Abstract PR007: Screening early detection of HPV-associated oropharynx cancers with multi-feature HPV whole genome sequencing liquid biopsy
Authors: Kuhs Krystle , Robbins Hilary , Das Dipon , Bryan Michael , Aye Ling , Al-Inaya Yana , Hirayama Shun , Adalsteinsson Viktor , Lawrence Michael , Waterboer Tim , Faden Daniel L 
Published: November 2024

Abstract
Early detection of HPV-associated oropharyngeal cancer (HPV+OPSCC), the most common HPV cancer in the United States, could reduce disease-related morbidity, yet currently there are no screening tests. Circulating tumor HPV DNA (ctHPVDNA) is a sensitive and specific biomarker for HPV+OPSCC at diagnosis. It was previously unknown if ctHPVDNA is detectable prior to HPV+OPSCC diagnosis, and thus it’s potential as a screening test. We recently reported (2023 AACR-AHNS Head and Neck Cancer Conference) detection of ctHPVDNA with 79% overall sensitivity at 100% specificity in a case-control cohort of HPV+OPSCC patients with plasma samples collected 1-11 years prior to diagnosis (n=28) and age- and sex-matched controls (n=28) from the MassGeneralBrigham Biobank (MGBB) using a custom multi-feature HPV whole genome sequencing liquid biopsy, termed HPV-DeepSeek, demonstrating for the first time, the feasibility of blood-based screening for HPV+OPSCC. Here, we extend and validate these finding in a second independent cohort and generate combined metrics for estimating HPV+OPSCC screening accuracy by HPV-DeepSeek. We conducted a blinded case-control study nested within the NCI PLCO Screening Trial. PLCO enrolled 155,000 healthy participants from November 1993-July 2001 with plasma sample collected at multiple time points. All patients were followed for cancer outcomes. PLCO participants who were diagnosed with OPSCC &gt;6 months after blood sample contribution were identified and matched 1:2 with controls based on smoking status, sex, race, year of blood collection, and year of birth. 400ul of plasma was retrieved, blinded, and transferred for testing. After quality control, the cohort included 72 OPSCC cases and 144 controls. Samples had previously underdone HPV E6 antibody testing which was used as a marker of HPV status. All samples were run on HPV- DeepSeek using pre-defined cut points and results were returned to NCI CDAS where case- control status was unblinded. 32 OPSCC cases were HPV E6 antibody positive and thus regarded as HPV16+OPSCC. 20/32 were ctHPVDNA positive and 12/32 were ctHPVDNA negative (overall sensitivity 63%). Specificity was 99%. The mean lead time of positive cases was 6.3 years, and the maximum lead time was 11.3 years. Sensitivity was highest closest to diagnosis and declined further from diagnosis (100% within 3 years of cancer diagnosis, 58% from 3-9 years, 20% from 9-12 years; p&lt;0.001). Four additional samples were positive for non- HPV16 genotypes (31, 33, 33, 39) in the overall cohort. When combined with the MGBB cohort, overall screening sensitivity was 70% and specificity was 99%. Sensitivity within 3 years of cancer diagnosis was 100%. ctHPVDNA can be detected in the blood up to 11 years prior to diagnosis with HPV+OPSCC, with ≥99% specificity, and an overall screening sensitivity of 70% in a cohort of 100 OPSCC cases and 172 controls using a multi-feature HPV WGS liquid biopsy. ctHPVDNA detection alone, or in combination with previously identified serological biomarkers, may be a feasible approach to screening for HPV+OPSCC.
Citation Format: Krystle Kuhs, Hilary Robbins, Dipon Das, Michael Bryan, Ling Aye, Yana Al-Inaya, Shun Hirayama, Viktor Adalsteinsson, Michael Lawrence, Tim Waterboer, Daniel L Faden. Screening early detection of HPV-associated oropharynx cancers with multi-feature HPV whole genome sequencing liquid biopsy [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr PR007.