GeneXpert for High Risk HPV Detection in FFPE Cervical Tissues: Diagnostic Value and Methodological Considerations

This papaer critically reviews the recent publication by Magaji et al. (2025) regarding the application of the cartridge-based GeneXpert assay for detecting high-risk human papillomavirus (hrHPV) in formalin-fixed paraffin-embedded (FFPE) cervical tissues. While the original study offers valuable proof-of-concept evidence for archival molecular epidemiology, significant methodological and diagnostic limitations warrant careful consideration. The high invalid test rate of 28.5% (57/200) underscores the adverse effects of formalin-induced DNA fragmentation and cross-linking, highlighting the necessity for optimized pre-analytical steps, such as extended proteinase K digestion and mandatory internal control pre-screening (e.g., β-globin or GAPDH). Furthermore, the assay demonstrated markedly low diagnostic sensitivity for pre-invasive lesions, with sensitivities of 9.1% for CIN1, 33.3% for CIN2, and 22.2% for CIN3, as well as very low positive predictive values of 2.1% for both CIN1 and CIN2. These findings indicate substantial underdetection, which may be attributable to the application of a cytology-optimized platform to solid tissue matrices. Consequently, the GeneXpert assay in its current format cannot be recommended for epidemiological prevalence estimation or standalone diagnosis in FFPE specimens, although its high negative predictive value may confer utility as a rule-out test. Standardized pre-analytical optimization is strictly required before routine clinical implementation.