Detection of NTRK Fusions: Merits and Limitations of Current Diagnostic Platforms

Abstract

Oncogenic fusions involving NTRK1, NTRK2, and NTRK3 with various partners are diagnostic of infantile fibrosarcoma and secretory carcinoma yet also occur in lower frequencies across many types of malignancies. Recently, targeted small molecular inhibitor therapy has been shown to induce a durable response in a high percentage of patients with NTRK fusion-positive cancers, which has made the detection of NTRK fusions critical. Several techniques for NTRK fusion diagnosis exist, including pan-Trk IHC, FISH, reverse transcription PCR, DNA-based next-generation sequencing (NGS), and RNA-based NGS. Each of these assays has unique features, advantages, and limitations, and familiarity with these assays is critical to appropriately screen for NTRK fusions. Here, we review the details of each existing methodology.

Figure 1.

Immunohistochemical staining with pan-Trk antibody (clone EPR 17341, Abcam) demonstrates a variety of staining patterns in malignancies with NTRK fusions, and the staining patterns correlate with the fusion partner. (A) A membranous staining pattern is seen in this case of intrahepatic cholangiocarcinoma with a PLEKHA6-NTRK1 fusion. (B) A nuclear and cytoplasmic staining pattern is seen in this case of secretory carcinoma of the salivary gland with the canonical ETV6-NTRK3 fusion. (C) Colonic adenocarcinoma with an LMNA-NTRK1 fusions exhibits a cytoplasmic and perinuclear staining pattern. (D) Physiologic staining can be seen in smooth muscle, as seen in arterial walls. (E-F) Physiologic staining can also be seen in tumors of neural differentiation, such as neuroblastoma (E) and glioblastoma (F), making interpretation difficult.