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Background  Gene fusion events resulting from chromosomal rearrangements play an important role in initiation of lung adenocarcinoma. The recent association of four oncogenic driver genes,  ALK ,  ROS1 ,  RET , and  NTRK1 , as lung tumor predictive biomarkers has increased the need for development of up-to-date technologies for detection of these biomarkers in limited amounts of material.    Methods  We describe here a multi-institutional study using the Ion  AmpliSeq ™ RNA Fusion Lung Cancer Research Panel to interrogate previously characterized lung tumor samples.    Results  Reproducibility between laboratories using diluted fusion-positive cell lines was 100%. A cohort of lung clinical research samples from different origins (tissue biopsies, tissue resections, lymph nodes and pleural fluid samples) were used to evaluate the panel. We observed 97% concordance for  ALK  (28/30 positive; 71/70 negative samples), 95% for  ROS1  (3/4 positive; 19/18 negative samples), and 93% for  RET  (2/1 positive; 13/14 negative samples) between the AmpliSeq assay and other methodologies.    Conclusion  This methodology enables simultaneous detection of multiple  ALK ,  ROS1 ,  RET , and  NTRK1  gene fusion transcripts in a single panel, enhanced by an integrated analysis solution. The assay performs well on limited amounts of input RNA (10 ng) and offers an integrated single assay solution for detection of actionable fusions in lung adenocarcinoma, with potential savings in both cost and turn-around-time compared to the combination of all four assays by other methods.    Electronic supplementary material  The online version of this article (10.1186/s12885-018-4736-4) contains supplementary material, which is available to authorized users.

Simultaneous detection of lung fusions using a multiplex RT-PCR next generation sequencing-based approach: a multi-institutional research study