Targeted Next Generation Sequencing for Human Papillomavirus Genotyping in Cervical Liquid-Based Cytology Samples

SIMPLE SUMMARY: Testing for Human Papillomavirus (HPV) is currently being implemented as part of cervical cancer (CC) screening in several countries. However, infections with all but one of the HPV types classified as possibly carcinogenic cannot be detected by the assays used for CC screening today. The aim of our study was to demonstrate the use of a targeted next generation sequencing (NGS) HPV panel for CC screening—both general practitioner-collected samples and self-samples. We here show that the targeted HPV panel can detect HPV with a sensitivity and specificity similar to commercial HPV assays, one of which is used for CC screening today. However, the targeted HPV panel possess several advantages compared to the screening assays, as it enables specific detection of all relevant HPV types and can identify viral integration, variants in the HPV genome, and dominant HPV types in multi-infected cases. ABSTRACT: At present, human papillomavirus (HPV) testing is replacing morphology-based cytology as the primary tool for cervical cancer screening in several countries. However, the HPV assays approved for screening lack detection for all but one of the possibly carcinogenic HPV types and do not genotype all included HPV types. This study demonstrates the use of a targeted HPV next generation sequencing (NGS) panel to detect and genotype all 25 carcinogenic, probably carcinogenic, and possibly carcinogenic HPV types as well as the low-risk types HPV6 and HPV11. The panel was validated using a cohort of 93 paired liquid-based cytology samples (general practitioner (GP)-collected cervical samples and cervico-vaginal self-samples (SS)). Overall, the targeted panel had a sensitivity (GP = 97.7%, SS = 92.1%) and specificity (GP = 98.0%, SS = 96.4%) similar to the commercial HPV assays, Cobas(®) 4800 HPV DNA test (Roche) and CLART(®) HPV4S assay (GENOMICA). Interestingly, of the samples that tested positive with the NGS panel, three (6.4%) of the GP-collected samples and four (9.1%) of the self-samples tested positive exclusively for HPV types only included in the NGS panel. Thus, targeted HPV sequencing has great potential to improve the HPV screening programs since, as shown here, it can identify additional HPV positive cases, cases with HPV integration, variants in the HPV genome, and which HPV type is dominant in multi-infected cases.