HPV Genotyping by Oxford Nanopore Sequencing
Human papillomavirus (HPV) is linked to various cancers, including cervical, anal, and head and neck cancers. Conventional methods for HPV genotyping and commercial platforms are limited to detecting high-risk HPV genotypes primarily in gynecological samples. Because of changing trends in the epidemiology and pathogenesis, there is a growing need for HPV genotyping techniques applicable to emerging clinical contexts involving diverse sample types, such as head and neck or anal samples, particularly for formalin-fixed paraffin-embedded (FFPE) tissues. This study aimed to validate amplicon-based sequencing with Oxford Nanopore Technologies for the detection and genotyping of HPV in 181 samples including FFPE head and neck samples, and ThinPrep® liquid-based cytology samples from anal and gynecological tissues. Sanger sequencing was used as a reference for genotyping accuracy. Our ONT sequencing method demonstrated a limit of detection of 1 copies/µL for HPV16 and HPV18. Perfect agreement (kappa coefficient = 1.0) was observed for HPV detection across all sample types. Genotyping accuracy exceeded 95%, and ONT identified additional genotypes in certain anal and gynecological samples that were undetected by Sanger sequencing. The assay showed high reproducibility, with consistent results across intra- and inter-run analyses. This study is the first to validate ONT sequencing for HPV genotyping in FFPE head and neck samples. ONT provides a rapid, cost-effective method for comprehensive HPV genotyping in diverse sample types.