Identification of Human Papillomavirus Infection in Cancer Tissue by Targeted Next-generation Sequencing

Abstract

Human papillomaviruses (HPV) are oncogenic DNA viruses implicated in squamous cell carcinomas of several anatomic sites, as well as endocervical adenocarcinomas. Identification of HPV is an actionable finding in some carcinomas, potentially influencing tumor classification, prognosis, and management. We incorporated capture probes for oncogenic HPV strains 16 and 18 into a broader next-generation sequencing (NGS) panel designed to identify actionable mutations in solid malignancies. A total of 21 head and neck, genitourinary and gynecological squamous cell carcinomas and endocervical adenocarcinomas were sequenced as part of the UNCSeq project. Using p16 immunohistochemical results as the gold standard, we set a cutoff for proportion of aligned HPV reads that maximized performance of our NGS assay (92% sensitive, 100% specific for HPV). These results suggest that sequencing of oncogenic pathogens can be incorporated into targeted NGS panels, extending the clinical utility of genomic assays.

The Human Virome: Implications for Clinical Practice in Transplantation Medicine

“…Use of metagenomic NGS approaches to broadly test for viruses in clinical samples has enabled the discovery of emerging and relevant viruses in global disease outbreaks and acute and chronic diseases, including in the immunocompromised host (36)(37)(38)(39). Many clinical syndromes for which an etiologic agent remains undetermined are believed to be viral in origin, particularly as current viral diagnostic methods used in the clinical laboratory do not detect the breadth of potentially causative viruses.…”

Current and Emerging Molecular Tests for Human Papillomavirus–Related Neoplasia in the Genomic Era

“…Mutation analyses have the potential to identify actionable mutations that predict treatment response or that confer prognostic information. 39 However, given that surgical excision and radiation therapy typically obviate the need for targeted therapy, the clinical utility of sequencing HPV þ carcinomas is limited. As the cost and convenience of performing next-generation sequencing in clinical laboratories continue to improve, it may become routine to sequence carcinomas at the time of diagnosis to identify patientspecific tumor mutations by which to track tumor burden and to predict recurrence, using either repeat biopsies or serial plasma DNA analysis.…”

“…40,42 Incorporating viral targets into next-generation sequencing panels could streamline the process of identifying viral and somatic tumor markers to be used to monitor tumor burden and to demonstrate efficacy of therapy. 39…”

“…The Hologic Cervista HPV HR assay detects 14 HPV types, including the 13 detected by the Hybrid Capture 2 (16,18,31,33,35,39,45,51,52,56,58,59, and 68) as well as type 66 using Invader probe technology. 61 The assay is FDA approved for essentially the same indications as the Qiagen Digene HC2 test.…”

“…There is interest in using massive parallel sequencing to simultaneously identify virus, assess viral types and additional viral genomic variants, and detect relevant human gene mutations in tissue, cytology, or body fluid samples. 39 Genomic methods have recently been described. 9,10,45,80 Cell-free DNA assays for HPV DNA in plasma show promise as a noninvasive measure of HPV þ carcinoma burden, and work is underway to evaluate this approach to monitor treatment efficacy, to identify recurrence, and to enhance early cancer detection.…”