ArticlePLoS genetics2013
Breakpoint analysis of transcriptional and genomic profiles uncovers novel gene fusions spanning multiple human cancer types.
Article in PLoS genetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers.
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Who cites it
70 citing papers in PubMed, 116 citations in OpenAlex.
- Identification of cryptic KMT2A-PTD and other novel fusion genes by transcriptome sequencing alters molecular risk stratification in AML-NK.Journal of molecular medicine (Berlin, Germany) · 2026Article
- Case Report: A case series on actionable genomic alterations guiding effective targeted therapy in rare sarcomas.Frontiers in oncology · 2026Article
- Jet lag-induced circadian disruption elevates glioma risk by altering molecular profiles in distinct brain regions.Discover oncology · 2025Article
- EWSR1::CREM rearranged intra-abdominal malignant epithelioid neoplasm: two new cases of an emerging entity with clinicopathological characteristics and histological pitfalls.Virchows Archiv : an international journal of pathology · 2025Article
- The genomic landscape of 2,023 colorectal cancers.Nature · 2024Article
- Decoding the Versatile Landscape of Autophagic Protein VMP1 in Cancer: A Comprehensive Review across Tissue Types and Regulatory Mechanisms.International journal of molecular sciences · 2024Review
- Kinase regulation by liquid-liquid phase separation.Trends in cell biology · 2023Review
- Routine Clinically Detected IncreasedJTO clinical and research reports · 2023Article
- A phase I trial of riluzole and sorafenib in patients with advanced solid tumors: CTEP #8850.Oncotarget · 2023Article
- The oncogenic properties of the EWSR1::CREM fusion gene are associated with polyamine metabolism.Scientific reports · 2023Article
- Metastatic sporadic paraganglioma with EWSR1::CREM gene fusion: A unique molecular profile that expands the phenotypic diversity of the molecular landscape of the EWSR1::CREM gene fusion positive tumors.Genes, chromosomes & cancer · 2023Article
- Landscape of potentially targetable receptor tyrosine kinase fusions in diverse cancers by DNA-based profiling.NPJ precision oncology · 2022Article
- Discovery and functional characterization of the oncogenicity and targetability of a novelCold Spring Harbor molecular case studies · 2022Article
- Structural insights into inhibitory mechanism of human excitatory amino acid transporter EAAT2.Nature communications · 2022Article
- Article
- The potential and limitation of targeted chromosomal breakpoint sequencing for theAmerican journal of cancer research · 2022Article
- Review
- Expression of Transcription FactorThe journal of histochemistry and cytochemistry : official journal of the Histochemistry Society · 2021Article
- Genomically Complex Human Angiosarcoma and Canine Hemangiosarcoma Establish Convergent Angiogenic Transcriptional Programs Driven by Novel Gene Fusions.Molecular cancer research : MCR · 2021Article
- Protein-gene Expression Nexus: Comprehensive characterization of human cancer cell lines with proteogenomic analysis.Computational and structural biotechnology journal · 2021Article
10 more citing papers are in PubMed but not listed here.
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Authors and funding
17 authors at 2 institutions in 1 country.
Funding
Abstract
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.
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