Target Capture Reagent Ratios for Cost-Effective Genomic Profiling
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Solution Overview
Problem
Whole exome sequencing for genomic profiling in cancer is not widely available and is expensive and time-intensive, posing a challenge for translating genomic studies into routine clinical practice for predicting patient treatment decisions.
Innovation Solution
A plurality of target capture reagents, comprising different ratios of functional and non-functional binding pair members, are used to selectively capture and sequence genomic intervals, allowing for high and low sequencing depth events to determine genomic alterations.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If whole exome sequencing is used for genomic profiling, then comprehensive genomic coverage is achieved, but cost and time requirements increase significantly
Solution Approach 1:
The patent divides the genome into specific regions of interest (ROIs) that are targeted for sequencing, rather than sequencing the entire exome. This segmentation allows focused genomic profiling on clinically relevant regions, reducing sequencing time and cost while maintaining precision for those specific areas.
Solution Approach 2:
The invention applies different sequencing depths to different genomic regions based on their clinical importance. High-precision sequencing is applied to critical regions with higher proportions of functional binding pair members, while less critical regions receive lower sequencing depth, optimizing resource allocation.
2Measurement precision
If whole exome sequencing is used for genomic profiling, then comprehensive genomic coverage is achieved, but cost increases significantly
Solution Approach 1:
By segmenting the genome into targeted regions of interest and sequencing only those regions with appropriate depth, the patent significantly reduces the amount of sequencing required, thereby lowering cost while maintaining comprehensive coverage of clinically relevant genomic areas.
Solution Approach 2:
The invention changes the sequencing depth parameter dynamically based on the proportion of functional binding pair members in each region. Regions with higher functional content receive higher sequencing depth, while regions with lower functional content receive reduced depth, optimizing cost-effectiveness.
3Measurement precision
If higher sequencing depth is applied to all regions, then detection sensitivity is improved, but resource consumption increases
Solution Approach 1:
The patent applies local quality by assigning different sequencing depths to different genomic regions based on their specific characteristics, particularly the proportion of functional binding pair members. This ensures high detection sensitivity in critical regions while conserving sequencing resources in less critical regions.
Solution Approach 2:
The invention dynamically adjusts the sequencing depth parameter for each region based on the proportion of functional binding pair members, optimizing detection sensitivity where needed while reducing resource consumption in regions where high sensitivity is less critical.
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
This approach enables efficient and cost-effective genomic profiling, facilitating the determination of biomarkers like tumor mutational burden and microsatellite instability, thereby guiding treatment decisions.
Implementation Method 1
R1s comprise R1s that comprise a functional first member of a binding pair (e.g., a binding pair described herein), and optionally, R1s that lack a functional first member of the binding pair; and R2s comprise R2s that comprise a functional first member of the binding pair and R2s that lack a functional first member of the binding pair; wherein the first member of the binding pair is capable of binding to a second member of the binding pair disposed on substrate
Data Source
AI summary
Compositions and methods of evaluating genomic alterations in a sample are disclosed.