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Efficient Identification of Patients With NTRK Fusions Using a Supervised Tumor-Agnostic Approach.

Susana Hernandez1, Esther Conde2, Aida Molero3

  • 1From the Department of Pathology, 12 de Octubre University Hospital, Research Institute 12 de Octubre University Hospital (i+12), Madrid, Spain (Hernandez, Alonso).

Archives of Pathology & Laboratory Medicine
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Identifying neurotrophic tropomyosin receptor kinase (NTRK) fusions is challenging due to low frequency. A multiparametric strategy combining histology and genomics significantly improved NTRK fusion detection rates in a single institution.

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Area of Science:

  • Oncology
  • Molecular Diagnostics
  • Genomics

Background:

  • Neurotrophic tropomyosin receptor kinase (NTRK) gene fusions are emerging as crucial tumor-agnostic biomarkers.
  • The low frequency of NTRK fusions (below 1%) presents significant challenges for patient identification.
  • Existing guidelines recommend diverse strategies, including next-generation sequencing (NGS) and immunohistochemistry (IHC), for NTRK fusion detection.

Purpose of the Study:

  • To implement and evaluate institutional triaging strategies for efficient NTRK fusion identification.
  • To provide pathologists with practical insights for initiating NTRK fusion detection workflows.
  • To enhance the diagnostic yield of NTRK fusions in clinical practice.

Main Methods:

  • A multiparametric strategy integrating histologic features (e.g., secretory carcinomas, papillary thyroid carcinomas, infantile fibrosarcoma) and genomic profiles (e.g., driver-negative NSCLC, MSI-high colorectal cancer, wild-type GIST) was employed.
  • Immunohistochemistry (IHC) using the VENTANA pan-TRK EPR17341 Assay served as the primary screening method for 323 tumor samples.
  • All IHC-positive cases underwent simultaneous confirmation via two NGS tests: Oncomine Comprehensive Assay v3 and FoundationOne CDx.

Main Results:

  • The multiparametric approach achieved a significantly higher NTRK fusion detection rate of 5.57% compared to the 0.30% reported in larger literature cohorts.
  • This represents a 20-fold increase in detection yield within the screened cohort of 323 patients.
  • The strategy effectively identified NTRK fusions in specific tumor types, demonstrating its utility in a clinical setting.

Conclusions:

  • A supervised tumor-agnostic approach, combining histologic and genomic data, is proposed for pathologists initiating NTRK fusion detection.
  • This strategy enhances the efficiency and yield of identifying patients with NTRK fusions.
  • The findings support the integration of multiparametric triaging for improved molecular diagnostics in oncology.