Targeted UMI Integration for Precise TCR Sequencing
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Solution Overview
Problem
Existing methods for high precision detection of cancer through next-generation sequencing (NGS) do not effectively integrate Unique Molecular Identifiers (UMIs) near the region of interest, leading to challenges in accurately sequencing and characterizing T cell and B cell receptor diversity, particularly for cancer diagnostics.
Innovation Solution
Integrate UMIs upstream or downstream of a region of interest (ROI) and perform two nested PCR amplifications for targeted DNA sequencing, using UMI integration primers with amplification adapters and sample identifiers, followed by pair-end sequencing.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If next-generation sequencing is used to detect genetic variations, then detection capability is improved, but cost and complexity increase
Solution Approach 1:
The patent extracts and isolates specific genetic variants of interest from the entire genome sequencing process. By using targeted enrichment methods to capture only relevant genomic regions containing disease-associated variants, the system achieves high detection precision for specific conditions while avoiding the cost and complexity of whole-genome sequencing.
Solution Approach 2:
The patent employs unique molecular identifiers (UMIs) to counterbalance sequencing errors and artifacts. By tagging individual DNA molecules with unique sequences before amplification and sequencing, the system can distinguish true biological variants from technical errors, maintaining high detection accuracy while reducing the need for redundant sequencing and associated costs.
2Measurement precision
If UMIs are integrated into targeted sequencing, then detection precision is improved, but protocol complexity increases
Solution Approach 1:
The patent merges UMI integration with targeted enrichment in a unified workflow. The UMI adapters are incorporated into the same library preparation process as the capture probes, allowing simultaneous tagging and enrichment in a single protocol rather than separate steps, thereby reducing overall complexity while maintaining precision.
Solution Approach 2:
The patent uses hybrid capture probes as intermediaries that simultaneously perform two functions: enriching for target genomic regions and facilitating UMI integration. These probes contain both the capture sequence for target binding and the UMI adapter sequence, streamlining the protocol by combining multiple functions into a single reagent.
Data Source
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AI summary
A high precision method and system for the detection of a medical or cosmetic condition. A unique molecular identifiers (UMI) is attached to a targeted DNA sequence comprising a region of interest (ROI) in a targeted manner. A NGS library enrichment using 2 nested ROI-specific enrichment PCR amplifications is performed followed by NGS sequencing. The precision to detect and characterize T cell receptors (TCR) diversity is substantially increased. This is particularly relevant for TCR monitoring applications such as cancer.