Multiplex Oncology Assay Primer Panel for Biomarker Detection
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Solution Overview
Problem
Current methods struggle to efficiently and systematically detect multiple relevant biomarkers in various sample types for cancer therapy, particularly in identifying responsive candidates and monitoring response, due to the complexity of tumor microenvironments and drug response biomarkers.
Innovation Solution
A single-stream multiplex assay using a composition of primer reagents targeting oncology gene sequences, including DNA hotspot mutation, copy number variation, and genetic fusion genes, allows for rapid detection of biomarkers like EGFR, ALK, BRAF, ROS1, HER2, MET, NTRK, and RET in samples such as FFPE tissue and plasma, integrated with next-generation sequencing workflows.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Quantity of substance
If multiple biomarkers are detected using conventional separate assays, then detection comprehensiveness is improved, but assay complexity and time consumption increase
Solution Approach 1:
The patent combines detection of multiple oncology biomarkers (EGFR, ALK, BRAF, ROS1, HER2, MET, NTRK, RET) into a single multiplex assay that processes all targets simultaneously in one reaction stream, eliminating the need for separate conventional assays for each biomarker
Solution Approach 2:
The assay system is designed to universally detect multiple different biomarker types (point mutations, copy number variations, gene fusions) using a single integrated workflow that handles diverse target sequences and mutation types through unified primer sets and amplification conditions
2Quantity of substance
If multiple biomarkers are detected using separate assays, then detection comprehensiveness is improved, but time consumption increases
Solution Approach 1:
The patent merges multiple detection processes into a single time-consuming step by performing multiplex amplification of all target biomarkers simultaneously in one reaction stream, reducing total assay time from multiple sequential tests to a single integrated test
Solution Approach 2:
The assay maintains continuous useful action through simultaneous amplification and detection of all biomarkers in parallel, eliminating idle time between separate assays and maintaining productive workflow throughout the entire detection process
3Measurement precision
If low level targets are detected, then detection sensitivity is improved, but false positive rate increases
Solution Approach 1:
The patent applies local quality through target-specific primer sets designed with unique characteristics for each biomarker, allowing optimized binding conditions and detection parameters for each specific target while maintaining overall assay consistency, thereby improving sensitivity without increasing false positives
Solution Approach 2:
The assay incorporates feedback mechanisms through internal controls and validation steps that monitor amplification efficiency and detect potential false positives, allowing real-time adjustment and verification of low-level target detections to ensure accuracy
4Measurement precision
If comprehensive biomarker panel is used, then diagnostic accuracy is improved, but cost increases
Solution Approach 1:
The patent combines multiple biomarker detections into a single assay, reducing the total number of reagents, instruments, and labor hours required compared to running separate conventional assays for each biomarker, thereby lowering overall cost while maintaining comprehensive diagnostic 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
Enables comprehensive detection of actionable oncology biomarkers in a single day, providing insights into diagnosis, prognosis, therapeutic regimens, and adverse events, with applications in clinical and research settings for tissue and plasma specimens.
Implementation Method 1
contacting at least a portion of the sample comprising multiple target sequences of interest using a plurality of target-specific primers in the presence of a polymerase under amplification conditions to produce a plurality of amplified target sequences
Data Source
AI summary
Provided are methods and compositions for preparing a library of target nucleic acid sequences that are useful for assessing gene mutations for oncology biomarker profiling of samples. In particular, a target-specific primer panel is provided that allows for selective amplification of oncology biomarker target sequences in a sample. In one aspect, the invention relates to target-specific primers useful for selective amplification of one or more target sequences associated with oncology biomarkers from two or more sample types. In some aspects, amplified target sequences obtained using the disclosed methods, and compositions can be used in various processes including nucleic acid sequencing and used to detect the presence of genetic variants of one or more targeted sequences associated with oncology.