Key differences between HPV-positive and HPV-negative head and neck squamous cell carcinomas (HNSCC)

Head and neck squamous cell carcinomas (HNSCC) develop from the mucosal epithelium in the oral cavity, pharynx, and larynx and are the most common malignancies that arise in the head and neck.1 Increasingly, tumors in the oropharynx are linked to prior infection with oncogenic strains of human papillomavirus (HPV), primarily HPV-16 and, to a lesser extent HPV-18 and others.2,3 HNSCCs of the oral cavity and larynx are primarily associated with tobacco-derived carcinogens, excessive alcohol consumption, or both, and are collectively referred to as HPV-negative HNSCC.4 The median age of diagnosis for non-virally associated HNSCC is 66 years, whereas the median age of diagnosis for HPV-associated oropharyngeal cancer is about 53 years.5

HPV-positive and HPV-negative HNSCC are two distinct diseases with different sites of origin, etiological agents, risk factors, and contributions to the development of oropharyngeal squamous cell carcinoma (OPSCC). The demographics, cause, and prevalence of HPV-positive and NPV-negative cancers are summarized in Table 1.

Table 1: Demographics, Cause, and Prevalence of HNSCC.

Whereas the incidence of smoking-related HNSCC continues to decline worldwide, that of HPV-positive HNSCC is on the rise.6 During 2007-2016, HPV-associated cancers increased by 2.1% per year on average, whereas cancers not associated with HPV decreased by 0.4% per year on average.6

HPV-positive and HPV-negative HNSCCs present with different molecular characteristics, immune landscapes, and clinical prognosis (Table 2) and lead to two fundamentally different diseases with distinct pathogenesis in terms of gene expression, tumor microenvironment (TME), and mutational burden.

Table 2. Pathology and Disease Signature in HNSCC.

Genomic and epigenetic analyses reveal extremely high heterogeneity in HNSCC in terms of characteristic mutations, molecular signature, cellular phenotype, composition of TME, and immune landscape (Table 3).

Table 3. Characteristic mutations in HPV-positive and HPV-negative HNSCC.

Various promising vaccine targets have been identified and treatment options employed for the treatment of HPV-positive and HPV-negative cancers with varying degrees of success (Table 4).

Table 4. Treatment options and targets.
Treatment personalization and de-escalation

According to Dr. Nishant Agrawal, Chief of Otolaryngology-Head & Neck Surgery UChicago Medicine, “We have seen a significant increase in the incidence of HPV-associated oropharyngeal cancer in relatively younger patients, with the median age of diagnosis in the 50s, even patients in their 30s.”32 He added that “Even at 2 years after radiation therapy, 15% of patients had grade 2 swallowing dysfunction and 8% had progressive dysphagia, so their swallowing is going to continue to get worse. Patients may also have chronic xerostomia. The dry mouth improves but it never gets back to 100%.”33 In contrast to patients with HPV-negative HNSCC, who have a five-year survival rate of about 25%-40%, patients with HPV-positive HNSCC fare much better with a disease-free survival rate of 85%-90% over five years. According to Dr. Agrawal, the better prognosis for HPV-positive patients suggests a need to de-escalate treatment while preserving survival.


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  3. Michaud, D.S. et al. (2014) High-risk HPV types and head and neck cancer. Int J Cancer. (135);1653-61.
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  10. Mahal, B.A. et al. (2019) Incidence and Demographic Burden of HPV-Associated Oropharyngeal Head and Neck Cancers in the United States. Cancer Epidemiol Biomark Prev. 28(10);1660-67.
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Sysmex Inostics Introduces CLIA-Validated Highly Sensitive HNSCC-SEQ Testing Services for Head and Neck Cancer at the 2022 Molecular Medicine Tri-Conference

Presenting Poster of Clinical Trial Findings at 2022 Multidisciplinary Head and Neck Cancers Symposium

Baltimore, MD, February 22, 2022 – Sysmex Inostics, a global leader in the liquid biopsy revolution for oncology, will introduce HNSCC-SEQ, a highly sensitive Plasma-Safe-SeqS and Next Generation Sequencing (NGS) assay service for head and neck squamous cell carcinomas (HNSCC), at the annual 2022 Molecular Medicine Tri-Conference being held Monday, February 21st through Wednesday, February 23rd in San Diego, California. The assay has a turn-around-time of 7-10 days and is available to researchers and clinicians.

Sysmex Inostics senior director of medical affairs, Dr. Fred Jones stated, “We see a huge opportunity for researchers and clinicians with our HNSCC-SEQ and HPV-SEQ assays being used in tandem to appropriately identify patients’ tumor mutational drivers.” Jones added, “We know the human papillomavirus (HPV) fuels a growing percentage of head and neck cancers, but there is also an unmet need to track HNSCC tumors via circulating tumor DNA (ctDNA) that are HPV-negative – that’s where HNSCC-SEQ comes in. This HNSCC panel helps researchers and clinicians identify patients quickly and accurately for the appropriate therapy and avoiding over-treatment.”

HNSCC develop from the mucosal tissue in the oral cavity, pharynx, and larynx and are the most common malignancies that arise in the head and neck regions.¹ HNSCC-SEQ was designed for HPV-negative patients and can be used to detect novel therapeutic targets and frequently occurring driver mutations for treatment response monitoring. HNSCC-SEQ delivers high-sensitivity mutation detection in HNSCC with a limit of detection of 0.05% MAF.2

HNSCC-SEQ can identify head and neck cancer mutational drivers from the genes: CDKN2A, EGFR, ERBB2, FGFR3, HRAS, KRAS, NOTCH1, PIK3CA, PTEN, and TP53, many of which are actively being pursued as therapeutic targets.3

Dr. Jones will discuss how Plasma-Safe-SeqS technology, including HNSCC-SEQ, can aid cancer drug development, treatment guidance and monitoring, in addition to post-treatment recurrence monitoring during the 2022 Molecular Medicine Tri- Conference’s C4B- Clinical Biomarkers & Companion Diagnostics presentation track in session room Indigo 206 on Tuesday, February 22nd at the Hilton San Diego Bayfront. More information about the presentation can be viewed here.

2022 Multidisciplinary Head and Neck Cancers Symposium

Additionally, Dr. Ari Rosenberg, Assistant Professor of Medicine at the University of Chicago will present findings from his study using Sysmex Inostics HPV-SEQ test at the 2022 Multidisciplinary Head and Neck Cancers Symposium being held February 24th through 26th in Phoenix, Arizona. The poster titled ‘Dynamic changes of cell-free HPV DNA in locoregional viral-associated oropharyngeal cancer receiving response-adaptive treatment’ will be presented Thursday, February 24th. More information can be viewed here.

HNSCC-SEQ and HPV-SEQ are available as a testing service provided by the Sysmex Inostics CLIA lab in Baltimore. MD.

About Sysmex Inostics

Sysmex Inostics, Inc., a US-based Sysmex Corporation subsidiary, empowers discoveries in oncology by providing investigators with ultra-sensitive, quantitative, and cost-effective CLIA-validated liquid biopsy services.

Since 2008, Sysmex Inostics has provided leading Pharma companies custom liquid biopsy assay services, first OncoBEAM™ and now Plasma-Safe-SeqS technology, to support real-time therapy selection and targeted-mutational monitoring during and after treatment throughout the clinical trial process.

Developed by experts at Johns Hopkins with the philosophy of “no molecule left behind,” Sysmex Inostics Plasma-Safe-SeqS technology has robust detection as low as 0.03% allele frequency (for input of 20,000 genomic equivalents) without sacrificing specificity. The venerable OncoBEAM™ digital PCR cell-free DNA (cfDNA) technology has been employed in hundreds of pivotal studies, publications, and numerous drug discoveries in oncology. Plasma-Safe-SeqS NGS technology, introduced in 2019, is currently being used in various clinical studies.

In July 2021, Sysmex Corporation announced a global strategic alliance with QIAGEN to expedite clinical trial timelines and CDx development by uniting QIAGEN’s commercial and regulatory expertise with the liquid biopsy scientific rigor and knowledge of Sysmex Inostics.

Sysmex Inostics offers Plasma-Safe-SeqS technology services in its CLIA-certified laboratory in Baltimore, Maryland.

For more information, refer to or email

Tracy Vandenbroek Director, Marketing Sysmex Inostics


  1. Stein, A. P. et al. (2015) Prevalence of human papillomavirus in oropharyngeal cancer: a systematic review. Cancer J. 21, 138-146.
  2. Internal validation data, Sysmex Inostics, Inc.
  3. Jiang X, Ye J, Dong Z, Hu S, Xiao M. Novel genetic alterations and their impact on target therapy response in head and neck squamous cell carcinoma. Cancer Manag Res. 2019;11:1321-1336. Published 2019 Feb 8. doi:10.2147/CMAR.S187780