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Efficient Identification of Patients With NTRK Fusions Using a Supervised Tumor-Agnostic Approach
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Efficient Identification of Patients With NTRK Fusions Using a Supervised Tumor-Agnostic Approach
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Journal Article
Efficient Identification of Patients With NTRK Fusions Using a Supervised Tumor-Agnostic Approach
2024
Overview
The available diagnostic strategies used to identify the NTRK rearrangements in the clinic include both traditional methodologies, such as immunohistochemistry (IHC), break-apart fluorescence in situ hybridization (FISH), and reverse transcriptase-polymerase chain reaction, as well as the increasingly popular next-generation sequencing (NGS).5 Each of these approaches has advantages and disadvantages that need to be carefully balanced given the low prevalence of NTRK fusions in unselected series of tumors.6,7 Along these lines, the European Society for Medical Oncology (ESMO) recommendations on the standard methods to detect NTRK fusions in daily practice have been released.8 The ESMO proposal encourages the use of NGS if available, or alternatively IHC could be used for screening with NGS confirmation of all positive IHC results.8 Subsequently, several other algorithms and consensuses have been published, acknowledging the need to incorporate histo.ogic and genomic triaging for more effective identification of NTRK-positive patients.5,8-16 It is important to emphasize that when pan-tumor strategies have been tested in the real clinical world, the overall frequency of NTRK fusions is less than 1 %.6,7,17-24 This situation prompted us to apply a pragmatic interpretation of these triaging proposals (ie, \"supervised tumor-agnostic approach\") in multiple cancer types to generate data using pan-TRK IHC and 2 different NGS panels. The series also considered cases with a lower probability of NTRK fusions in which histologybased or genomic-based triaging strategies were proposed based on published evidence (Figure 1; Table l).5'25,26 Histologic criteria were defined by the corresponding World Health Organization (WHO) classification scheme (data not shown). The analysis by in-house NGS test required that for each FFPE tumor sample, freshly cut 5-pm-thick sections were collected on separate Eppendorf tubes for DNA and RNA extraction: 3 sections for surgical specimens and 5 sections for small biopsy specimens for each nucleic acid. Orthogonal Testing Orthogonal testing was used to resolve the NGS discordant results. Because of the characteristics of the discrepancies (see below) either NTRK FISH (ZytoLight SPEC NTRK1 Dual Color Break Apart Probe, ZytoLight SPEC NTRK3 Dual Color Break Apart Probe, ZytoVision GMbH, Bremerhaven, Germany) or ETV6 FISH (Vysis ETV6 Break Apart FISH Probe Kit, Abbott Molecular, Illinois) was used.
Publisher
College of American Pathologists
Subject
