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Additional file 1: Supplementary material. Supplementary Methods. Supplementary Results. Figure S1. Gene fusions supported by one or more SV tools. Figure S2. Allele fraction of distinct fusions per SV type. Figure S3. Filtering predicted gene fusions to a high confidence subset. Figure S4. High gene fusion burden is associated with copy number instability. Figure S5. Osteosarcomas with TP53 gene fusion. Figure S6. Potentially pathogenic gene fusion candidates in individual patients. Figure S7. HOXA9 gene expression and gene fusion status. Figure S8. Association between ZBTB20 gene expression and survival. Figure S9. Co-occurring fusions and SNVs indicative of TSG disruption. Figure S10. MTAP--CDKN2B-AS1 fusions and associated expression changes of CDKNB-AS1 and CDKN2A. References for supplementary methods and results.

Additional file 1:. This files contains supplementary Fig. 1–9 and the supplementary figure legends.

Additional file 3:. This files contains the references of supplementary Table 1.

Additional file 3:. This files contains the references of supplementary Table 1.

Contains fulltext : 153045.pdf (Publisher’s version ) (Open Access) MET has gained interest as a therapeutic target for a number of malignancies because of its involvement in tumorigenesis, invasion and metastasis. At present, a number of inhibitors, both antibodies against MET or its ligand hepatocyte growth factor, and small molecule MET tyrosine kinase inhibitors are in clinical trials. We here describe a novel variant of MET that is expressed in 6 % of high-grade gliomas. Characterization of this mutation in a glioma cell line revealed that it consists of an intronic deletion, resulting in a splice event connecting an intact splice donor site in exon 6 with the next splice acceptor site being that of exon 9. The encoded protein lacks parts of the extracellular IPT domains 1 and 2, encoded by exons 7 and 8, resulting in a novel pseudo-IPT and is named MET(Delta7-8). MET(Delta7-8) is located predominantly in the cytosol and is constitutively active. The auto-activating nature of MET(Delta7-8), in combination with a lack of transmembrane localization, renders MET(Delta7-8) not targetable using antibodies, although the protein is efficiently deactivated by MET-specific tyrosine kinase inhibitors. Testing of MET-expressing tumors for the presence of this variant may be important for treatment decision making.