Gene fusions, like BCR/ABL1 in
chronic myelogenous leukemia, have long been recognized in hematologic and mesenchymal
malignancies. The recent finding of gene fusions in prostate and
lung cancers has motivated the search for pathogenic gene fusions in other
malignancies. Here, we developed a "breakpoint analysis" pipeline to discover candidate gene fusions by tell-tale transcript level or genomic
DNA copy number transitions occurring within genes. Mining data from 974 diverse
cancer samples, we identified 198 candidate fusions involving annotated cancer genes. From these, we validated and further characterized novel gene fusions involving ROS1
tyrosine kinase in
angiosarcoma (CEP85L/ROS1), SLC1A2
glutamate transporter in
colon cancer (APIP/SLC1A2), RAF1
kinase in
pancreatic cancer (ATG7/RAF1) and
anaplastic astrocytoma (BCL6/RAF1), EWSR1 in
melanoma (EWSR1/CREM), CDK6
kinase in T-cell
acute lymphoblastic leukemia (FAM133B/CDK6), and CLTC in
breast cancer (CLTC/VMP1). Notably, while these fusions involved known cancer genes, all occurred with novel fusion partners and in previously unreported
cancer types. Moreover, several constituted druggable targets (including
kinases), with therapeutic implications for their respective
malignancies. Lastly, breakpoint analysis identified new cell line models for known rearrangements, including
EGFRvIII and FIP1L1/PDGFRA. Taken together, we provide a robust approach for gene fusion discovery, and our results highlight a more widespread role of fusion genes in
cancer pathogenesis.