DNA Methylation Marker Panel for Non-Invasive Cancer Detection
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Solution Overview
Problem
Current multi-cancer screening methods are laborious, complex, and lack sufficient sensitivity and specificity for detecting multiple types of cancers non-invasively, particularly in early stages, and fail to accurately predict the tissue source of cancer.
Innovation Solution
Identification of specific DNA methylation markers in cell-free DNA samples, including pan-cancer markers (SEQ ID NO: 1-6) and tissue-specificity markers (SEQ ID NO: 5, 8-15), which are hypermethylated in cancer DNA, allowing for sensitive and specific detection of cancer presence and tissue origin using methylation-sensitive enzymatic digestion and PCR analysis.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If ultra-sensitive biochemical methods are used to detect tumor derived DNA in liquid biopsies, then detection sensitivity is improved, but the complexity and cost of the assay increases
Solution Approach 1:
The patent segments the DNA methylation analysis into distinct functional regions: pan-cancer markers (SEQ ID NO: 1-6) for cancer detection and tissue-specificity markers (SEQ ID NO: 5, 8-15) for cancer type identification. This segmentation allows the assay to systematically address multiple detection challenges through specialized marker panels, improving sensitivity while managing complexity through organized analysis frameworks.
Solution Approach 2:
The patent creates a universal multi-cancer detection system that uses the same liquid biopsy platform to detect multiple cancer types simultaneously. The assay integrates pan-cancer markers that work across all cancer types with tissue-specific markers that differentiate between them, enabling one assay to serve multiple detection functions and improving overall system efficiency.
2Productivity
If multiple cancer types are detected in a single assay, then screening efficiency is improved, but the specificity and accuracy for tissue source identification decreases
Solution Approach 1:
The patent divides the marker panel into two functional segments: pan-cancer markers (SEQ ID NO: 1-6) that provide broad cancer detection across all tissue types, and tissue-specificity markers (SEQ ID NO: 5, 8-15) that provide differentiated identification. This segmentation enables the assay to first efficiently detect cancer presence using pan-markers, then accurately identify tissue origin using tissue-specific markers, resolving the contradiction between screening efficiency and identification accuracy.
Solution Approach 2:
The patent applies local quality by using different marker sets with specialized functions at different analytical stages. Pan-cancer markers provide general detection capability for all cancer types, while tissue-specific markers provide specialized identification for specific cancer origins. This localized specialization allows the assay to maintain high accuracy for tissue source identification while preserving overall screening efficiency.
3Reliability
If early stage cancers are detected, then patient prognosis is improved, but the sensitivity of current screening methods for early stage cancers is insufficient
Solution Approach 1:
The patent employs preliminary action by using pan-cancer markers (SEQ ID NO: 1-6) that are designed to detect cancer presence at early stages before symptoms manifest. These markers are selected for their ability to show methylation changes early in cancer development, allowing the assay to detect early stage cancers and improve patient prognosis by enabling early intervention.
Solution Approach 2:
The patent utilizes parameter changes by detecting DNA methylation status as a biomarker for early cancer detection. Methylation changes occur early in cancer development and serve as sensitive parameters that can be detected in liquid biopsies, enabling the identification of early stage cancers with high sensitivity and improving patient outcomes through early detection.
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 achieves 62% sensitivity and 94% specificity for detecting multiple cancer types, with high sensitivity for early-stage cancers and accurate tissue source identification, providing a non-invasive and clinically useful screening tool.
Implementation Method 1
using methylation-sensitive enzymatic digestion and PCR analysis
Implementation Method 2
using methylation-sensitive enzymatic digestion and PCR analysis
Data Source
AI summary
Methods and systems for assessing the presence of cancer in a subject and predicting the tissue source of the cancer are provided, by analyzing DNA methylation markers in cell- free DNA samples, particularly cell-free DNA from plasma samples.