Hybrid Capture Sequencing for T-Cell Clonality

Resolve Bottlenecks,
Find Innovative SolutionsGenerate Solutions

Solution Overview

Problem

Current T-cell receptor gene rearrangement (TRGR) testing methods, such as the BIOMED-2 assay, face limitations due to amplicon size restrictions, interpretative errors, and diagnostic bias, particularly in sequencing the TRA locus and requiring large DNA amounts, which hampers comprehensive clonality assessment and immunotherapy guidance.

Innovation Solution

A novel next-generation sequencing (NGS)-based T-cell clonality assay that captures and sequences all four T-cell receptor loci using hybrid capture probes, enriching for V, D, and J gene segments, and identifying CDR3 regions to provide a comprehensive and quantitative analysis of T-cell clonality.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Measurement precision

If traditional PCR-based TRGR testing methods are used, then the assay can be performed with existing technology, but the amplicon size restrictions limit comprehensive sequencing capability and require large DNA amounts

Engineering Contradiction:

Improveclonality assessment accuracyVSAvoidDNA amount required

Core Design Contradiction:

Measurement precisionVSQuantity of substance

Solution Approach 1:

The patent extracts and enriches specific target regions (V, D, and J gene segments) from the total genomic DNA using hybrid capture probes. This extraction approach allows comprehensive sequencing of TR loci without requiring large amounts of input DNA, as only the relevant portions are amplified and sequenced rather than the entire genome.

Inventive Principle:

Principle #2Taking out (Extraction)

Solution Approach 2:

The patent segments the TR gene loci into distinct V, D, and J regions, and uses separate hybrid capture probes for each segment. This segmentation enables comprehensive coverage of all TR loci (TRA, TRB, TRG, TRD) with targeted enrichment, overcoming the amplicon size restrictions of traditional PCR methods while reducing DNA requirements.

Inventive Principle:

Principle #1Segmentation

2Reliability

If traditional TRGR testing methods are used, then the assay protocol is established, but interpretative errors and diagnostic bias occur

Engineering Contradiction:

Improvediagnostic accuracyVSAvoidinterpretative accuracy

Core Design Contradiction:

ReliabilityVSLoss of information

Solution Approach 1:

The patent replaces traditional PCR-based mechanical amplification with a hybrid capture-based enrichment system followed by next-generation sequencing. This substitution eliminates interpretative errors associated with gel electrophoresis and manual fragment size analysis, providing automated, high-resolution sequence data that reduces diagnostic bias and improves reliability.

Inventive Principle:

Principle #28Mechanics substitution (Replace mechanical system)

Solution Approach 2:

The patent introduces hybrid capture probes as an intermediary between the genomic DNA and the sequencing process. These probes specifically enrich for TR loci sequences, acting as a mediator that guides the sequencing process to focus on relevant regions, thereby reducing misinterpretation and improving diagnostic accuracy through targeted analysis.

Inventive Principle:

Principle #24Intermediary (Mediator)

3Adaptability or versatility

If comprehensive sequencing of all TR loci is performed, then complete clonality assessment is achieved, but the complexity of the assay increases

Engineering Contradiction:

Improvecomprehensive clonality assessmentVSAvoidassay complexity

Core Design Contradiction:

Adaptability or versatilityVSDevice complexity

Solution Approach 1:

The patent designs a universal hybrid capture probe set that simultaneously targets all four TR loci (TRA, TRB, TRG, TRD) and their respective V, D, and J segments. This multi-functional probe system enables comprehensive sequencing of all TR loci in a single assay, achieving complete clonality assessment without proportionally increasing assay complexity through standardized protocols.

Inventive Principle:

Principle #6Universality (Multi-functionality)

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

The NGS-based assay offers a robust, high-throughput method for accurate T-cell clonality assessment, overcoming previous limitations by enabling complete sequence analysis of all TR loci, reducing interpretative errors, and providing quantitative data for improved diagnostic accuracy and immunotherapy monitoring.

Implementation Method 1

capturing DNA fragments existing in the patient sample using a collection of nucleic acid hybrid capture probes, wherein each capture probe is designed to hybridize to a known V gene segment and/or a J gene segment within the T cell receptor and/or immunoglobulin genomic loci

Methodology Applied

Scientific EffectHybridization:

Data Source

PatentUS11788136B2Hybrid-capture sequencing for determining immune cell clonality

Publication Date: 2023.10.17 UNIV HEALTH NETWORK

AI summary

A method of capturing a population of T-Cell receptor and/or immunoglobulin sequences with variable regions within a patient sample, the method comprising: extracting and/or preparing DNA fragments from the patient sample; ligating a nucleic acid adapter to the DNA fragments, the nucleic acid adapter suitable for recognition by a pre-selected nucleic acid probe; capturing DNA fragments existing in the patient sample using a collection of nucleic acid hybrid capture probes, wherein each capture probe is designed to hybridize to a known V gene segment and/or a J gene segment within the T cell receptor and/or immunoglobulin genomic loci.