Pan-tumor screening for NTRK gene fusions using pan-TRK immunohistochemistry and RNA NGS fusion panel testing

Area of Science:

• Oncology
• Molecular Diagnostics
• Genetics

Background:

• Neurotrophic tyrosine receptor kinase (NTRK) gene fusions are targetable oncogenic drivers across various cancers.
• Clinical implementation of NTRK fusion testing faces challenges including variable prevalence, TRK expression levels, and numerous fusion partners.

Purpose of the Study:

• To evaluate the utility of pan-TRK immunohistochemistry (IHC) and RNA-based next-generation sequencing (NGS) for detecting NTRK gene fusions in specific cancer types.
• To assess the performance of pan-TRK IHC in identifying actionable NTRK fusions, particularly in driver mutation-negative lung, urothelial, and cholangiocarcinoma cases.

Main Methods:

• Retrospective analysis of 127 driver mutation-negative lung, urothelial, and cholangiocarcinoma cases.
• Initial screening using pan-TRK IHC, followed by confirmatory RNA fusion panel testing for positive, equivocal, or weak staining cases.

Main Results:

• 4 out of 127 cases (3.1%) harbored NTRK fusions confirmed by RNA NGS.
• Pan-TRK IHC showed positive staining in 49.6% of cases, with 71.4% of these being weak or focal, potentially due to non-specific TRK expression.
• Pan-TRK IHC demonstrated limited sensitivity for NTRK3 fusions and reduced specificity, necessitating RNA NGS for accurate diagnosis.

Conclusions:

• NTRK gene fusions can be successfully identified for targeted therapy, but confirmatory testing is vital.
• Pan-TRK IHC has limitations in sensitivity and specificity, especially for NTRK3 fusions and in tumors with physiologic TRK expression.
• RNA-based NGS is crucial for confirming NTRK fusions, overcoming the challenges posed by pan-TRK IHC variability.