Modified Oligonucleotide Probes for Tumor-Derived Viral DNA Detection
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Solution Overview
Problem
Current PCR-based methods for detecting viral nucleic acids, such as HPV DNA, lack specificity in distinguishing between tumor-derived and non-tumor-derived DNA, leading to insufficient sensitivity and accuracy in cancer detection, with false positives common in healthy individuals.
Innovation Solution
The use of structurally modified DNA oligonucleotide primer and probe combinations, including locked nucleic acids, quenchers, and dyes, to detect tumor-derived HPV DNA by amplifying and distinguishing it from non-tumor sources through digital PCR in micro-droplets, utilizing specific amplicon signals to identify tumor-derived fragments.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If PCR-based methods are used to detect viral nucleic acids in circulation, then the detection sensitivity can be improved, but the specificity deteriorates due to inability to distinguish tumor-derived DNA from non-tumor-derived DNA
Solution Approach 1:
The invention divides the detection process into two distinct stages: first detecting the presence of viral nucleic acids, then separately analyzing fragment characteristics (size, shape, conformation) to determine tumor origin. This segmentation allows each stage to optimize for its specific function, resolving the contradiction between sensitivity and specificity.
Solution Approach 2:
The invention applies different detection qualities to different aspects of the same target: high sensitivity is applied to viral nucleic acid detection, while high specificity is applied to fragment characteristic analysis. This local quality differentiation allows the system to excel at both sensitivity and specificity simultaneously.
2Reliability
If PCR-based methods detect viral DNA in circulation, then early cancer detection capability is improved, but false positive rate increases due to detection of non-tumor viral DNA
Solution Approach 1:
The detection system segments the analysis into presence detection (high sensitivity) and origin determination (high specificity) phases. This eliminates false positives by requiring both viral presence and tumor-derived fragment characteristics to be positive for cancer diagnosis.
Solution Approach 2:
Fragment characteristics (size, shape, conformation) serve as an intermediary marker that indirectly indicates tumor origin without requiring direct detection of tumor cells. This intermediary approach reduces false positives by providing additional verification beyond simple viral DNA detection.
3Ease of operation
If standard PCR methods are used for viral DNA detection, then the ease of operation is maintained, but the manufacturing precision of detection accuracy deteriorates
Solution Approach 1:
The invention segments detection into simple presence testing and enhanced fragment analysis. The segmented approach allows standard PCR to maintain ease of operation while adding fragment characteristic analysis to improve manufacturing precision of detection accuracy.
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
Achieves high sensitivity and specificity in detecting tumor-derived HPV DNA, enabling early cancer detection and monitoring treatment efficacy with improved accuracy, allowing for personalized treatment strategies.
Implementation Method 1
structurally modified DNA oligonucleotide primer and probe combinations, including locked nucleic acids
Implementation Method 2
quenchers, and dyes, to detect tumor-derived HPV DNA by amplifying and distinguishing it
Implementation Method 3
amplifying and distinguishing it from non-tumor sources through digital PCR in micro-droplets
Data Source
Figure 1A~1B
Figure 2~3A
Figure 3B~3C
AI summary
The present disclosure provides methods and compositions of modified oligonucleotide primer and probe combinations, structurally modified with locked nucleic acids, quenchers, and dyes, effective to detect tumor-derived Human Papilloma Virus (HPV) and tumor-derived Epstein-Barr virus (EBV) and, especially, to distinguish viral DNA derived from tumors from viral DNA derived from infectious viral particles.