Identification and validation of a 3-gene methylation classifier for hpv-based cervical screening on self-samples
Clinical Cancer Research , Volume 24 - Issue 14 p. 3456- 3464
Purpose: Offering self-sampling of cervico-vaginal material for high-risk human papillomavirus (hrHPV) testing is an effective method to increase the coverage in cervical screening programs. Molecular triage directly on hrHPV-positive self-samples for colposcopy referral opens the way to full molecular cervical screening. Here, we set out to identify a DNA methylation classifier for detection of cervical precancer (CIN3) and cancer, applicable to lavage and brush self-samples. Experimental Design: We determined genome-wide DNA methylation profiles of 72 hrHPV-positive self-samples, using the Infinium Methylation 450K Array. The selected DNA methylation markers were evaluated by multiplex quantitative methylation-specific PCR (qMSP) in both hrHPV-positive lavage (n ¼ 245) and brush (n ¼ 246) self-samples from screening cohorts. Subsequently, logistic regression analysis was performed to build a DNA methylation classifier for CIN3 detection applicable to self-samples of both devices. For validation, an independent set of hrHPV-positive lavage (n ¼ 199) and brush (n ¼ 287) self-samples was analyzed. Results: Genome-wide DNA methylation profiling revealed 12 DNA methylation markers for CIN3 detection. Multiplex qMSP analysis of these markers in large series of lavage and brush self-samples yielded a 3-gene methylation classifier (ASCL1, LHX8, and ST6GALNAC5). This classifier showed a very good clinical performance for CIN3 detection in both lavage (AUC ¼ 0.88; sensitivity ¼ 74%; specificity ¼ 79%) and brush (AUC ¼ 0.90; sensitivity ¼ 88%; specificity ¼ 81%) self-samples in the validation set. Importantly, all self-samples from women with cervical cancer scored DNA methylation–positive. Conclusions: By genome-wide DNA methylation profiling on self-samples, we identified a highly effective 3-gene methylation classifier for direct triage on hrHPV-positive self-samples, which is superior to currently available methods.
|Clinical Cancer Research|
|This work was funded by the European Commission 7th Framework Programme; grant id erc/322986 - Molecular Self Screening for Cervical Cancer Prevention (MASS-CARE)|
Verlaat, W. (Wina), Snoek, B.C. (Barbara C.), Heideman, D.A.M, Wilting, S.M, Snijders, P.J.F, Novianti, P.W, … Steenbergen, R.D.M. (2018). Identification and validation of a 3-gene methylation classifier for hpv-based cervical screening on self-samples. Clinical Cancer Research, 24(14), 3456–3464. doi:10.1158/1078-0432.CCR-17-3615