Prevalence and characteristics of NTRK fusions in 25,946 patients with non-small cell lung cancer.

BACKGROUND

Functional NTRK1-2-3 fusions are rare, tumor-agnostic, targetable alterations. Accurate detection is essential to ensure optimal treatment. We investigated the prevalence of NTRK fusions in two cohorts of patients with NSCLC.

METHODS

The Lungscape Cohort, comprising of tissue microarrays from 1703 resected stage I-III NSCLC cases (52% adenocarcinomas, 40% squamous cell carcinomas), was screened using pan-TRK immunohistochemistry (IHC, EPR17341, Ventana) and positive cases were confirmed by next-generation sequencing (NGS). The NGS Cohort of 24,243 NSCLC was screened by NGS within the European Lungscape Center Network and positive cases were retested using IHC. Functional fusions were defined as in-frame fusions containing an intact NTRK kinase domain.

RESULTS

In the Lungscape Cohort of resected NSCLC panTRK IHC was found positive in 69 (60squamous cell carcinoma, 5 adenocarcinoma, 4 large cell carcinoma) of 1703 patients (4%, median H-score: 37, range 5-200). Sixty-five samples underwent confirmatory testing by NGS and one fusion was found, which after manual review was classified as non-functional. The NGS Cohort yielded 11 fusions in tumors of 24,243 patients of which eight were functional (0.03%; 5 in NTRK1, 1 in NTRK2 and 2 in NTRK3) and five were retested using IHC (median H score 200, range 50-300). Of the three non-functional fusions, two were IHC negative and 1 weakly positive (H-score 30).

CONCLUSION

Pan-TRK IHC has a false-positive rate of ∼4%, particularly in squamous cell carcinomas, underscoring the need for confirmatory NGS to validate IHC findings and assess fusion functionality. Functional NTRK1/2/3 fusions remain exceedingly rare in NSCLC, with a detection rate of 0.03% across our combined cohorts.