Detection of chromosomal rearrangements involving tyrosine kinase genes such as ALK, NTRK1, ROS1 is of great importance for diagnosis of non-small cell lung cancer (NSCLC) and selection of targeted therapies. Herein, we present an extended, multiplexed Oncomine targeted RNA sequencing research assay for detection of fusion transcripts and intragenic rearrangements (exon deletion/skipping). In addition, we present our studies towards development of a transcript-based expression imbalance research assay designed to identify gene fusions in a partner agnostic manner, and apply the method for multiple key driver genes as a potential complementary method to our core fusion detection method.