Characterization of High-Risk Human Papillomavirus Genotypes in Formalin-Fixed Paraffin-Embedded Cervical Tissues Using Genexpert®

Backgrounds: There is a growing need for human papillomavirus (HPV) annotation of formalin-fixed paraffin-embedded (FFPE) tissues. This study was carried out to characterize high-risk human papillomavirus genotypes in formalin-fixed paraffin-embedded cervical tissues using GeneXpert®
Materials & Methods: In this study, 200 formalin-fixed paraffin-embedded (FFPE) cervical tissue samples were collected from women with pre-invasive and invasive cervical diseases and screened for high-risk human papillomavirus (hrHPV) using GeneXpert®.
Findings: Analysis of the results showed that 47 (23.5%) samples were positive for hrHPV, with HPV 16 being the most common type (16.5%), followed by other high risk (OHR) types (31, 33, 35, 52, 58, 51, 59, 39, 56, 66, 68) (4.5%) and HPV 18/45 (2.5%). Ninety-six (48%) samples were negative for hrHPV, while 57 (28.5%) samples were invalid. GeneXpert® had low sensitivity for hrHPV in CIN 1 (cervical intraepithelial neoplasia) (9.1%), CIN 2 (33.3%), CIN 3 (22.2%), and cervical cancer (50.7%). However, the specificity of the test was much better, with values ranging from 64.9-83.8%. Apart from cervical cancer, which had a positive predictive value of 74.5%, the positive predictive value of all pre-invasive diseases was very poor. However, the negative predictive value of the test was very good, with CIN 2 having a high value of 97.9%.

Conclusion: This study findings show that FFPE cervical tissue is functional for HPV detection, although HPV detection and characterization by the GeneXpert® assay is still recommended only after full optimization.