1. The Clinical Utility of a Next-Generation Sequencing-Based Approach to Detecting Circulating HPV DNA in Patients with Advanced Anal Cancer.
- Author
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Bhamidipati, Deepak, Johnson, Jay R., Lin, Kangyu, Pelicano, Helene, Eng, Cathy, Huey, Ryan, Wolff, Robert A., Halperin, Daniel M., Frumovitz, Michael F., Wistuba, Ignacio I., Duose, Dzifa Y., Mallampati, Saradhi, Luthra, Rajyalakshmi, and Morris, Van K.
- Subjects
PAPILLOMAVIRUS diseases ,RESEARCH funding ,DNA ,METASTASIS ,LONGITUDINAL method ,ANAL tumors ,EPITHELIAL cell tumors ,SEQUENCE analysis ,MOLECULAR diagnosis - Abstract
Simple Summary: Detecting circulating tumor DNA (ctDNA) in the blood has emerged as a valuable method for evaluating several different cancers. Most anal cancers are caused by HPV infection, which is typically identified through the examination of tissue specimens. In this study, we describe a novel method for detecting HPV in the ctDNA using next-generation DNA sequencing on blood samples from patients with advanced anal cancer. The assay was able to detect multiple types of HPV, including uncommon variants. Additionally, the assay appeared to correlate with the disease burden and response to treatment. HPV DNA can often integrate into cancer DNA, which was detectable using our assay, and we show that this may prognosticate which patients are more resistant to treatment. Background: To extend the practicality of liquid biopsy beyond the historical HPV circulating tumor DNA (ctDNA) assays, we evaluated the clinical relevance of a novel next-generation sequencing HPV ctDNA assay in patients with locally advanced and metastatic squamous cell cancer of the anal canal (mSCCA). Methods: ctDNA isolated from the plasma of patients with mSCCA was sequenced using a 1.4 Mb hybrid-capture target-enrichment panel covering the whole genome sequences of all 193 HPV types. The HPV type, copy number (CN), and integration sites were determined using a bioinformatic pipeline. Results: A total of 77 plasma samples from 28 patients with HPV-related SCCA were retrospectively analyzed. HPV ctDNA was detected in 26 cases (93%) (including uncommon subtypes). The median HPV CN was higher in metastatic versus locally recurrent/unresectable SCCA (p = 0.043). Changes in the HPV CN were concordant with the radiographic response (p = 0.027). An integration event was detected in 23 patients (82%), with presumed episomal HPV DNA present in the remaining patients. Higher HPV integration (a mean of ≥1 integration across samples) was associated with a worse overall survival from the start of immunotherapy (13.6 months versus 36.0 months; p = 0.003). Conclusions: Using HPV-informed next-generation sequencing of the ctDNA, we found changes in the HPV CN correlated with the treatment response and that HPV integration detected in the ctDNA is an unfavorable prognostic biomarker. [ABSTRACT FROM AUTHOR]
- Published
- 2025
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