OncoPrism-HNSCC uses RNA-sequencing and machine learning (ML) to analyse cancer cells from patients with head and neck cancer. Credit: Pormezz via Shutterstock.

Cofactor Genomics has showcased positive data highlighting that its clinical biomarker assay OncoPrism-HNSCC could guide doctors in choosing more effective treatments for head and neck squamous cell carcinoma (HNSCC) patients.

OncoPrism-HNSCC uses RNA-sequencing and machine learning (ML) to analyse cancer cells from patients, producing a score that sorts patients into groups of low, medium, or high based on how likely they are to benefit from immune checkpoint inhibitor (ICI) treatments.

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Cofactor said that current methods used to predict patient responses to ICIs like measuring PD-L1 combined positive score (CPS) and tumour mutational burden (TMB) are not effective. Both scores can show inconsistent predictive value, resulting in over-treatment and poorer outcomes for HNSCC patients.

Data from the PREDAPT clinical trial (NCT04510129) showed that the OncoPrism test improved the prediction of patient benefit from anti-PD-1 ICIs as both a monotherapy and in combination with chemotherapy. Results indicate a 300% improvement in specificity over PD-L1 CPS and a 400% improvement in sensitivity over TMB.

The study enrolled 1,650 patients with recurrent or metastatic HNSCC. Patients either had a tumour biopsy taken before anti-PD-1/PD-L1 treatment or were scheduled for biopsy before treatment. According to a report on GlobalData’s Pharma Intelligence Center, there will be 338,790 cases of HNSCC by 2030 in the eight major markets (US, France, Germany, Italy, Spain, UK, Japan, and urban China).

ICIs are blockbuster drugs that help the immune system recognise and attack cancer cells. They work by blocking certain proteins, such as PD-L1 or PD-1, which cancer cells often use to evade immune detection. ICIs have become an important treatment option for patients with HNSCC, however, not all patients respond well to them, making predictive tests important.  

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Douglas Adkins, head and neck oncologist and professor of medicine at Washington University School of Medicine, said: “The OncoPrism assay provides a new and important tool to help clinicians decide about treatment options for their patients with recurrent or metastatic head and neck cancer.”  

In December 2017, Cofactor secured $18m in a series A funding round led by Menlo Ventures and joined by existing investor Data Collective Venture Capital LLC. 

Other companies have demonstrated good results in the predictive biomarker test space. In August 2024, Software company io9 released data showing that its AI-powered biomarker test DeepHRD could identify biomarkers that help determine the best initial treatment for patients with ovarian and breast cancer. Results showed superior performance of DeepHRD compared to companion diagnostics approved by the US Food and Drug Administration for the same biomarker.