ctDNA Biomarker Panel for Early HNSCC Recurrence Detection

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Solution Overview

Problem

Current methods for monitoring HPV-positive head and neck cancer (HNSCC) have limited sensitivity and specificity, leading to delayed detection of recurrences and unnecessary treatments, and there is a need for improved surveillance strategies to detect residual and recurrent disease early.

Innovation Solution

A method involving target-enrichment sequencing analysis of HPV and human genes, such as HPV16, E7 sequences, and frequently mutated genes like AJUBA, TP53, to detect head and neck cancer markers in biological samples, using a biomarker panel with probes for capture hybridization.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Measurement precision

If current monitoring methods (MRI/PET-CT and clinical follow-up) are used, then disease monitoring is performed according to WHO guidelines, but sensitivity and specificity are limited leading to delayed detection of recurrences and unnecessary treatments

Engineering Contradiction:

Improvedetection accuracyVSAvoidmonitoring reliability

Core Design Contradiction:

Measurement precisionVSReliability

Solution Approach 1:

The patent introduces plasma circulating tumor DNA (ctDNA) as an intermediary biomarker to detect head and neck cancer recurrence. Instead of directly imaging tumors or performing invasive biopsies, the method detects tumor-derived DNA fragments in plasma samples, providing a non-invasive liquid biopsy approach that overcomes the limitations of current imaging and clinical follow-up methods

Inventive Principle:

Principle #24Intermediary (Mediator)

Solution Approach 2:

The patent replaces mechanical imaging systems (MRI/PET-CT) and invasive mechanical biopsy procedures with a molecular detection system. By using PCR-based methods to amplify and detect specific tumor DNA sequences in plasma, the system substitutes physical imaging and surgical intervention with biochemical detection, achieving higher sensitivity and specificity

Inventive Principle:

Principle #28Mechanics substitution (Replace mechanical system)

2Measurement precision

If imaging is performed to detect residual disease, then residual disease can be detected in 10-20% of cases, but pathological examination is often not conclusive leading to potentially unnecessary treatments

Engineering Contradiction:

Improveresidual disease detection accuracyVSAvoiddiagnostic simplicity

Core Design Contradiction:

Measurement precisionVSEase of operation

Solution Approach 1:

The patent extracts tumor-specific genetic information from complex plasma samples containing mixed DNA from multiple sources. By using targeted PCR amplification of tumor-specific mutations or viral sequences (such as HPV in head and neck cancer), the method isolates and detects only the relevant tumor-derived DNA signals, filtering out background noise from normal cells

Inventive Principle:

Principle #2Taking out (Extraction)

Solution Approach 2:

The patent changes the detection parameter from anatomical imaging (MRI/PET-CT) to molecular genetic markers. By detecting specific DNA sequences, mutation patterns, or viral integration signatures in plasma, the method transforms the diagnostic approach from visualizing tumor mass to detecting molecular evidence of tumor presence, achieving higher precision in residual disease detection

Inventive Principle:

Principle #35Parameter changes

3Measurement precision

If examination under general anesthesia is performed for recurrent disease diagnosis, then diagnosis can be obtained, but it is obviously unsuited for screening and only applied on clinical indications

Engineering Contradiction:

Improverecurrence diagnosis accuracyVSAvoiddiagnostic procedure complexity

Core Design Contradiction:

Measurement precisionVSDevice complexity

Solution Approach 1:

The patent enables the diagnostic system to serve itself by using readily accessible plasma samples that can be collected through simple venipuncture without requiring general anesthesia or complex procedural infrastructure. The liquid biopsy approach allows patients to undergo screening in routine outpatient settings, eliminating the need for specialized surgical facilities and anesthesia services

Inventive Principle:

Principle #25Self-service

Applied Scientific Principles

This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.

Function Achieved in This Case

The method provides high sensitivity and specificity for early detection of head and neck cancer, particularly recurrent cases, allowing for timely intervention and improved patient outcomes.

Implementation Method 1

Methodology Applied

Scientific EffectHybridization:

Data Source

PatentEP4678765A1A biomarker panel and method(s) for monitoring of head and neck cancer

Publication Date: 2026.01.14 STICHTING AMSTERDAM UMC

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AI summary

The present disclosure provides a method and a biomarker panel for early detection, monitoring and prognosis of head and neck cancer and its recurrence. Particularly, the method(s) and biomarker panel rely on the enrichment and sequencing of DNA isolated from a biological sample to identify the presence of and/or measure the level of marker(s) selected from a group comprising whole genome of HPV16, E7 sequence(s) of one of more of HPV18, HPV31, HPV33, HPV35, HPV39, HPV45, HPV51, HPV52, HPV56, HPV58, HPV59, HPV68, HPV73 and HPV82, human gene(s) selected from a group comprising AJUBA, ASXL1, CASP8, CDKN2A, CUL3, DDX3X, EPHA2, FAT1, FBXW7, FGFR3, HRAS, KDM6A, KEAP1, KMT2D, KRAS, NFE2L2, NOTCH1, NOTCH2, NSD1, PIK3CA, PTEN, RB1, RHOA, TERT promotor, TGFBR2, TP53, TP53 5'UTR and TP63, and combination(s) thereof.