Target-Enriched Multiplexed Sequencing for Low-Abundance Tumor Biomarkers
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Solution Overview
Problem
Existing methods for detecting tumor biomarkers are inadequate for non-invasive detection and require excessive sequencing, failing to reliably identify genetic aberrations present in low amounts, particularly in early cancer detection.
Innovation Solution
The use of a pool of Target Capture Sequences (TACS) that are 100-500 base pairs long, with optimized GC content and staggered binding to tumor biomarker sequences, followed by enrichment and statistical analysis to enhance read-depth and specificity, allowing for the detection of tumor biomarkers in various biological samples.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If whole genome-based massively parallel shotgun sequencing is used for tumor biomarker detection, then comprehensive genomic coverage is achieved, but sequencing requirements and cost increase excessively
Solution Approach 1:
The patent extracts and sequences only the specific tumor biomarker regions of interest from the whole genome, using targeted capture methods to isolate and enrich for cancer-relevant sequences. This eliminates the need to sequence the entire genome while maintaining detection sensitivity for tumor biomarkers.
Solution Approach 2:
The genome is segmented into specific regions of interest (tumor biomarker loci) that are separately captured and sequenced. The patent divides the genomic landscape into target regions (containing tumor biomarkers) and non-target regions, focusing sequencing resources only on the relevant segments.
2Productivity
If targeted NGS approaches are used to reduce sequencing requirements, then sequencing efficiency improves, but detection sensitivity for low-abundance genetic aberrations decreases
Solution Approach 1:
The patent performs preliminary enrichment of target sequences before sequencing by hybridizing capture probes to the fragmented genomic DNA. This preliminary capture step concentrates the tumor biomarker sequences of interest, increasing their abundance and signal-to-noise ratio before the actual sequencing occurs.
Solution Approach 2:
The patent uses composite capture probe structures with optimized characteristics (including GC content optimization between 40-60% and specific length parameters) to enhance binding efficiency and specificity. These optimized composite probes improve the enrichment of low-abundance target sequences.
3Ease of manufacture
If capture probes with non-optimized characteristics are used, then probe design is simpler, but enrichment efficiency and specificity decrease
Solution Approach 1:
The patent systematically optimizes key probe parameters including length (100-500 base pairs), GC content (40-60%), and binding position relative to tumor biomarker sequences. These parameter optimizations enhance hybridization efficiency, specificity, and uniformity of enrichment while maintaining practical probe design and synthesis.
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 significantly increases the detection sensitivity and accuracy of tumor biomarkers, enabling non-invasive cancer diagnosis, screening, and treatment monitoring by reducing sequencing requirements and improving read-depth in regions of interest.
Implementation Method 1
hybridizing the sequencing library to a pool of double-stranded TArget Capture Sequences (TACS) that bind to one or more tumor biomarker sequences of interest
Data Source
AI summary
The invention provides methods for assessment of tumor biomarkers using target-enriched multiplexed parallel analysis. The methods of the invention utilize Target Capture Sequences (TACS) to thereby enrich for target sequences of interest, followed by massive parallel sequencing and statistical analysis of the enriched population. The methods can be used with DNA samples from a patient, such as a tissue biopsy or plasma sample (liquid biopsy), for detection of the presence of tumor biomarkers, e.g., for purposes of diagnosis, screening, therapy selection and/or treatment monitoring. Kits for carrying out the methods of the invention are also provided.