A multimodal sequencing framework to define viral and host genomic heterogeneity in HPV associated head and neck cancer

Background: This study aims to integrate viral and host genomic analyses with social determinants of health (SDOH) to improve biologic risk stratification in patients with human papillomavirus-associated head and neck cancer (HPV+ HNC). Methods: Patients with biopsy-proven, p16-positive HPV+ HNC were enrolled. Archived or fresh tumor tissue underwent DNA extraction followed by HPV consensus-primer genotyping targeted to the L1 locus (MY09/MY11 primer sequences) to determine viral type. Samples with confirmed HPV infection proceed to short-read sequencing for viral genotype characterization and host mutational profiling, and long-read sequencing to define HPV integration architecture, HPV-host fusion events, and larger structural variants. Demographic, clinical, and SDOH variables were collected to explore associations between patient context and genomic heterogeneity. Results: To date, 10 patients have provided informed consent and have been enrolled in this study. Additionally, eights archived tumor specimens have been analyzed. The cohort consists of seven White male, two Hispanic or Latino male, and one White female patients. Archived specimens were derived from three White, two Asian, two Black, and one Hispanic patient. Preliminary HPV genotyping demonstrates a distribution of high-risk HPV types, including HPV16, HPV18, HPV33, HPV35, and HPV59. These early results suggest a potential variation across ancestry and SDOH-defined clusters, with White patients predominantly demonstrating the HPV16 genotype, while there is a higher prevalence of non-16 types amongst other racial and ethnic groups. Conclusions: These early findings highlight the value of broadening HPV genotype characterization and capturing patient diversity to uncover the full spectrum of viral and host genomic variation in HPV+ HNC. Ongoing expansion of the cohort and completion of sequencing analyses will be critical next steps toward defining clinically meaningful genomic subgroups and developing future frameworks for precision risk stratification, surveillance, and treatment personalization in HPV-associated head and neck cancer.