The Valgent4 protocol: Robust analytical and clinical validation of 11 HPV assays with genotyping on cervical samples collected in SurePath medium

Background: The VALidation of HPV GENoyping Tests (VALGENT) is an international initiative designed to validate HPV assays with genotyping capability. The VALGENT4 protocol differs from previous VALGENT installments as the sample collection medium is SurePath, and exclusively includes samples from women >= 30 years of age which is concordant with the majority of HPV primary screening guidelines. Here we present the protocol for the fourth installment of the VALGENT framework. Objectives: In VALGENT4 11 HPV assays will be evaluated using two comparator assays based on PCR with the GP5+/6+ primers. Study design: Overall, the VALGENT4 panel consists of 1,297 routine samples comprised of 998 unselected, consecutive samples, of which 51 samples had abnormal cytology with 13 women diagnosed with >= CIN2, and 299 consecutive samples enriched for >= ASCUS cytology (100 ASCUS, 100 LSIL, 99 HSIL) with 106 >= CIN2 upon follow up. Manipulated and DNA extracted panel samples were characterized with respect to human beta globin (HBB) and overall DNA content and composition to quality assess the panel prior to distribution to the collaborating sites. Result: The relative cellularity (mean CT value of HBB from the Onclarity assay) on the 1,297 LBC samples (CT=24.8) was compared with 293 un-manipulated routine cytology screening samples (CT=23.8). Furthermore, the DNA extracted panel samples was characterized using the Exome iPLEX pro assay, which reports amplifiable copies on individual samples as well as copies of five different base pair lengths. Here the data showed a slightly lower number of amplifiable DNA copies (ratio: 0.7, p = < 0.01)) in the VALGENT4 panel samples compared to routine extracted cervical DNA samples Conclusion: The present manuscript details the manipulation, processing and quality assessment of samples used in VALGENT-4. This methodological document may be of value for future international projects of HPV test validation.