Multiplex TCR Sequencing with Error Correction
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Solution Overview
Problem
Current methods for high-resolution analysis of the immune repertoire, particularly for T cell receptors, face challenges in efficiently capturing the diversity and accuracy of immune cell receptor sequences due to limitations in sequencing technologies and the introduction of sequence errors, making it difficult to effectively profile vast repertoires and understand immune responses.
Innovation Solution
A multiplex library preparation technology and sequencing workflow that uses specific primer sets targeting variable and joining gene regions of TCR beta and gamma chains, enabling a single reaction for profiling T cell receptor beta and gamma chains, which enhances clonality detection and rare clone detection, and incorporates error correction methods to improve sequencing accuracy.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If next generation sequencing is used to capture the immune repertoire, then the throughput and coverage are improved, but sequence errors are introduced that reduce measurement precision
Solution Approach 1:
The patent applies preliminary action by performing error correction and consensus building during the library preparation and amplification stages, before final sequencing. Multiple rounds of PCR amplification with error correction algorithms identify and eliminate sequencing errors in advance, ensuring high accuracy in the final repertoire analysis while maintaining NGS throughput capabilities
Solution Approach 2:
The patent implements feedback mechanisms through iterative error correction algorithms that analyze sequencing data, identify errors, and generate corrected consensus sequences. The system uses feedback loops where initial sequencing results inform subsequent amplification and correction steps, continuously improving sequence accuracy while maintaining high throughput
2Measurement precision
If multiple separate reactions are used for TCR beta and gamma chain profiling, then the measurement precision for each chain is improved, but the device complexity and time required are increased
Solution Approach 1:
The patent merges the profiling of TCR beta and gamma chains into a single multiplexed library preparation reaction. By designing primers that simultaneously target both TCR chains and using a unified amplification and sequencing workflow, the patent reduces the number of separate reactions required while maintaining the measurement precision needed for accurate clonality detection
Solution Approach 2:
The patent creates a universal library preparation protocol that handles both TCR beta and gamma chains through the same workflow. The primer design and amplification conditions are optimized to universally capture diverse TCR repertoires, eliminating the need for separate specialized reactions for each chain type
3Device complexity
If conventional sequencing methods are used, then the equipment complexity is reduced, but the ability to detect rare clones and complex repertoires is insufficient
Solution Approach 1:
The patent applies preliminary action by performing extensive error correction and consensus building during library preparation and amplification before sequencing. This preliminary processing enhances the detection sensitivity for rare clones by eliminating background noise and errors, allowing conventional or simplified sequencing systems to achieve high measurement precision for rare clone detection
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 allows for high-accuracy amplification and sequencing of immune cell receptor sequences, improving the detection of complex immune cell repertoires and reducing false positives, thereby enhancing diagnostic and therapeutic capabilities.
Implementation Method 1
amplification and sequencing of immune cell receptor sequences
Data Source
AI summary
The present disclosure provides methods, compositions, kits, and systems useful in the determination and evaluation of the immune repertoire. In one aspect, methods provide for determining convergence of T cell receptor beta and T cell receptor gamma repertoires in samples prior to a treatment and predicting a subject's response to the treatment. In another aspect, methods provide predicting a subject's potential or predisposition to be protected from or vulnerable to an adverse event following a treatment.