gene fusion


Summary: The GENETIC RECOMBINATION of the parts of two or more GENES resulting in a gene with different or additional regulatory regions, or a new chimeric gene product. ONCOGENE FUSION includes an ONCOGENE as at least one of the fusion partners and such gene fusions are often detected in neoplastic cells and are transcribed into ONCOGENE FUSION PROTEINS. ARTIFICIAL GENE FUSION is carried out in vitro by RECOMBINANT DNA technology.

Top Publications

  1. Kinsella M, Harismendy O, Nakano M, Frazer K, Bafna V. Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs. Bioinformatics. 2011;27:1068-75 pubmed publisher
    ..A C++ and Python implementation of the method demonstrated in this article is available at Supplementary data are available at Bioinformatics online. ..
  2. Wang Q, Xia J, Jia P, Pao W, Zhao Z. Application of next generation sequencing to human gene fusion detection: computational tools, features and perspectives. Brief Bioinform. 2013;14:506-19 pubmed publisher
    ..In this article, we review the NGS and computational features of existing methods for fusion gene detection and suggest directions for future development. ..
  3. Rogers R, Bedford T, Lyons A, Hartl D. Adaptive impact of the chimeric gene Quetzalcoatl in Drosophila melanogaster. Proc Natl Acad Sci U S A. 2010;107:10943-8 pubmed publisher
    ..Together, these results show that chimeric genes can produce structural and regulatory changes in a single mutational step and may be a major factor in adaptive evolution. ..
  4. Dimitriadis D, Koumandou V, Trimpalis P, Kossida S. Protein functional links in Trypanosoma brucei, identified by gene fusion analysis. BMC Evol Biol. 2011;11:193 pubmed publisher
    Domain or gene fusion analysis is a bioinformatics method for detecting gene fusions in one organism by comparing its genome to that of other organisms...
  5. Gasi D, Trapman J. Androgen regulation of ETS gene fusion transcripts in prostate cancer. Methods Mol Biol. 2011;776:335-48 pubmed publisher
    ..Despite its high frequency, the biological and molecular effects of ETS gene fusion in prostate cancer development and progression are unknown...
  6. Lawson A, Hindley G, Forshew T, Tatevossian R, Jamie G, Kelly G, et al. RAF gene fusion breakpoints in pediatric brain tumors are characterized by significant enrichment of sequence microhomology. Genome Res. 2011;21:505-14 pubmed publisher
    ..Here, we present a detailed analysis of RAF gene fusion breakpoints from a well-characterized cohort of 43 low-grade astrocytomas...
  7. Rao Q, Liu B, Cheng L, Zhu Y, Shi Q, Wu B, et al. Renal cell carcinomas with t(6;11)(p21;q12): A clinicopathologic study emphasizing unusual morphology, novel alpha-TFEB gene fusion point, immunobiomarkers, and ultrastructural features, as well as detection of the gene fusion by fluorescence in situ. Am J Surg Pathol. 2012;36:1327-38 pubmed publisher
    ..TFEB RCC seemed to be an indolent tumor. During a mean follow-up of 31 months, none of the cases developed tumor recurrence, progression, or metastasis. ..
  8. Pflueger D, Terry S, Sboner A, Habegger L, Esgueva R, Lin P, et al. Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing. Genome Res. 2011;21:56-67 pubmed publisher
    ..than 1 billion sequence reads and used a novel computational approach (FusionSeq) in order to identify novel gene fusion candidates with high confidence...
  9. Berger M, Levin J, Vijayendran K, Sivachenko A, Adiconis X, Maguire J, et al. Integrative analysis of the melanoma transcriptome. Genome Res. 2010;20:413-27 pubmed publisher
    ..Taken together, these results may indicate new avenues for target discovery in melanoma, while also providing a template for large-scale transcriptome studies across many tumor types. ..

More Information


  1. Erickson Johnson M, Chou M, Evers B, Roth C, Seys A, Jin L, et al. Nodular fasciitis: a novel model of transient neoplasia induced by MYH9-USP6 gene fusion. Lab Invest. 2011;91:1427-33 pubmed publisher
    ..Considering the self-limited nature of the lesion, NF may represent a model of 'transient neoplasia', as it is, to our knowledge, the first example of a self-limited human disease characterized by a recurrent somatic gene fusion event.
  2. Kim D, Salzberg S. TopHat-Fusion: an algorithm for discovery of novel fusion transcripts. Genome Biol. 2011;12:R72 pubmed publisher
    ..Using RNA-seq data from breast and prostate cancer cell lines, we detected both previously reported and novel fusions with solid supporting evidence. TopHat-Fusion is available at ..
  3. Park K, Dalton J, Narayanan R, Barbieri C, Hancock M, Bostwick D, et al. TMPRSS2:ERG gene fusion predicts subsequent detection of prostate cancer in patients with high-grade prostatic intraepithelial neoplasia. J Clin Oncol. 2014;32:206-11 pubmed publisher
    ..The predictive value of ERG gene fusion in HGPIN for PCa was interrogated as a post hoc analysis in the context of a randomized clinical trial.
  4. Wang X, Prensner J, Chen G, Cao Q, Han B, Dhanasekaran S, et al. An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer. Nat Biotechnol. 2009;27:1005-11 pubmed publisher
    ..Knockdown of NFE2 decreased proliferation and invasion of H1792 cells. Together, these results present a systematic analysis of gene fusions in cancer and describe key characteristics that assist in new fusion discovery. ..
  5. Iyer M, Chinnaiyan A, Maher C. ChimeraScan: a tool for identifying chimeric transcription in sequencing data. Bioinformatics. 2011;27:2903-4 pubmed publisher
    Next generation sequencing (NGS) technologies have enabled de novo gene fusion discovery that could reveal candidates with therapeutic significance in cancer...
  6. Pierron G, Tirode F, Lucchesi C, Reynaud S, Ballet S, Cohen Gogo S, et al. A new subtype of bone sarcoma defined by BCOR-CCNB3 gene fusion. Nat Genet. 2012;44:461-6 pubmed publisher
    ..Thus, the intrachromosomal X-chromosome fusion described here represents a new subtype of bone sarcoma caused by a newly identified gene fusion mechanism.
  7. Asmann Y, Hossain A, Necela B, Middha S, Kalari K, Sun Z, et al. A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines. Nucleic Acids Res. 2011;39:e100 pubmed publisher
    ..Executables in PERL are available for download from our web site: ..
  8. Barwick B, Abramovitz M, Kodani M, Moreno C, Nam R, Tang W, et al. Prostate cancer genes associated with TMPRSS2-ERG gene fusion and prognostic of biochemical recurrence in multiple cohorts. Br J Cancer. 2010;102:570-6 pubmed publisher
    Recent studies have indicated that prostate cancer patients with the TMPRSS2-ERG gene fusion have a higher risk of recurrence...
  9. Errani C, Zhang L, Sung Y, Hajdu M, Singer S, Maki R, et al. A novel WWTR1-CAMTA1 gene fusion is a consistent abnormality in epithelioid hemangioendothelioma of different anatomic sites. Genes Chromosomes Cancer. 2011;50:644-53 pubmed publisher
    ..of epithelioid hemangioendothelioma (EHE), however, no follow-up studies have been performed to identify the gene fusion or to assess its prevalence in a larger cohort of patients...
  10. Ha K, Lalonde E, Li L, Cavallone L, Natrajan R, Lambros M, et al. Identification of gene fusion transcripts by transcriptome sequencing in BRCA1-mutated breast cancers and cell lines. BMC Med Genomics. 2011;4:75 pubmed publisher
    ..We then refined our approach by identifying misaligned paired reads, which may flank a putative gene fusion junction...
  11. Lee K, Chae J, Kwak C, Ku J, Moon K. TMPRSS2-ERG gene fusion and clinicopathologic characteristics of Korean prostate cancer patients. Urology. 2010;76:1268.e7-13 pubmed publisher
    ..The fusion rate of the TMPRSS2-ERG gene was 20.9% (53/254). TMPRSS2-ERG gene fusion was identified more frequently in patients with low Gleason grade (primary Gleason pattern ? 3 or sum of ..
  12. Brenner J, Ateeq B, Li Y, Yocum A, Cao Q, Asangani I, et al. Mechanistic rationale for inhibition of poly(ADP-ribose) polymerase in ETS gene fusion-positive prostate cancer. Cancer Cell. 2011;19:664-78 pubmed publisher
    ..the mechanisms by which ETS fusions mediate their effects, and find that the product of the predominant ETS gene fusion, TMPRSS2:ERG, interacts in a DNA-independent manner with the enzyme poly (ADP-ribose) polymerase 1 (PARP1) and ..
  13. Costa S, Almeida A, Castro A, Domingues L, Besir H. The novel Fh8 and H fusion partners for soluble protein expression in Escherichia coli: a comparison with the traditional gene fusion technology. Appl Microbiol Biotechnol. 2013;97:6779-91 pubmed publisher
  14. Reid A, Ranea J, Clegg A, Orengo C. CODA: accurate detection of functional associations between proteins in eukaryotic genomes using domain fusion. PLoS ONE. 2010;5:e10908 pubmed publisher
    ..b>Gene fusion prediction is one approach to detection of such functional relationships...
  15. Rubio Briones J, Fernandez Serra A, Calatrava A, Garcia Casado Z, Rubio L, Bonillo M, et al. Clinical implications of TMPRSS2-ERG gene fusion expression in patients with prostate cancer treated with radical prostatectomy. J Urol. 2010;183:2054-61 pubmed publisher
    ..TMPRSS2-ERG fusion gene status classifies patients with prostate cancer treated with radical prostatectomy into groups defined by different prognostic factors. This could be the basis for designing more refined treatment strategies. ..
  16. Li Y, Chien J, Smith D, Ma J. FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq. Bioinformatics. 2011;27:1708-10 pubmed publisher
    ..The purpose of FusionHunter is to identify potential fusions with high sensitivity and specificity and to guide further functional validation in the laboratory. ..
  17. Banerji S, Cibulskis K, Rangel Escareño C, Brown K, Carter S, Frederick A, et al. Sequence analysis of mutations and translocations across breast cancer subtypes. Nature. 2012;486:405-9 pubmed publisher
    ..The MAGI3-AKT3 fusion leads to constitutive activation of AKT kinase, which is abolished by treatment with an ATP-competitive AKT small-molecule inhibitor. ..
  18. Benelli M, Pescucci C, Marseglia G, Severgnini M, Torricelli F, Magi A. Discovering chimeric transcripts in paired-end RNA-seq data by using EricScript. Bioinformatics. 2012;28:3232-9 pubmed publisher
    ..computational framework, named chimEric tranScript detection algorithm (EricScript), for the identification of gene fusion products in paired-end RNA-seq data...
  19. Malfavon Borja R, Wu L, Emerman M, Malik H. Birth, decay, and reconstruction of an ancient TRIMCyp gene fusion in primate genomes. Proc Natl Acad Sci U S A. 2013;110:E583-92 pubmed publisher
    ..Despite its decayed status, we found TRIMCypA3 gene fusion transcripts in several primates...
  20. Yu J, Yu J, Mani R, Cao Q, Brenner C, Cao X, et al. An integrated network of androgen receptor, polycomb, and TMPRSS2-ERG gene fusions in prostate cancer progression. Cancer Cell. 2010;17:443-54 pubmed publisher
    ..These findings provide a working model in which TMPRSS2-ERG plays a critical role in cancer progression by disrupting lineage-specific differentiation of the prostate and potentiating the EZH2-mediated dedifferentiation program. ..
  21. Malouf G, Camparo P, Oudard S, Schleiermacher G, Theodore C, Rustine A, et al. Targeted agents in metastatic Xp11 translocation/TFE3 gene fusion renal cell carcinoma (RCC): a report from the Juvenile RCC Network. Ann Oncol. 2010;21:1834-8 pubmed publisher
    ..Median OS was 27 months with a 19 months median follow-up. In Xp11 translocation RCC, targeted therapy achieved objective responses and prolonged PFS similar to those reported for clear-cell RCC. ..
  22. Wu C, Wyatt A, McPherson A, Lin D, McConeghy B, Mo F, et al. Poly-gene fusion transcripts and chromothripsis in prostate cancer. Genes Chromosomes Cancer. 2012;51:1144-53 pubmed publisher
    ..One such poly-gene fusion transcript appeared to be expressed from a chain of small genomic fragments...
  23. Tatevossian R, Lawson A, Forshew T, Hindley G, Ellison D, Sheer D. MAPK pathway activation and the origins of pediatric low-grade astrocytomas. J Cell Physiol. 2010;222:509-14 pubmed publisher
    ..In this review we summarize these findings, discuss how these gene fusions may arise and consider possible implications for diagnosis and treatment...
  24. Liu C, Ma J, Chang C, Zhou X. FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq. BMC Bioinformatics. 2013;14:193 pubmed publisher
    ..FusionQ is a novel tool for fusion detection and quantification based on RNA-Seq data. It has both good specificity and sensitivity performance. FusionQ is free and available at ..
  25. Robinson D, Kalyana Sundaram S, Wu Y, Shankar S, Cao X, Ateeq B, et al. Functionally recurrent rearrangements of the MAST kinase and Notch gene families in breast cancer. Nat Med. 2011;17:1646-51 pubmed publisher
    ..These findings show that recurrent gene rearrangements have key roles in subsets of carcinomas and suggest that transcriptome sequencing could identify individuals with rare, targetable gene fusions. ..
  26. Chmielecki J, Crago A, Rosenberg M, O Connor R, Walker S, Ambrogio L, et al. Whole-exome sequencing identifies a recurrent NAB2-STAT6 fusion in solitary fibrous tumors. Nat Genet. 2013;45:131-2 pubmed publisher
  27. Yin L, Rao P, Elson P, Wang J, Ittmann M, Heston W. Role of TMPRSS2-ERG gene fusion in negative regulation of PSMA expression. PLoS ONE. 2011;6:e21319 pubmed publisher
    ..The purpose of this investigation is to determine whether PSMA expression can be regulated by the TMPRSS2-ERG gene fusion. We employed two PSMA positive cell lines: VCaP cells, which harbor TMPRSS2-ERG fusion, and LNCaP cells, which ..
  28. Ge H, Liu K, Juan T, Fang F, Newman M, Hoeck W. FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution. Bioinformatics. 2011;27:1922-8 pubmed publisher
    ..FusionMap includes reference indexing, read filtering, fusion alignment and reporting in one package. The software is free for noncommercial use at ( ..
  29. Kangaspeska S, Hultsch S, Edgren H, Nicorici D, Murumägi A, Kallioniemi O. Reanalysis of RNA-sequencing data reveals several additional fusion genes with multiple isoforms. PLoS ONE. 2012;7:e48745 pubmed publisher
    ..This illustrates the importance of reanalyzing sequencing data as gene definitions change and bioinformatic methods improve, and highlights the previously unforeseen isoform diversity among fusion transcripts. ..
  30. Robinson D, Wu Y, Kalyana Sundaram S, Cao X, Lonigro R, Sung Y, et al. Identification of recurrent NAB2-STAT6 gene fusions in solitary fibrous tumor by integrative sequencing. Nat Genet. 2013;45:180-5 pubmed publisher
    ..A gene fusion of the transcriptional repressor NAB2 with the transcriptional activator STAT6 was detected...
  31. Parker B, Annala M, Cogdell D, Granberg K, Sun Y, Ji P, et al. The tumorigenic FGFR3-TACC3 gene fusion escapes miR-99a regulation in glioblastoma. J Clin Invest. 2013;123:855-65 pubmed publisher
    ..These results demonstrated that the FGFR3-TACC3 gene fusion is expressed in human cancer and generates an oncogenic protein that promotes tumorigenesis in glioblastoma.
  32. Francis R, Thompson Wicking K, Carter K, Anderson D, Kees U, Beesley A. FusionFinder: a software tool to identify expressed gene fusion candidates from RNA-Seq data. PLoS ONE. 2012;7:e39987 pubmed publisher
    ..We present FusionFinder, a Perl-based software designed to automate the discovery of candidate gene fusion partners from single-end (SE) or paired-end (PE) RNA-Seq read data...
  33. Zhu Q, Wang Z, Zhu W, Chen W, Wu J. The multislice CT findings of renal carcinoma associated with XP11.2 translocation/TFE gene fusion and collecting duct carcinoma. Acta Radiol. 2013;54:355-62 pubmed publisher
    Renal cell carcinoma associated with Xp11.2 translocation and TFE gene fusion (Xp11.2/TFE RCC), and collecting duct carcinoma (CDC) are uncommon subtypes of renal cell carcinomas...
  34. Nord K, Lilljebjörn H, Vezzi F, Nilsson J, Magnusson L, Tayebwa J, et al. GRM1 is upregulated through gene fusion and promoter swapping in chondromyxoid fibroma. Nat Genet. 2014;46:474-7 pubmed publisher
    ..found that the glutamate receptor gene GRM1 recombines with several partner genes through promoter swapping and gene fusion events...
  35. Mitani Y, Rao P, Futreal P, Roberts D, Stephens P, Zhao Y, et al. Novel chromosomal rearrangements and break points at the t(6;9) in salivary adenoid cystic carcinoma: association with MYB-NFIB chimeric fusion, MYB expression, and clinical outcome. Clin Cancer Res. 2011;17:7003-14 pubmed publisher
    ..6%) tumors. Detailed FISH analysis of 11 out the 15 tumors with gene fusion without transcript formation showed translocation of NFIB sequences to proximal or distal sites of the MYB gene...
  36. Sboner A, Habegger L, Pflueger D, Terry S, Chen D, Rozowsky J, et al. FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data. Genome Biol. 2010;11:R104 pubmed publisher
    ..It also has a module to identify exact sequences at breakpoint junctions. FusionSeq detected known and novel fusions in a specially sequenced calibration data set, including eight cancers with and without known rearrangements. ..
  37. Kato H, Kanematsu M, Yokoi S, Miwa K, Horie K, Deguchi T, et al. Renal cell carcinoma associated with Xp11.2 translocation/TFE3 gene fusion: radiological findings mimicking papillary subtype. J Magn Reson Imaging. 2011;33:217-20 pubmed publisher
    ..2 translocation/transcription factor E3 (TFE3) gene fusion (Xp11 translocation carcinoma)...
  38. Magi Galluzzi C, Tsusuki T, Elson P, Simmerman K, Lafargue C, Esgueva R, et al. TMPRSS2-ERG gene fusion prevalence and class are significantly different in prostate cancer of Caucasian, African-American and Japanese patients. Prostate. 2011;71:489-97 pubmed publisher
    ..We examined the prevalence and class of TMPRSS2-ERG gene fusion in PCa from Caucasian, African-American, and Japanese patients...
  39. Buljan M, Frankish A, Bateman A. Quantifying the mechanisms of domain gain in animal proteins. Genome Biol. 2010;11:R74 pubmed publisher
    ..Here we show that the major mechanism for gains of new domains in metazoan proteins is likely to be gene fusion through joining of exons from adjacent genes, possibly mediated by non-allelic homologous recombination...
  40. Guo C, Dancer J, Wang Y, Aparicio A, Navone N, Troncoso P, et al. TMPRSS2-ERG gene fusion in small cell carcinoma of the prostate. Hum Pathol. 2011;42:11-7 pubmed publisher
    Recent studies have shown that most prostate cancers carry the TMPRSS2-ERG gene fusion. Here we evaluated the TMPRSS2-ERG gene fusion in small cell carcinoma of the prostate (n = 12) in comparison with small cell carcinoma of the urinary ..
  41. Kalyana Sundaram S, Shankar S, Deroo S, Iyer M, Palanisamy N, Chinnaiyan A, et al. Gene fusions associated with recurrent amplicons represent a class of passenger aberrations in breast cancer. Neoplasia. 2012;14:702-8 pubmed
    ..As illustrative examples of the "amplicon-associated" gene fusions, we examined here a recurrent gene fusion involving the mediator of mammalian target of rapamycin signaling, RPS6KB1 kinase in BT-474, and the ..
  42. Nacu S, Yuan W, Kan Z, Bhatt D, Rivers C, Stinson J, et al. Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples. BMC Med Genomics. 2011;4:11 pubmed publisher
    ..Tissue specificity of TIC events is correlated with expression patterns of the upstream gene. Some TIC events, such as MSMB-NCOA4, may play functional roles in cancer. ..
  43. Tanas M, Sboner A, Oliveira A, Erickson Johnson M, Hespelt J, Hanwright P, et al. Identification of a disease-defining gene fusion in epithelioid hemangioendothelioma. Sci Transl Med. 2011;3:98ra82 pubmed publisher
    ..This WWTR1/CAMTA1 gene fusion is under the transcriptional control of the WWTR1 promoter and encodes a putative chimeric transcription factor ..
  44. Cheng G, Hu Y, Yin Y, Yang X, Xiang C, Wang B, et al. Functional screening of antibiotic resistance genes from human gut microbiota reveals a novel gene fusion. FEMS Microbiol Lett. 2012;336:11-6 pubmed publisher
    ..SSC/2. A functional study on the novel kanamycin resistance gene showed that only the N-terminus conferred kanamycin resistance. Our results showed that functional metagenomics is a useful tool for the identification of new ARGs. ..
  45. Abate F, Acquaviva A, Paciello G, Foti C, Ficarra E, Ferrarini A, et al. Bellerophontes: an RNA-Seq data analysis framework for chimeric transcripts discovery based on accurate fusion model. Bioinformatics. 2012;28:2114-21 pubmed publisher
    ..Bellerophontes performs a selection of putative junctions on the basis of a match to an accurate gene fusion model...
  46. Edwards P. Fusion genes and chromosome translocations in the common epithelial cancers. J Pathol. 2010;220:244-54 pubmed publisher
  47. Saljoughian N, Taheri T, Zahedifard F, Taslimi Y, Doustdari F, Bolhassani A, et al. Development of novel prime-boost strategies based on a tri-gene fusion recombinant L. tarentolae vaccine against experimental murine visceral leishmaniasis. PLoS Negl Trop Dis. 2013;7:e2174 pubmed publisher
    ..Altogether, these results indicate the promise of the A2-CPA-CPB(-CTE)-recombinant L. tarentolae as a safe live vaccine candidate against VL. ..
  48. Attard G, Jameson C, Moreira J, Flohr P, Parker C, Dearnaley D, et al. Hormone-sensitive prostate cancer: a case of ETS gene fusion heterogeneity. J Clin Pathol. 2009;62:373-6 pubmed publisher
    ..This is exemplified by the case presented here of a patient diagnosed in 1991 who remains asymptomatic and chemotherapy-naïve after having long-lasting tumour responses to multiple lines of systemic hormonal treatments. ..
  49. Kasyapa C, Kunapuli P, Cowell J. HSPA1A is an important regulator of the stability and function of ZNF198 and its oncogenic derivative, ZNF198-FGFR1. J Cell Biochem. 2007;102:1308-17 pubmed
    ..These observations suggest an important role for HSPA1A in ZNF198 and ZNF198-FGFR1 mediated cellular function. ..
  50. Vu H, Xinh P, Masuda M, Motoji T, Toyoda A, Sakaki Y, et al. FLT3 is fused to ETV6 in a myeloproliferative disorder with hypereosinophilia and a t(12;13)(p13;q12) translocation. Leukemia. 2006;20:1414-21 pubmed
    ..FLT3 receptor in leukemic cells might be inappropriately activated through dimerization by HLH domain of ETV6, which consequently interfered with proliferation and differentiation of hematopoietic cells. ..
  51. Prensner J, Chinnaiyan A. Oncogenic gene fusions in epithelial carcinomas. Curr Opin Genet Dev. 2009;19:82-91 pubmed publisher
    ..tumors and highlighted important advances in bioinformatics, sequencing, and microarray technology as tools for gene fusion discovery...
  52. Caudell D, Aplan P. The role of CALM-AF10 gene fusion in acute leukemia. Leukemia. 2008;22:678-85 pubmed
  53. Buzdin A, Gogvadze E, Lebrun M. Chimeric retrogenes suggest a role for the nucleolus in LINE amplification. FEBS Lett. 2007;581:2877-82 pubmed
    ..These hypotheses will be discussed in this review. ..