Cell-Free DNA Methylation Analysis for Early Tumor Origin Detection
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Solution Overview
Problem
Current cancer detection methods are limited by a focus on symptom-based screening and often detect cancers at later stages, lacking effective population-scale techniques for early detection with high specificity and accuracy in identifying the tissue of origin.
Innovation Solution
A computer-implemented method utilizing molecular phenotypes from test samples, including epigenetic data, to perform binary and multiclass classifications using logistic regression, Naïve Bayes, decision trees, SVM, random forest, and neural networks to determine cancer status and tissue of origin, leveraging methylation patterns and other genetic markers.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If symptom-based screening and traditional detection methods are used, then cancer detection is performed, but detection occurs at later stages with reduced sensitivity and inability to identify tissue of origin
Solution Approach 1:
The patent replaces traditional mechanical and visual inspection methods (physical exams, imaging) with molecular analysis of cell-free DNA. By substituting mechanical screening with biochemical detection of methylation patterns and genetic mutations in circulating DNA, the system achieves early detection without relying on symptom presentation or late-stage physical manifestations of cancer.
Solution Approach 2:
The patent uses cell-free DNA as an intermediary biomarker to detect cancer indirectly. Instead of directly observing tumors or symptoms, the system analyzes DNA fragments circulating in body fluids that originate from tumor cells. This intermediary approach enables detection of cancer at molecular levels before physical symptoms or visible tumors develop.
2Adaptability or versatility
If comprehensive cancer screening is performed across multiple cancer types, then tissue of origin identification capability is improved, but diagnostic evaluation complexity and cost increase
Solution Approach 1:
The patent develops a universal cell-free DNA analysis platform that can detect multiple cancer types simultaneously through a single test. The same analytical methodology (sequencing and analysis of methylation patterns, genetic mutations, and fragment characteristics) applies across all cancer types, eliminating the need for separate diagnostic pathways for each cancer type and reducing overall system complexity.
Solution Approach 2:
The patent analyzes multiple parameters of cell-free DNA including methylation status, genetic mutations, fragment length, and sequence composition. By simultaneously measuring these different molecular parameters, the system achieves comprehensive multi-cancer detection capability from a single sample analysis, reducing the need for multiple separate tests and simplifying the diagnostic workflow.
Data Source
AI summary
Described herein are methods and compositions related to differentiating cancer and non-cancer signals, including from cell free nucleic acids. Further described herein are methods and compositions to discriminate the origin of a tumor, including use of methylation detection in a test sample obtained from a test subject at least partially using a computer. Other aspects related methods of treating disease in subjects. Yet other aspects include related systems and computer readable media used to implement the aforementioned methods.