Abstract A012: Analytical validation of a cfDNA-based fragmentomic profiling assay for the detection and quantification of 14 HPV types in cervical cancer
Authors: Sunil Kumar, Joshua Hutcheson, David Conway, Michael Horan, Syandan Chakraborty, Chloe Wiseman, Alicia Gunning, Evgeny Skyrypkin, Cassin Williams, Catherine Del Vecchio Fitz, Piyush B Gupta
Journal: Clinical Cancer Research (2024)

Abstract Purpose: Human papillomavirus (HPV) is the primary cause of cervical cancer, one of the most common cancers affecting women globally. Despite advances in prevention and screening, there remains a critical need for reliable, non-invasive assays to detect and monitor HPV-driven cervical cancers. Liquid biopsy offers a promising solution to meet this need. Here, we report the analytical validation of a plasma-based fragmentomic profiling assay designed to detect and characterize circulating tumor tissue modified viral (TTMV)-HPV DNA from 14 HPV types associated with cervical cancer. Methods: A high-complexity, laboratory-developed test was developed that employs 68 primers and 34 probes to target 14 HPV types via droplet digital PCR (ddPCR). A quantitative algorithm was applied to integrate fragment counts to generate a TTMV-HPV DNA Score, reflective of the quantity of circulating tumor-derived HPV DNA. Analytical validation was performed by determining the limit of blank (LOB), limit of quantitation (LOQ), and limit of detection (LOD) for each HPV type. To measure the limits of assay performance, engineered samples were used for reference interval studies. Synthesized target-specific DNA regions of HPV16, HPV18, HPV31, HPV33, HPV35, HPV39, HPV45, HPV51, HPV52, HPV56, HPV58, HPV59, HPV66, and HPV68 were diluted to varying concentrations to perform assay validation. Results: The assay demonstrated excellent specificity, with LOBs ranging from 0 to 0.07 copies/µL across the 14 HPV types. LODs ranged from 0.20 to 1.02 copies/µL, indicating a high level of sensitivity. The assay also showed high accuracy and precision, with coefficients of variation (CV) below 20% for all HPV types across both intra- and inter-assay precision studies. Regression analysis confirmed strong linearity (R2 &amp;gt; 0.99) across a wide range of analyte concentrations. Conclusion: These results demonstrate that TTMV-HPV DNA assay accurately and reproducibly detects circulating HPV DNA for 14 HPV types commonly associated with cervical cancer, offering a valuable tool for both diagnosis and ongoing surveillance in clinical settings. Future studies will present the clinical validation in order to establish the prognostic utility of the assay in predicting the likelihood of HPV-driven cervical cancer in patients. Citation Format: Sunil Kumar, Joshua Hutcheson, David Conway, Michael Horan, Syandan Chakraborty, Chloe Wiseman, Alicia Gunning, Evgeny Skyrypkin, Cassin Williams, Catherine Del Vecchio Fitz, Piyush B Gupta. Analytical validation of a cfDNA-based fragmentomic profiling assay for the detection and quantification of 14 HPV types in cervical cancer [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 A012.