Methylation Analysis to Detect CIN3+ in High-Risk Human Papillomavirus-Positive Self-Samples From the Population-Based Cervical Cancer Screening Program

Abstract

Since 2017, a self-sampling device has been introduced to the Dutch population-based screening program to enable higher participation rates. However, routine triage cytology cannot be performed on self-sampling material. Methylation is an alternative triage method that can be performed directly on DNA extracted from self-samples. Recently, we tested a set of 15 published cervical intraepithelial neoplasia grade 3 or worse (CIN3+)-specific methylation markers and found a panel of 3 markers with a sensitivity of 82% and a specificity of 74%. In this study, we determined the sensitivity and specificity of 2 commercial assays using quantitative methylation-specific PCR. DNA from the same cohort of high-risk human papillomavirus-positive self-sampled material obtained through the population-based screening program in the North of the Netherlands from women with CIN2 or less (<CIN3, n = 208) and women with CIN3+ (n = 96) was used. The QIAsure methylation test (consisting of 2 methylation markers) showed a sensitivity of 65% and a specificity of 72%, whereas the Gyntect assay (consisting of 6 methylation markers) showed a sensitivity of 59% and a specificity of 91% for CIN3+. When we compared all individual 23 methylation markers, receiver operating characteristic analysis showed an area under the curve of ≥0.7 for 11 of 23 markers (P < .001). By model-based recursive partitioning and robustness analysis, we found a panel with a better sensitivity compared with QIAsure and Gyntect (P < .001). This new panel, consisting of ITGA4, ASCL1, and FAM19A4, has a sensitivity of 84% and a specificity of 70%, similar to our previously identified panel (ANKRD18CP, LHX8, and EPB41L3). Thus, in addition to our previously identified panel, the combination of ITGA4, ASCL1, and FAM19A4 showed good diagnostic performance and potentially can replace cytology, thereby avoiding additional doctor visits for many women worldwide and reducing the time for decision making for referral to the gynecologist.

Keywords: DNA methylation markers; cervical cancer screening; human papillomavirus; quantitative methylation-specific PCR; self-sampling.