Generation Sequencing in GTL16. At this point we cannot rule out the possibility of a small pre-existing pool of SND1-BRAF expressing clones in GTL16. The clinical significance of the SND1-BRAF fusion is unknown. A computational search of publically available CNV arrays representing more than 5000 cell lines and primary samples did not identify any co-occurring SND1-BRAF breakpoints consistent with the known fusion. It is likely that selective pressure from prolonged drug treatment is required to generate SND1-BRAF fusions in primary tumors. The acquisition of additional oncogenic drivers has important implications for targeted therapy. The sequential treatment of tumors with targeted agents may allow sequential resistance to develop if inhibitors are applied individually. Conceivably, resistance mechanisms to BRAF inhibition like IGF-1R [52], COT [53], NRAS [54], or PDGFRbeta [54] could also provide alternate survival pathways in the context of c-Met inhibition. For example, EGFR signaling is one example of a resistance mechanism common to both c-Met inhibition [2] and BRAF inhibition [55]. Additionally, in a study of BRAF mutated Papillary Thyroid Carcinoma (PTC), c-Met expression was 3-fold higher in the BRAF aggressive PTC vs. the BRAF non-aggressive PTC [56]. Furthermore, c-Met amplification is a primary resistance mechanism to the BRAF inhibitor PLX4032 in patient derived melanoma cell lines [57]. Hence, c-Met and BRAF co- activation may increase tumor robustness and resistance to targeted therapy due to activation of multiple growth and survival pathways. Further studies are needed to understand the comple- mentarity and essential elements of c-Met and BRAF inhibition. Supporting Information Figure S1 Kinase Selectivity Screen of METi. (A) Kinase selectivity screen (KSS) performed at Upstate Biotechnology. Values in % inhibition of phosphorylation given 1 mM of METi compared to control. (B) KSS performed at University of Dundee (Division of Signal Transduction Therapy). Values in % inhibition of phosphorylation given 1 mM of METi compared to control. (C) Cell based dose response kinase inhibition of indicated kinases by METi. (PDF) References 1. Janne PA, Gray N, Settleman J (2009) Factors underlying sensitivity of cancers to small-molecule kinase inhibitors. Nat Rev Drug Discov 8: 709–723. 2. McDermott U, Pusapati RV, Christensen JG, Gray NS, Settleman J (2010) Acquired resistance of non-small cell lung cancer cells to MET kinase inhibition is mediated by a switch to epidermal growth factor receptor dependency. Cancer Res 70: 1625–1634. 3. Engelman JA, Zejnullahu K, Mitsudomi T, Song Y, Hyland C, et al. (2007) MET amplification leads to gefitinib resistance in lung cancer by activating ERBB3 signaling. Science 316: 1039–1043. 4. Ercan D, Zejnullahu K, Yonesaka K, Xiao Y, Capelletti M, et al. (2010) Amplification of EGFR T790M causes resistance to an irreversible EGFR inhibitor. Oncogene 29: 2346–2356. 5. Guix M, Faber AC, Wang SE, Olivares MG, Song Y, et al. (2008) Acquired resistance to EGFR tyrosine kinase inhibitors in cancer cells is mediated by loss of IGF-binding proteins. J Clin Invest 118: 2609–2619. 6. Comoglio PM, Giordano S, Trusolino L (2008) Drug development of MET inhibitors: targeting oncogene addiction and expedience. Nat Rev Drug Discov 7: 504–516. 7. Lutterbach B, Zeng Q, Davis LJ, Hatch H, Hang G, et al. (2007) Lung cancer cell lines harboring MET gene amplification are dependent on Met for growth and survival. Cancer Res 67: 2081–2088. 8. Smolen GA, Sordella R, Muir B, Mohapatra G, Barmettler A, et al. (2006) Amplification of MET may identify a subset of cancers with extreme sensitivity to the selective tyrosine kinase inhibitor PHA-665752. Proc Natl Acad Sci U S A 103: 2316–2321. BRAF Fusion Confers Resistance to c-Met Inhibitor Figure S2 Kinase Selectivity Screen of RAFi. (A) Kinase selectivity screen (KSS) performed at University of Dundee (Division of Signal Transduction Therapy). Values in % inhibition of phosphorylation given 1 mM of RAFi compared to control. (B) KSS performed at Invitrogen (Selectscreen Service) compared to control. Values in % inhibition of phosphorylation given 1 mM of RAFi. (C) Cell based dose response kinase inhibition of indicated kinases by RAFi. (PDF) Figure S3 Phosphorylation fold decreases upon PF-04217903 treatment of GTL16, GTL16R1 and GTL16R3 cells compared to vehicle. Values are taken from RPPA analysis of cells treated with 2.5 mM METi for 1 hr. (PDF) Figure S4 Amplification at regions 7q34 and 7q32 form a fusion transcript. (A) CNV data show breakpoints between exons 16–17 of SND1 and 8–9 of BRAF. (B) RNA-Seq paired end reads aligned to the putative fusion transcript show reads that overlap or span the SND/BRAF junction only in clone GTL16R3 but not GTL16. (PDF) Figure S5 (A) Table of raw coverage or normalized Reads/ Base/Million (RBM) reads of RNA-Seq that align to full length or fusion regions of SND1 or BRAF. Fold is calculated relative to GTL16. Fusion regions are overrepresented in GTL16R1 and GTL16R3 relative to GTL16. (B) Graphic of the raw coverage and RBM at each base position in SND1 and BRAF shows the uneven distribution of coverage and high expression of the fusion transcript. (PDF) Author Contributions Conceived and designed the experiments: NVL MEL KAC SS. Performed the experiments: NVL MEL KAC DB. Analyzed the data: NVL MEL AP JY SA KAC. Contributed reagents/materials/analysis tools: KAC AP YZ SA SB. Wrote the paper: NVL MEL KAC JGC PAR SA. 9. Cepero V, Sierra JR, Corso S, Ghiso E, Casorzo L, et al. 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