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H&N chipHead/neck carcinoma HNSCCNGS mutational panelTNM stagingTP53/CDKN2A/FAT1 genes


The invention relates to an in vitro diagnosis method of head and/or neck cancer in tissue samples and/or biological liquids. The aim is to provide a diagnosis of primary cancer, tumor recurrence and the presence of residual cancer cells in the resection margins of a surgical removal of the tumor. HNSCC carcinoma is the 6th most common malignant tumor today.

Technical features

The most common site of HNSCC cancer is the oral cavity (70%) followed by the larynx and pharynx. It has local spread and a low tendency to develop distant metastases. The absence of symptoms leads to a diagnosis already in the presence of metastases, with recurrence rates (50-60%) even after surgical resection that appears complete. TNM staging is the 1st classification system for HNSCC tumors, however it does not discriminate the heterogeneity of tumors; patients with the same clinical stage do not have the same course, response to therapy, relapse rate and survival. The TP53 tumor suppressor gene mutation is the most frequent in HNSCC. The invention detects mutations in 3 specific genes TP53, CDKN2A and FAT1 providing a sensitive diagnostic method. Gene sequencing identifies known and unknown mutations. For example, the method can foresee a specific mutational panel based on NGS (also called H&N chip) with DNA coding sequence of the TP53, CDKN2A and FAT1 genes in tissue or liquid samples (plasma/saliva). Most HNSCCs contain mutations identifying large numbers of patients. The method detects mutations with very low allele frequencies (<1%). In particular, through the TP53, CDKN2A and FAT1 sequence assay mutations with allelic frequency> 0.2% are detected.

Possible Applications

  • Detect, monitor and predict the course of head and neck squamous cell carcinoma (HNSCC) with high specificity and sensitivity;
  • Applicable technique to characterize tumor heterogeneity and diagnose residual tumor cells in the resection margins.


  • High precision in screening assay and diagnostics;
  • The presence of only 3 genes makes the panel more sensitive than traditional ones;
  • There are no panels that use FAT1 in the mutational profile;
  • DNA detection of cancer cells in tissue, liquid and lymph node samples.