Trk Fusion Protein Staining With Confirmatory Scoring in Solid Tumors
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Solution Overview
Problem
Current methods for detecting NTRK gene fusions in tumors lack a gold standard due to inconsistent specificity and sensitivity, with fluorescence in situ hybridization (FISH), in situ hybridization (ISH), Next Generation Sequencing (NGS), and immunohistochemistry (IHC) each having limitations such as difficulty in optimization and interpretation, and IHC detecting protein expression rather than actual fusion presence.
Innovation Solution
A method involving affinity histochemical staining using biomarker-specific reagents that bind to specific amino acid sequences of TrkA, TrkB, or TrkC, followed by scoring based on staining patterns and intensity thresholds, and confirming with sequencing or in situ hybridization for NTRK rearrangements.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If immunohistochemistry (IHC) is used to detect NTRK fusions, then sensitivity is improved, but specificity deteriorates because it detects protein expression rather than actual fusion presence
Solution Approach 1:
The patent segments the detection approach into two distinct parts: IHC staining to identify potential fusion-positive cases (sensitivity step), followed by FISH or ISH confirmation to verify actual fusion presence (specificity step). This segmentation allows each method to excel at its intended function without compromising overall diagnostic accuracy.
Solution Approach 2:
The patent introduces FISH or ISH as an intermediary confirmation step between initial IHC screening and final diagnosis. This intermediary method specifically detects the fusion event itself rather than just protein expression, serving as a mediator that bridges the sensitivity of IHC with the specificity needed for accurate fusion detection.
2Measurement precision
If fluorescence in situ hybridization (FISH) or in situ hybridization (ISH) is used to detect NTRK fusions, then specificity is improved, but ease of operation deteriorates due to difficulty in optimization and interpretation
Solution Approach 1:
The patent performs preliminary IHC staining before FISH/ISH analysis to pre-identify cases that are likely to be fusion-positive. This preliminary action filters the sample set, allowing FISH/ISH to be applied more selectively and reducing the overall complexity of optimization and interpretation across all cases.
Solution Approach 2:
The patent establishes a feedback loop where IHC results guide the decision to proceed with FISH/ISH confirmation. The IHC staining pattern and intensity provide feedback that determines which cases require further specific fusion verification, streamlining the overall process and reducing unnecessary FISH/ISH applications.
3Measurement precision
If Next Generation Sequencing (NGS) is used to detect NTRK fusions, then specificity is improved, but sensitivity deteriorates
Solution Approach 1:
The patent inverts the conventional approach by using protein detection (IHC) as the primary sensitive screen rather than starting with nucleic acid sequencing (NGS). This inversion allows the method to first capture all potential fusion-positive cases through sensitive protein detection, then apply specific fusion verification only to those cases.
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
Provides a reliable and sensitive method for detecting NTRK fusion proteins in non-neuroendocrine tumors, enabling accurate selection of patients for Trk-directed therapy.
Implementation Method 1
affinity histochemically staining the sample with a biomarker-specific reagent that specifically binds to one or more of: an amino acid sequence comprising, consisting essentially of, or consisting of residues 363-760 of SEQ ID NO: 1; an amino acid sequence comprising, consisting essentially of, or consisting of residues 646-838 of SEQ ID NO: 2; or an amino acid sequence comprising, consisting essentially of, or consisting of residues 718-839 of SEQ ID NO: 3
Data Source
AI summary
Materials and methods for detecting NTRK rearrangements via affinity staining. Samples are stained with a biomarker-specific reagent (such as an antibody) that binds to a retained portion of TrkA, TrkB, and/or TrkC. The staining pattern is evaluated, and the presence of a Trk fusion is determined by detecting whether or not the sample has at least a threshold number of cells having a threshold staining intensity. In some cases, the same scoring methodology is applied regardless of the staining localization pattern. In other cases, a cytoplasmic and/or membranous localization is scored by a first methodology, whereas a nuclear localization is scored by a second methodology. The methods disclosed herein may be applied across non-endocrine solid tumor types.