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Figure S8. RT-PCR analysis of EML4 in four tissue specimens. The relative EML4 mRNA expression at each exon in NAT specimens was calculated as the ratio of the normalized values with GAPDH mRNA to those in tumor tissues. Each bar represents the mean + SD (n = 3) (PPTX 45 kb)

Table S1. Taqman probes for fusion (DOCX 26 kb)

Figure S5. RT-PCR analysis of ALK, RET, or ROS1 fusion in 4 tumor tissues. The mRNA expression of variant 1, 2, 3a, or 3b of EML4-ALK (a), KIF5B-RET, CCDC6-RET (b) or SLC34A2-ROS1 (c) was determined by RT-PCR using the Taqman probes shown in Additional file 1: Table S1. Red lines show fusion geneâ positive tumor tissue, and green lines show fusion geneâ negative tumor tissue (PPTX 122 kb)

Figure S11. Western blotting analysis in five cancer cell lines without any fusion gene. Cell lysates were harvested after 2â h of treatment with each drug at the concentrations shown (nM) (PPTX 2123 kb)

Figure S3. Western blotting analysis in 3 cancer cell lines with ALK fusion. Cell lysates were harvested after 2â h of treatment with each drug at the concentration shown (nM). The antibodies were obtained from Cell signaling technology. (PPTX 2483 kb)

Figure S1. RT-PCR analysis of ALK, RET, or ROS1 fusion in 37 cancer cell lines. The mRNA expression of variant 1, 2, 3a, or 3b of EML4-ALK (a), KIF5B-RET, CCDC6-RET (b) or SLC34A2-ROS1 (c) was determined by RT-PCR using the Taqman probes shown in Additional file 1: Table S1. Red lines show fusion geneâ positive cell lines and green lines show fusion geneâ negative cell lines (PPTX 129 kb)

Table S4. Exon count of mRNA (DOCX 26 kb)

Table S5. IC50s of ALK-TKIs and erlotinib (DOCX 28 kb)

Figure S9. Western blotting analysis in three cancer cell lines with or without RET fusion. Cell lysates were harvested after 2â h of treatment with each drug at the concentrations shown (nM). The levels of RET phosphorylation in LC-2/ad were undetectable by this western blotting system (PPTX 2307 kb)

Figure S6. Summary of ALK, RET, or ROS1 fusion in 4 tumor tissue specimens. Plot of normalized values calculated from the data in Additional file 9: Figure S5 (PPTX 45 kb)

Figure S7. Analysis by IHC and FISH of ALK in ILS31007 tissue specimen. The FFPE specimens with tumor tissue (upper panel) and the paired NAT specimens (lower panel) were obtained from BioreclamationIVT. IHC (left panel) and FISH (right panel) analyses for ALK rearrangement were performed with, respectively, the N-Histofine ALK detection kit (Nichirei Biosciences; Tokyo, Japan) and the Vysis ALK break apart FISH probe kit (Abbott laboratories; Abbott Park, IL) at a commercial clinical laboratory, LSI Medience (Tokyo, Japan). Images were captured using standard settings by the BZ900 (Keyence; Osaka, Japan) (PPTX 754 kb)

Table S3. Target terminus of antibody (DOCX 28 kb)

Figure S4. Comparison of molecular weights between wild-type and fusion protein. After high exposure of N-terminal EML4 in the results shown in Fig. 2, two sizes of EML4 protein were detected in NCI-H2228 and SNU-2292 cell lines (left-hand figure), and we assumed that the larger protein was wild-type EML4 (arrow) and the smaller protein was ALK-fused EML4 (arrowhead), after referring to the protein weight of EML4-ALK detected by an ALK C-terminus antibody (right-hand figure) (a). In the same way, we assumed that the larger and smaller proteins were respectively wild-type EML4 (arrow) and ALK-fused EML4 (arrowhead) in the results for the ILS31007 tumor tissue specimen shown in Fig. 3b (b), and the larger and smaller proteins were respectively wild-type CCDC6 (arrow) and RET-fused CCDC6 (arrowhead) in the results for CCDC6 in the LC-2/ad cell line shown in Fig. 2 (c) (PPTX 600 kb)

Figure S2. Summary of ALK, RET, or ROS1 fusion in 37 cancer cell lines. Plot of normalized values calculated from the data in Additional file 5: Figure S1 (PPTX 50 kb)

Table S2. Taqman probes for exons of mRNA (DOCX 28 kb)