Abstract 363: Investigating the potential clinical predictive value of virus genotype, menopausal status and mutational landscape in cervical cancer tissue using a NGS based human papillomavirus (HPV) assay and whole exome sequencing (WES)
Authors: Pignon Jean-Christophe , Giese Heidi , Foernzler Dorothee , McDaniel Lee D. , Bartha Gabor , Scheuenpflug Juergen , Feng Zheng 
Published: July 2021

Abstract
Purpose: Persistent HPV infections are associated with nearly all cervical cancers and some head & neck and genitourinary cancers. In cervical cancer, 14 high risk HPV genotypes have been previously identified with varying geographical prevalence and carcinogenicity. HPV16 and 18 account for &gt;70% of cervical cancer incidence worldwide. There is an unmet need to explore HPV-associated cancer pathology, HPV infection status and molecular profiles to detect virus load and identify predictive gene signatures. We investigated the association between HPV genotypes and clinicopathological features and analyzed the mutational landscape using the ImmunoID NeXT Platform®.
Methods: Early stage cervical cancer FFPE tissue samples (n=38) were analyzed. We detected and quantified oncoviral DNA, identified likely somatic mutations, and quantified genome-wide mutational burden. Any sample with at least one filtered read of HPV evidence was considered positive; zero such evidential reads were reported across a negative control cohort of &gt; 439 non-cervical cancer samples. Oncovirus DNA counts and HPV genotype status were then evaluated against covariates (age; menopausal status) for statistical significance. Finally, mutation frequency was assessed in genes comprising major cervical cancer driver pathways from the KEGG and Biocarta databases.
Results: Oncoviral HPV infections were detected using a NGS based approach in all tumor tissue with demonstrated robust assay performance. A statistically significant difference in viral DNA counts was observed between high risk genotypes HPV16 and 18 (n=27) and all other genotypes (n=10), (p=0.028, Student's t). Genotypes were also significantly associated with menopausal status (p=0.01, Fisher's Exact Test) and age at surgical resection (p=0.011, Student's t). Among the pathways considered, TGF-β and MAP-kinase were the most frequently mutated across 38 samples and multiple pathway annotations.
Conclusions: We applied a powerful NGS based WES approach that enables accurate detection of HPV genotypes with quantification of HPV viral DNA. This quantitative approach represents a possible promising clinical benefit over existing qualitative HPV genotyping assays and may have the potential for further development to define cancer type and treatment specific cutoff values for cancer prognosis. Furthermore, our results demonstrate that a WES based approach provides clinically valuable insights into the constitutive molecular mechanisms of cervical cancer. The association of HPV genotypes with clinical patient characteristics and/or mutational profiles has the potential to identify prognostic and predictive clinical biomarkers and to provide critical information for treatment defining strategies.
Citation Format: Jean-Christophe Pignon, Heidi Giese, Dorothee Foernzler, Lee D. McDaniel, Gabor Bartha, Juergen Scheuenpflug, Zheng Feng. Investigating the potential clinical predictive value of virus genotype, menopausal status and mutational landscape in cervical cancer tissue using a NGS based human papillomavirus (HPV) assay and whole exome sequencing (WES) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 363.