Liver Tumorigenic Phenotype Detection Using TET-Converted cfDNA
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Solution Overview
Problem
Current diagnostic methods for hepatocellular carcinoma (HCC) are inadequate for early detection, often relying on serum tumor markers like AFP, which are not efficient, and lack predictive tools for risk assessment, leading to poor prognosis due to late detection.
Innovation Solution
A method involving RNA sequencing and analysis of viral oncogene expression, methylation patterns, and transcriptional changes in exosomes and circulating tumor cells from blood samples to identify pre-tumorigenic and tumorigenic phenotypes, using targeted sequencing technologies and bioinformatics tools for early detection and monitoring.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If current diagnostic methods using serum tumor markers like AFP are used, then the diagnostic process is simple and inexpensive, but the detection precision and early detection capability are insufficient
Solution Approach 1:
The diagnostic approach is segmented into multiple layers: first using simple serum tumor markers for initial screening, then applying RNA sequencing and methylation analysis specifically to high-risk cases or cases with indeterminate results. This segmentation allows the system to maintain high detection precision while avoiding the complexity of advanced methods for all patients.
Solution Approach 2:
The patent introduces intermediate diagnostic markers including RNA expression levels of viral oncogenes and methylation patterns of specific genes (such as RASSF1A, APC, and p16) that serve as mediators between simple serum markers and complex tissue biopsy. These intermediate markers provide earlier and more precise detection capability while maintaining a relatively streamlined diagnostic workflow.
2Loss of time
If RNA sequencing and methylation analysis are implemented for early detection, then the early detection capability and prognosis are improved, but the cost and complexity of the diagnostic process increase
Solution Approach 1:
The patent implements preliminary action by analyzing RNA expression levels and methylation patterns in blood-derived exosomes before clinical symptoms appear or before tumors become detectable by conventional imaging. This allows detection at the pre-tumorigenic or early tumorigenic stage, significantly reducing the time loss between disease onset and diagnosis.
Solution Approach 2:
The diagnostic method uses a multi-functional approach where a single blood sample can be analyzed for multiple parameters simultaneously: viral load, RNA expression levels of multiple oncogenes, and methylation patterns of multiple genes. This universality allows comprehensive early detection without requiring multiple separate diagnostic procedures, thereby managing complexity efficiently.
3Measurement precision
If comprehensive metabolic panels and imaging techniques are used for cirrhosis monitoring, then the monitoring coverage is comprehensive, but the early detection of HCC before cirrhosis symptoms appear is limited
Solution Approach 1:
The patent extracts and analyzes specific molecular markers (RNA from viral oncogenes and methylation patterns from tumor suppressor genes) from blood-derived exosomes, separating these early detection markers from the comprehensive metabolic panel and imaging procedures. This extraction allows focused, high-precision early detection without requiring the full resource consumption of comprehensive monitoring for all patients.
Solution Approach 2:
The diagnostic approach applies local quality by using advanced molecular analysis methods specifically for detecting early HCC risk, rather than applying comprehensive metabolic panels and imaging to all monitoring scenarios. The patent tailors the intensity and type of monitoring to the specific need for early HCC detection in high-risk patients with hepatitis B or C infection.
Data Source
AI summary
In an aspect, a method comprises (a) isolating cell-free DNA molecules obtained or derived from a blood sample of a subject; (b) subjecting the cfDNA molecules to TET-associated sequencing comprising: (i) using a TET enzyme to oxidize 5-mC residues and 5-hmC residues of the cfDNA molecules, (ii) sequencing the TET-converted cfDNA molecules to produce a set of cfDNA methylation sequencing reads; (c) processing the set of cfDNA methylation sequencing reads to determine a liver-specific methylation pattern of the cfDNA molecules across a set of liver-specific differentially methylated genomic regions, wherein the processing comprises distinguishing between 5-mC and 5-hmC residues and cytosine residues; (d) determining a presence of a tumorigenic phenotype of the liver, based at least in part on the determined liver-specific methylation pattern; and (e) administering a treatment to the subject to treat the tumorigenic phenotype.