Evidence map›Paper›PMID 39793474›Full record

ArticleJournal of clinical virology : the official publication of the Pan American Society for Clinical Virology2025

Highly-multiplex detection of plasma cell-free human papillomavirus-16 DNA in oropharyngeal carcinoma.

Payton Clark, Natalya Karasik, Shauna R Campbell, Neil M Woody, Jamie A Ku, Natalie Silver, Danielle Bottalico, Brandon L Prendes, Eric D Lamarre, Joseph Scharpf and 6 more

Abstract read
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In one paragraph

Article in Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

16 authors.

Payton ClarkCenter for Immunotherapy and Precision Immuno-Oncology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
Natalya KarasikDepartment of Radiation Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.
Shauna R CampbellDepartment of Radiation Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.
Neil M WoodyDepartment of Radiation Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.
Jamie A KuDepartment of Head and Neck Surgery, Head and Neck Institute, Cleveland Clinic, Cleveland, OH, USA.
Natalie SilverDepartment of Head and Neck Surgery, Head and Neck Institute, Cleveland Clinic, Cleveland, OH, USA.
Danielle BottalicoDepartment of Head and Neck Surgery, Head and Neck Institute, Cleveland Clinic, Cleveland, OH, USA.
Brandon L PrendesDepartment of Head and Neck Surgery, Head and Neck Institute, Cleveland Clinic, Cleveland, OH, USA.
Eric D LamarreDepartment of Head and Neck Surgery, Head and Neck Institute, Cleveland Clinic, Cleveland, OH, USA.
Joseph ScharpfDepartment of Head and Neck Surgery, Head and Neck Institute, Cleveland Clinic, Cleveland, OH, USA.
Tamara A SussmanDepartment of Medical Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.
Jessica L GeigerDepartment of Medical Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.
Hannah WangDepartment of Laboratory Medicine, Diagnostics Institute, Cleveland Clinic, Cleveland, OH, USA.
Timothy A ChanCenter for Immunotherapy and Precision Immuno-Oncology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Department of Radiation Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.
Shlomo A KoyfmanDepartment of Radiation Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.
Jacob A MillerCenter for Immunotherapy and Precision Immuno-Oncology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Department of Radiation Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA. Electronic address: millerj73@ccf.org.

Funding

Translational and Clinical Trial Correlates CoreU54CA274513 · NCI · CLEVELAND CLINIC LERNER COM-CWRU · PI Timothy An-thy Chan · 2022 to 2026
$9.3M
NCI NIH HHS U54 CA274513
6 · The paper itself

Abstract

backgroundPlasma cell-free Human Papillomavirus DNA (cfHPVDNA) is a biomarker for oropharyngeal carcinoma. Existing diagnostics may be limited by inadequate sensitivity or high cost/complexity for longitudinal monitoring.

objectivesWe hypothesized that sensitive and specific plasma cfHPVDNA detection may be achieved via a highly-multiplex qPCR method. STUDY

designWe designed and validated a single-tube one-step genotype-specific qPCR assay for detection of cfHPV16DNA in human plasma using >8,000 genomes spanning 18 genotypes. Amplicons were optimized for cfHPVDNA fragment size.

resultsThe cfHPV16DNA qPCR amplicons spanned 16 % of the HPV16 genome. Amplicons were conserved in a median of 99.0 % of 3,944 genomes in silico. The 95 % lower limit of detection was 0.35 genome copies/reaction and the limit of blank was 0. Multiplexing achieved a tenfold improvement in sensitivity compared with single amplicons using in silico simulations of cfHPVDNA fragmentation, which was in close agreement with experimental observations. An assay was replicated for HPV18 with similar observations. Among 36 patients with head/neck mucosal carcinomas (26 HPV-positive, 12 HPV-negative), there was 100 % concordance with tissue HPV status and with NavDx digital PCR. Pre-treatment specimens with sub-genomic cfHPVDNA concentration were detected. False negatives were observed with single amplicons but not with this multiplexed method. Among 17 patients with post-treatment landmark specimens, there was 100 % PPV and 100 % NPV for recurrence.

conclusionsThis assay is specific for plasma cfHPVDNA detection and prognostic for recurrence. Sub-genomic sensitivity was in close agreement with in silico simulations. The format might be more accessible than dPCR or NGS for longitudinal testing.

Indexed as

Cell-Free Nucleic AcidsDNA, ViralHuman papillomavirus 16Oropharyngeal NeoplasmsPapillomavirus InfectionsAgedFemaleGenotypeHuman Papillomavirus VirusesHumansMaleMiddle AgedReal-Time Polymerase Chain ReactionSensitivity and SpecificityCell-Free Nucleic AcidsDNA, ViralCell free DNAHuman papillomavirusOropharyngeal carcinoma

Identifiers

PMID39793474
PMCPMC13292461

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.