The role of cell-free circulating tumor DNA (ctDNA) for detection of minimal residual disease (MRD) and recurrence in head and neck cancer

By Karen Howarth, PhD, Senior Director of Clinical Genomics, Inivata

Despite intensive therapies and improved treatment options, head and neck squamous cell carcinomas (HNSCC) remain a substantial burden to global health, with 5-year survival rates standing at less than 50%. In order to achieve better treatment outcomes, new diagnostic and therapeutic approaches are needed that can benefit from the identification of new and personalized biomarkers.¹ The use of liquid biopsy to detect tumor cells and nucleic acids, proteins or metabolites is becoming increasingly important in this regard.²⁻³ In particular, the analysis of cell-free circulating tumor DNA – or ctDNA – as a potential biomarker for tumor detection and monitoring is becoming increasingly useful for routine clinical practice.

The Department of Otorhinolaryngology, Head and Neck Surgery at the Hospital of the Ludwig-Maximilians-University Munich, Germany, set up the Liquid bIOpsy for miNimal rESidual diSease detection in Head and Neck Squamous Cell Carcinoma (LIONESS) study in collaboration with Inivata. The aims of the study were twofold; to determine whether post-operative ctDNA detection can act as a biomarker for surgical tumor clearance, and to evaluate the potential of personalized ctDNA analysis for early molecular-level detection of relapse before recurrence is clinically confirmed.

The single-center prospective cohort study is ongoing, but data is now available on the first 17 patients with p16-negative HNSCC who have received primary surgical treatment with curative intent. Whole exome sequencing (WES) was performed on formalin-fixed paraffin-embedded (FFPE) tissue obtained from each patient’s primary tumor.

Inivata’s RaDaRTM, a highly sensitive personalized assay that tracks multiple tumor-specific variants in a patient using a liquid biopsy, was used. Analysis was conducted on serial pre- and post-operative plasma samples for evidence of minimal residual disease (MRD) and recurrence.

In post-surgery samples, RaDaRTM detected ctDNA at levels as low as 0.0006% variant allele frequency (VAF). In all cases with clinical recurrence to date, ctDNA was detected prior to progression, with lead times, i.e. the interval between detection of the first ctDNA positive sample post-surgery and confirmation of clinical recurrence, ranging from 108 to 253 days. In the remaining patients there was no recurrence detected, indicating a 100% clinical specificity of the RaDaRTM assay, and confirming post-operative tumor clearance.

In conclusion, the study illustrates the potential of ctDNA as a biomarker for monitoring MRD as well as recurrence in patients with HNSCC and demonstrates the feasibility of personalized ctDNA assays for the detection of disease post-treatment and with consequences for further therapy planning.

Data produced from the LIONESS study has recently been published in the British Journal of Cancer and can be viewed here.


  1. Gatta G, Botta L, Sánchez MJ, Anderson LA, Pierannunzio D, Licitra L, et al. Prognoses and improvement for head and neck cancers diagnosed in Europe in early 2000s: The EUROCARE-5 population-based study. European Journal of Cancer. 2015 Oct;51(15):2130–43.
  2. Corcoran RB, Chabner BA. Application of Cell-free DNA Analysis to Cancer Treatment. New England Journal of Medicine. 2018 Nov;379(18):1754–65.
  3. Egyud M, Sridhar P, Devaiah A, Yamada E, Saunders S, Ståhlberg A, et al. Plasma circulating tumor DNA as a potential tool for disease monitoring in head and neck cancer. Head & Neck. 2018 Dec 15;68(1):7–8.
  4. Ignatiadis M, Sledge GW, Jeffrey SS. Liquid biopsy enters the clinic — implementation issues and future challenges. Nature Reviews Clinical Oncology. 2021 Apr 27;1–16.
  5. Cristiano S, Leal A, Phallen J, Fiksel J, Adleff V, Bruhm DC, et al. Genome-wide cell-free DNA fragmentation in patients with cancer. Nature. 2019 May 29;570(7761):385–9.
  6. Adalsteinsson VA, Ha G, Freeman SS, Choudhury AD, Stover DG, Parsons HA, et al. Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors. Nature Communications. 2017 Nov 6;8(1):985–13.
  7. Dawson S-J, Tsui DWY, Murtaza M, Biggs H, Rueda OM, Chin S-F, et al. Analysis of Circulating Tumor DNA to Monitor Metastatic Breast Cancer. The New England journal of medicine. 2013 Mar 13;368(13):1199–209.
  8. Goodwin S, McPherson JD, McCombie WR. Coming of age: ten years of next-generation sequencing technologies. Nature Reviews Genetics. 2016 Jun 1;17(6):333–51.
  9. Leary RJ, Kinde I, Diehl F, Schmidt K, Clouser C, Duncan C, et al. Development of personalized tumor biomarkers using massively parallel sequencing. Science translational medicine. 2010 Feb 24;2(20):20ra14.
  10. Wang Y, Springer S, Mulvey CL, Silliman N, Schaefer J, Sausen M. Detection of somatic mutations and HPV in the saliva and plasma of patients with head and neck squamous cell carcinomas. Science translational medicine. 2015 Jun 24;7(293):1–8.
  11. Bettegowda C, Sausen M, Leary RJ, Kinde I, Wang Y, Agrawal N, et al. Detection of Circulating Tumor DNA in Early- and Late-Stage Human Malignancies. Science translational medicine. 2014 Feb 19;6(224):224ra24-224ra24.
  12. Hamana K, Uzawa K, Ogawara K, Shiiba M, Bukawa H, Yokoe H, et al. Monitoring of circulating tumour-associated DNA as a prognostic tool for oral squamous cell carcinoma. British journal of cancer. 2005 May 31;92(12):2181–4.
  13. Schirmer MA, Beck J, Leu M, Oellerich M, Rave-Fränk M, Walson PD, et al. Cell-Free Plasma DNA for Disease Stratification and Prognosis in Head and Neck Cancer. Clinical Chemistry. 2018 Jun;64(6):959–70.

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