-ribose) polymerase inhibitors (PARPis). Several promising tests to detect HRD have been developed based on different HRD definitions, biomarkers, and algorithms. However, no consensus on a gold standard HRD test has been established. In this systematic review, a comprehensive list of tests for the detection of HRD was identified and compared regarding HRD definition, biomarkers, and algorithms. PubMed’s Medline and Elsevier’s Embase were systematically searched, resulting in 27 eligible articles meeting the inclusion criteria. The primary challenge when comparing HRD tests lies in the lack of a consensus definition of HRD, as the HRD definition influences the proportion of samples being classified as HRD and impacts the classification performance. This systematic review provides an overview of available HRD tests that can inspire other researchers in searching for a gold standard HRD definition and highlights the importance of the factors that should be considered when choosing an HRD definition and tests for future planning of clinical trials and studies.

Background: Ovarian cancer remains the most lethal gynecological cancer, primarily due to its asymptomatic nature in early stages and consequent late diagnosis. Early detection improves survival, but current biomarkers lack sensitivity and specificity. Cell-free DNA (cfDNA) released from tumor cells captures tumor-associated epigenetic alterations and represents a promising source for minimally invasive biomarkers. Among these, aberrant DNA methylation occurs early in tumorigenesis and may reflect underlying disease biology. This study aimed to investigate genome-wide cfDNA methylation profiles in patients with ovarian cancer, benign ovarian conditions, and healthy controls to identify cancer-associated methylation patterns that may inform future biomarker development. Results: We performed genome-wide cfDNA methylation profiling using cell-free methylated DNA immunoprecipitation sequencing (cfMeDIP-seq) on plasma samples from 40 patients with high-grade serous ovarian carcinoma, 38 patients with benign ovarian conditions, and 38 healthy postmenopausal women. A total of 536 differentially methylated regions (DMRs) were identified between ovarian cancer and controls (n = 76), with 97% showing hypermethylation in ovarian cancer. DMRs were enriched in CpG islands and gene bodies and depleted in repetitive elements, consistent with known cancer-associated methylation patterns. Fifteen genes showed robust hypermethylation across analyses. These genes exhibited methylation across intronic, exonic, and upstream regulatory regions. Separate comparisons of ovarian cancer to each control group (benign and healthy) supported the reproducibility of these findings. Gene Ontology enrichment analysis revealed enrichment in gland development, embryonic morphogenesis, and endocrine regulation, suggesting biological relevance to ovarian tumorigenesis. Conclusions: This study identifies consistent cfDNA hypermethylation patterns in ovarian cancer, affecting genes involved in developmental regulation and hormone-related processes. Our findings underscore the potential of cfMeDIP-seq for detecting tumor-specific methylation signatures in plasma and highlight these 15 hypermethylated genes as biologically relevant targets for future studies on cfDNA methylation in ovarian cancer.

Homologous recombination deficiency (HRD) is a predictive biomarker for response to platinum-based chemotherapy in ovarian cancer. In this retrospective study, we benchmarked three HRD detection algorithms - CHORD, ShallowHRD, and OvaHRDscar - alongside BRCA1/2 mutation status in a cohort of 100 patients with high-grade serous ovarian carcinoma (HGSC). HRD status was derived from whole genome sequencing of tumor/normal samples, and progression-free survival (PFS) was used as the primary endpoint. All three HRD algorithms showed a statistically significant association with improved PFS. In multivariate Cox regression models adjusted for age, FIGO stage, tissue type, and neoadjuvant chemotherapy, HRD-positive status was significant associated with reduced hazard of progression or death: OvaHRDscar (HR = 0.41, 95% CI: 0.25–0.67), ShallowHRD (HR = 0.50, 95% CI: 0.31–0.79), and CHORD (HR = 0.47, 95% CI: 0.24–0.94). In contrast, BRCA1/2 mutation status did not show a significant association (HR = 0.64, 95% CI: 0.35–1.16). These findings support that HRD algorithms may aid in the diagnostic assessment of HRD and support broader genomic profiling to enhance clinical decision-making. Future studies should focus on refining algorithm thresholds and validating these results in larger, multi-center cohorts to facilitate clinical translation.