Circulating Tumor DNA Probe Enrichment for Low-Fraction Mutation Detection
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Solution Overview
Problem
Existing methods struggle to accurately detect disease-associated mutations, particularly in low concentrations of cell-free tumor DNA and fetal DNA, hindering non-invasive diagnosis of cancer and prenatal genetic testing.
Innovation Solution
An assay using a unique combination of probes to detect segregating markers or mutations, combined with personalized methods to determine tumor fraction by screening genomic DNA from tumor tissue and identifying a signature panel of somatic mutations.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If conventional detection methods are used, then the detection process is simple, but the detection precision is insufficient for low concentration tumor DNA and fetal DNA
Solution Approach 1:
The detection method is divided into multiple sequential steps: (1) enrichment of cell-free DNA fragments containing target sequences using hybridization capture with probes, (2) amplification of enriched DNA, and (3) sequencing and analysis. This segmentation allows each step to be optimized independently, achieving high detection precision for low-concentration tumor and fetal DNA while maintaining manageable procedural complexity through systematic organization.
Solution Approach 2:
The method performs preliminary enrichment of target DNA sequences before sequencing by hybridizing probes to cell-free DNA fragments containing tumor-specific or fetal-specific sequences. This preliminary action concentrates the rare target molecules from low-concentration samples, enabling subsequent detection with high precision even when tumor DNA or fetal DNA constitutes only a small fraction of total cell-free DNA.
2Reliability
If the concentration of tumor DNA is very low, then the non-invasive detection capability is maintained, but the ability to determine disease presence is hindered
Solution Approach 1:
The method uses hybridization probes as intermediaries to bridge the gap between low-concentration tumor DNA and detection capabilities. These probes specifically bind to tumor-specific sequences, enabling reliable detection of disease presence even when tumor DNA concentration is extremely low (e.g., 0.1% or less of total cell-free DNA), thereby maintaining both non-invasive sampling and high detection reliability.
Solution Approach 2:
The method changes the concentration parameter by performing targeted enrichment that increases the relative concentration of tumor-specific DNA sequences from trace levels to detectable levels. Through hybridization capture and selective amplification, the method transforms the extremely low concentration of tumor DNA in initial cell-free samples into sufficient quantities for reliable sequencing and disease determination.
3Measurement precision
If the concentration of fetal DNA in maternal blood is low, then the non-invasive prenatal testing is feasible, but the detection of fetal mutations becomes difficult
Solution Approach 1:
The method applies local quality enhancement by designing probes that specifically target fetal-specific or paternally-inherited sequences, concentrating detection efforts on regions where fetal DNA can be distinguished from maternal background. This localized approach to sequence-specific enrichment enables precise fetal mutation detection despite the low overall concentration of fetal DNA in maternal blood.
Solution Approach 2:
The method employs sequence-specific probes as intermediaries to selectively capture and enrich fetal DNA fragments from the mixture of maternal and fetal cell-free DNA in maternal blood. These intermediaries enable the detection system to distinguish and analyze fetal-specific mutations even when fetal DNA constitutes only a small fraction of total circulating DNA.
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
Enhances the detection of disease-associated mutations and tumor fraction, providing accurate non-invasive diagnosis of cancer and fetal genetic disorders.
Implementation Method 1
identifying a plurality of probes useful in the detection of at least one segregating marker; selecting a unique combination of probes wherein the probes are designed to detect either (i) a marker of interest or (ii) a segregating sequence at a marker of interest
Implementation Method 2
contacting said unique combination of probes to a nucleic acid sample; and determining the presence or absence of a segregating sequence at the marker of interest
Data Source
AI summary
The present disclosure relates to a laboratory execution system that provides for automation of laboratory processes. A centralized data management system may be dynamically updated and used to facilitate management of components of the laboratory execution system, such as an automation system and an analytics results management system that may facilitate complex analytical functions, such as synthesizing raw test data. Potential workflows include the detection of specific molecules of interest.