TCR Vbeta Repertoire Detection via Family-Specific PCR Primers

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Solution Overview

Problem

Current methods for determining T-cell receptor (TCR) clonality are insensitive, complex, and impractical, lacking the ability to quickly and accurately monitor changes in TCR V beta clonality, which is crucial for assessing therapeutic effectiveness in diseases such as HIV/AIDS and cancers.

Innovation Solution

A novel method using specific primers for PCR reactions combined with analytical software and gel fractionation to rapidly detect and quantify TCR V beta repertoire clonality, allowing for the identification of monoclonal, oligoclonal, or polyclonal repertoires in T-cell populations, enabling monitoring of immune responses and therapeutic efficacy within a day.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Measurement precision

If conventional methods are used to determine TCR clonality, then the process can be performed, but the methods are insensitive, complex, and impractical

Engineering Contradiction:

Improveclonality detection sensitivityVSAvoidmethod complexity

Core Design Contradiction:

Measurement precisionVSDevice complexity

Solution Approach 1:

The method segments the TCR repertoire analysis by targeting specific Vbeta gene families (e.g., Vbeta 7, Vbeta 9, Vbeta 14) with family-specific primers, allowing independent detection of clonality in each segment rather than analyzing the entire repertoire at once, thereby improving sensitivity while managing complexity

Inventive Principle:

Principle #1Segmentation

Solution Approach 2:

The patent introduces PCR amplification as an intermediary step that converts difficult-to-detect clonal TCR transcripts into detectable DNA fragments, enabling sensitive clonality detection without requiring direct observation of the original TCR molecules

Inventive Principle:

Principle #24Intermediary (Mediator)

2Productivity

If conventional methods are used to determine TCR clonality, then analysis can be performed, but results take more than a day and are impractical for rapid monitoring

Engineering Contradiction:

Improvedetection speedVSAvoidanalysis time

Core Design Contradiction:

ProductivityVSLoss of time

Solution Approach 1:

The method performs preliminary PCR amplification of TCR transcripts before analysis, pre-processing the samples to convert them into a format suitable for rapid detection, thereby reducing the overall analysis time from more than a day to less than a day

Inventive Principle:

Principle #10Preliminary action

Solution Approach 2:

The patent replaces time-consuming conventional analysis methods with a streamlined PCR-based system that uses thermal cycling and DNA fragment analysis, substituting the mechanical complexity of traditional methods with a more efficient molecular biology approach that completes analysis in less than a day

Inventive Principle:

Principle #28Mechanics substitution (Replace mechanical system)

3Reliability

If conventional methods are used, then TCR clonality can be assessed, but the methods lack reliability for monitoring therapeutic effectiveness

Engineering Contradiction:

Improveclonality monitoring reliabilityVSAvoidclonality detection accuracy

Core Design Contradiction:

ReliabilityVSMeasurement precision

Solution Approach 1:

The method applies local quality by using family-specific primers tailored to each Vbeta gene family, ensuring that detection is optimized for the specific characteristics of each TCR family rather than using a generic approach, thereby improving both reliability and precision of clonality monitoring

Inventive Principle:

Principle #3Local quality

Solution Approach 2:

The patent implements feedback by comparing detected clonal expansions against established criteria and patterns, allowing interpretation of the results in the context of therapeutic response, where changes in clonality patterns provide feedback on treatment effectiveness

Inventive Principle:

Principle #23Feedback

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 method provides a sensitive and reliable means to detect TCR V beta clonality changes, facilitating the assessment of therapeutic effectiveness and immune response monitoring in diseases like HIV/AIDS, hepatitis, and cancers, with results obtained in less than a day, improving upon the limitations of existing techniques.

Implementation Method 1

The method relies on subsets of unique primers that quantitatively determine the extent of clonal expansions of TCR VβT-cell repertoires

Methodology Applied

Scientific EffectPCR amplification:

Implementation Method 2

specific primers for PCR reactions combined with analytical software and gel fractionation to rapidly detect and quantify TCR V beta repertoire clonality

Methodology Applied

Scientific EffectGel electrophoresis:

Data Source

PatentUS7375211B2Method for detection and quantification of T-cell receptor Vβ repertoire

Publication Date: 2008.05.20 SHANGHAI ABELZETA LTD

AI summary

The invention is a method for detecting and measuring T-cell receptor (TCR) repertoires from mammalian lymphocytes. The method is based on the use of the multiple sets of unique primers to amplify 22 regions of the TCR Vβ region and thereby detect clonal expansions related to antigen stimulation of the immune system. Kits containing sets of primers and specialized analytical statistical software for use in determining clonal expansion in humans and mice are disclosed. The reliability, efficiency and short assay time in using the method is well suited to monitoring immune response to vaccination and therapeutic treatments for immune disorders.