CANTRK: A Canadian Ring Study to Optimize Detection of NTRK Gene Fusions by Next Generation RNA Sequencing.

CANTRK is a ring study to optimize testing for neurotrophic receptor tyrosine kinase (NTRK) fusions in Canadian laboratories. Sixteen diagnostic laboratories used next generation sequencing (NGS) for NTRK1, NTRK2 or NTRK3 fusions. Each laboratory received 12 formalin fixed, paraffin embedded (FFPE) tumor samples with unique NTRK fusions, and 2 control non-NTRK fusion samples (1 ALK and 1 ROS1). Laboratories used validated protocols for NGS fusion detection. Panels included Oncomine Comprehensive Assay v3, Oncomine Focus, Oncomine Precision, AmpliSeq Focus, TruSight RNA Pan-Cancer Panel, FusionPlex Lung and QIAseq Multimodal Lung. One sample was withdrawn from analysis due to sample quality issues. Of the remaining 13 samples, 6 of 11 NTRK fusions and both control fusions were detected by all labs. Two fusions, WNK2::NTRK2 and STRN3::NTRK2, were not detected by 10 labs using Comprehensive or Focus panels, due to absence of WNK2 and STRN3 in panel designs. Two fusions TPM3::NTRK1 and LMNA::NTRK1 were challenging to detect on AmpliSeq for Illumina Focus panel due to bioinformatic issues. One ETV6::NTRK3 fusion at low levels was not detected by two labs using TruSight Pan-cancer Panel. Panels detecting all fusions included FusionPlex Lung, Oncomine Precision, and QIAseq Multimodal Lung. The CANTRK study demonstrated competency in detection of NTRK fusions by NGS across different panels in 16 Canadian laboratories, and identified key test issues as targets for improvements.