Circulating Tumor DNA Detection Using CAPP-Seq Selectors
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Solution Overview
Problem
Existing methods for detecting and monitoring tumor-related nucleic acids in cancer patients are limited by the need for patient-specific optimization, sensitivity to a subset of patients, inability to detect genomic fusions, and reliance on a small number of known cancer genes, failing to effectively identify relevant mutations in the majority of serum samples.
Innovation Solution
A method called CAPP-Seq, which involves producing a selector set of oligonucleotides targeting recurrently mutated genomic regions, enriching cell-free DNA samples using hybrid selection, and sequencing to detect circulating tumor DNA, allowing for the detection of somatic mutations even at low percentages.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If PCR-based assays are used to detect recurrent point mutations in plasma DNA, then detection of specific mutations (e.g., KRAS or EGFR) is achieved, but the majority of patients without these gene mutations cannot be detected
Solution Approach 1:
The patent creates a universal assay platform that can detect multiple types of genetic alterations (point mutations, insertions, deletions, chromosomal rearrangements, copy number changes) across many different genes simultaneously. This multi-functional approach allows a single test to serve diverse patient populations with various cancer types and genetic profiles, rather than requiring separate patient-specific assays
2Measurement precision
If whole genome sequencing followed by breakpoint qPCR is used to identify patient-specific chromosomal rearrangements, then sensitivity is improved, but the requirement for patient-specific optimization limits widespread clinical application
Solution Approach 1:
The patent performs preliminary identification of recurrently mutated genes and their mutation hotspots across many patients before creating the assay. This pre-characterization allows the development of a standardized panel that targets the most common cancer mutations, eliminating the need for patient-specific optimization while maintaining high detection sensitivity for the majority of cases
3Measurement precision
If amplicon-based deep sequencing methods are used to detect cfDNA mutations in up to 6 recurrently mutated genes, then detection capability is improved, but the number of mutations that can be interrogated is limited
Solution Approach 1:
The patent segments the genome into many small amplicons (typically 100-500 base pairs) that can be efficiently amplified and sequenced. By dividing the target regions into numerous small segments across hundreds or thousands of genes, the assay can interrogate a much larger number of potential mutation sites than previous methods that targeted only 6 genes, while maintaining deep sequencing capability
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
CAPP-Seq enables the sensitive detection and monitoring of tumor-specific somatic mutations in blood samples, providing insights into tumor burden, response to therapy, and enabling biopsy-free tumor genotyping with high sensitivity and specificity.
Implementation Method 1
producing a selector set corresponding to one or more genomic regions comprising the one or more mutations specific to the sequencing information of the tumor sample, wherein the selector set comprises a plurality of oligonucleotides that selectively hybridize the one or more genomic regions
Implementation Method 2
performing hybrid selection on the cfDNA sample using the selector set to enrich for cfDNA corresponding to genomic regions known to contain tumor-specific somatic mutations
Data Source
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Figure 2a~2c
AI summary
Methods for creating a selector of mutated genomic regions and for using the selector set to analyze genetic alterations in a cell-free nucleic acid sample are provided. The methods can be used to measure tumor-derived nucleic acids in a blood sample from a subject and thus to monitor the progression of disease in the subject. The methods can also be used for cancer screening, cancer diagnosis, cancer prognosis, and cancer therapy designation.