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Standard methods to detect NTRK fusions in daily practice and clinical research: ESMO recommendations

NTRK1, NTRK2 and NTRK3 fusions are present in a plethora of malignancies across different histologies.
These fusions represent the most frequent mechanism of oncogenic activation of these receptor tyrosine kinases, and biomarkers for the use of TRK small molecule inhibitors.
Given the varying frequency of NTRK1/2/3 fusions, crucial to the administration of NTRK inhibitors is the development of optimal approaches for the detection of human cancers harbouring activating NTRK1/2/3 fusion genes.

Experts from several Institutions were recruited by the European Society for Medical Oncology ( ESMO ) Translational Research and Precision Medicine Working Group ( TR and PM WG ) to review the available methods for the detection of NTRK gene fusions, their potential applications, and strategies for the implementation of a rational approach for the detection of NTRK1/2/3 fusion genes in human malignancies.

The main techniques employed for NTRK fusion gene detection include immunohistochemistry, fluorescence in situ hybridization ( FISH ), RT-PCR, and both RNA-based and DNA-based next generation sequencing ( NGS ).
Each technique has advantages and limitations, and the choice of assays for screening and final diagnosis should also take into account the resources and clinical context.

In conclusion, in tumours where NTRK fusions are highly recurrent, FISH, RT-PCR or RNA-based sequencing panels can be used as confirmatory techniques, whereas in the scenario of testing an unselected population where NTRK1/2/3 fusions are uncommon, either front-line sequencing ( preferentially RNA-sequencing ) or screening by immunohistochemistry followed by sequencing of positive cases should be pursued. ( Xagena )

Marchiò C et al, Annals of Oncology, Volume 30, Issue 9, Pages 1417–1427, 2019