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Published on: April 11, 2016
Clearance of circulating HPV DNA during chemoradiation using a next-generation sequencing liquid biopsy
Mina Bakhtiar1, Yana Al-Inaya2, Dipon Das2
1Department of Radiation Oncology, Mass General Brigham, Boston, MA, USA.
Background And Purpose:
Next-generation sequencing (NGS) assays are being evaluated to measure circulating tumor DNA (ctDNA) in human papilloma virus-driven oropharynx squamous cell carcinoma (HPV-OPSCC). This technology has not yet been explored in patients receiving definitive therapy. Here, we employ HPV-DeepSeek, a whole-genome NGS assay, to interrogate ctHPVDNA levels in patients receiving chemoradiation for HPV-OPSCC.
Materials And Methods:
This was a secondary analysis of plasma samples from a single-institution prospective biomarker study. Plasma samples from adults treated with definitive chemoradiation for HPV-OPSCC were analyzed using HPV-DeepSeek. Clinical and patient factors were abstracted from the electronic medical record. Spearman correlation, Kruskal-Wallis/Mann-Whitney U testing and univariable linear regression were used to test the association between baseline ctHPVDNA reads and clearance rate by patient and disease features.
Results:
Twenty-three patients with AJCC 8th edition clinical stage I-II HPV-OPSCC were included. HPV-DeepSeek detected ctHPVDNA in 100% of samples collected in week 1. Twenty-six percent of patients cleared ctHPVDNA by week 4, 52% cleared by week 6, and 17% cleared by first follow-up. One patient did not clear ctHPVDNA and was lost to follow-up. On univariable regression, ctHPVDNA level was associated with AJCC 8th edition nodal stage (coeff = 44831, p = 0.022), overall stage (coeff = 43907, p = 0.05), and viral integration (coeff = 61813, p = 0.008). Median follow-up was 7.3 years. There were no recurrences.
Conclusions And Relevance:
HPV-DeepSeek, an ultra-sensitive NGS assay, can detect ctHPVDNA clearance in patients receiving definitive chemoradiation for HPV-OPSCC.
Insights
An ultra-sensitive next-generation sequencing (NGS) assay, HPV-DeepSeek, effectively detects circulating tumor human papillomavirus DNA (ctHPVDNA) clearance in patients undergoing chemoradiation for HPV-OPSCC, showing promise for monitoring treatment response.
Area of Science:
- Oncology
- Genomics
- Molecular Diagnostics
Background:
- Human papillomavirus-driven oropharynx squamous cell carcinoma (HPV-OPSCC) is a growing concern.
- Next-generation sequencing (NGS) assays are emerging tools for detecting circulating tumor DNA (ctDNA).
- The utility of NGS for monitoring ctDNA during definitive therapy for HPV-OPSCC remains largely unexplored.
Purpose of the Study:
- To evaluate the HPV-DeepSeek whole-genome NGS assay for measuring ctHPVDNA levels in patients with HPV-OPSCC receiving chemoradiation.
- To assess the ability of HPV-DeepSeek to detect ctHPVDNA clearance during definitive therapy.
Main Methods:
- Secondary analysis of plasma samples from a prospective biomarker study.
- Utilized the HPV-DeepSeek NGS assay to analyze ctHPVDNA in adult patients treated with definitive chemoradiation for HPV-OPSCC.
- Employed statistical methods including Spearman correlation and univariable linear regression to associate ctHPVDNA levels with clinical and disease features.
Main Results:
- HPV-DeepSeek detected ctHPVDNA in 100% of samples from 23 patients with AJCC 8th edition stage I-II HPV-OPSCC.
- ctHPVDNA clearance was observed in 26% by week 4, 52% by week 6, and 17% by first follow-up.
- Baseline ctHPVDNA levels correlated with AJCC nodal stage, overall stage, and viral integration.
Conclusions:
- The ultra-sensitive HPV-DeepSeek NGS assay can successfully detect ctHPVDNA clearance in patients undergoing chemoradiation for HPV-OPSCC.
- This assay shows potential as a tool for monitoring treatment response in this patient population.
- No recurrences were observed during a median follow-up of 7.3 years.
