Technological Advances in the Detection of Novel Fusion Genes


Since their first discovery in chronic myeloid leukaemia, fusion genes have been shown to play a central role in haematologic cancers. However, aberrations arising from this type of somatic mutations have been neglected in common solid tumours, largely because of limitations of current cytogenetic techniques. The recent discovery of recurrent gene fusions in prostate and lung cancer has led to a renewed interest in the identification of novel fusion genes in solid tumours. In this review, we discuss the technical challenges of studying gene fusions in solid tumours, appraise the application of newer molecular techniques and highlight emerging technologies, with the focus on next‐generation sequencing and chromogenic in situ hybridisation, that have greatly enhanced the speed and reliability of gene fusion discovery in malignant solid tumours.

Key Concepts:

  • A fusion gene is a gene hybrid formed from linking two physically separated genes.

  • A fusion gene can occur as a result of chromosomal rearrangements such as translocations, insertions, deletions and inversions, which lead to novel protein fusion products.

  • The detection of fusion genes is being recognised as a promising clinical tool for the diagnosis, staging classification, prognosis and treatment of cancer.

  • Gene fusions have been an underappreciated class of mutation in solid tumours.

  • The identification of gene fusions in solid tumours is technically challenging due to the complex and often chaotic karyotypic profiles of solid cancers.

  • Recent advances in genomics obtained from next generation sequencing, coupled with the emerging field of bioinformatics and ever‐advancing molecular techniques, have uncovered many novel oncogenic fusion genes in solid tumours that were unable to be detected by traditional cytogenetic methods.

  • Fluorescence In‐Situ Hybridisation (FISH) is recognised as the most effective diagnostic methods for the detection of gene fusions.

  • Transcriptome‐sequencing (also known as RNA‐sequencing), a recently introduced high‐throughput method of characterising ribonucleic acid (RNA) transcribed from the genome is rapidly emerging as the key method for the discovery of gene fusions.

  • Numerous challenges and unanswered issues remained with the discovery of novel gene fusions and their development as effective targeted cancer therapies or as clinical diagnostic and/or prognostic tools.

Keywords: fusion genes; genomic rearrangement; next‐generation sequencing; cancer genomics; chromogenic in‐situ hybridisation; fluorescence in‐situ hybridisation

Figure 1.

Fusion genes in cancer. Chromosomal aberrations (including translocation, insertion, deletion and inversion) can result in either fusion of an oncogene with another gene (a) or forced activation of an oncogene or down‐regulation of a tumour suppressor gene (b). P1 and P2 represent regulatory promoter elements for Gene 1 and 2, respectively. Arrows indicate locations of chromosomal breakpoints. The boxes represent exons whereas the lines between the boxes represent introns.

Figure 2.

Molecular and cytological techniques used in fusion gene discovery studies. (a) Exon‐walking quantitative real‐time PCR: an obvious over‐expression pattern from only the 3′ regions of the candidate gene suggests the presence of a genetic rearrangement. Arrows represent primer pairs. (b) 5′ RACE assay for the identification of unknown 5′ fusion partner. (c) Fusion‐specific RT‐PCR, where arrows represent forward and reverse primers set spanning the junction between the two fused genes. (d) FISH: Break‐apart (left) and fusion probe (right) strategies.

Figure 3.

Paired‐end sequencing versus single‐end sequencing. Paired‐end strategy (above) linked two reads as belonging to the same transcribed unit. With single‐end approach (below) individual reads are associated with independent genes, thus this method requires that the read spans the fusion junction.



Akasaka T, Ueda C, Kurata M et al. (2000) Nonimmunoglobulin (non‐Ig)/BCL6 gene fusion in diffuse large B‐cell lymphoma results in worse prognosis than Ig/BCL6. Blood 96(8): 2907–2909.

de Alava E, Kawai A, Healey JH et al. (1998) EWS‐FLI1 fusion transcript structure is an independent determinant of prognosis in Ewing's sarcoma. Journal of Clinical Oncology 16(4): 1248–1255.

Beuzeboc P, Soulie M, Richaud P et al. (2009) Fusion genes and prostate cancer. From discovery to prognosis and therapeutic perspectives. Progrès en Urologie 19(11): 819–824.

Braun M, Stomper J, Boehm D et al. (2012) Improved method of detecting the ERG gene rearrangement in prostate cancer using combined dual‐colour chromogenic and silver in situ hybridization. Journal of Molecular Diagnostics (Ahead of print).

Campbell PJ, Stephens PJ, Pleasance ED et al. (2008) Identification of somatically acquired rearrangements in cancer using genome‐wide massively parallel paired‐end sequencing. Nature Genetics 40(6): 722–729.

Charest A, Lane K, McMahon K et al. (2003) Fusion of FIG to the receptor tyrosine kinase ROS in a glioblastoma with an interstitial del(6)(q21q21). Genes, Chromosomes and Cancer 37(1): 58–71.

Cimino G, Elia L, Mancini M et al. (2003) Clinico‐biologic features and treatment outcome of adult pro‐B‐ALL patients enrolled in the GIMEMA 0496 study: absence of the ALL1/AF4 and of the BCR/ABL fusion genes correlates with a significantly better clinical outcome. Blood 102(6): 2014–2020.

Dockhorn‐Dworniczak B, Schafer KL, Dantcheva R et al. (1994) Detection of EWS‐/FLI‐1 gene fusion transcripts by RT‐PCR as a tool in the diagnosis of tumors of the Ewing sarcoma group. Verhandlungen der Deutschen Gesellschaft für Pathologie 78: 214–219.

French CA, Miyoshi I, Aster JC et al. (2001) BRD4 bromodomain gene rearrangement in aggressive carcinoma with translocation t(15;19). American Journal of Pathology 159(6): 1987–1992.

French CA, Ramirez CL, Kolmakova J et al. (2008) BRD‐NUT oncoproteins: a family of closely related nuclear proteins that block epithelial differentiation and maintain the growth of carcinoma cells. Oncogene 27(15): 2237–2242.

Gnirke A, Melnikov A, Maguire J et al. (2009) Solution hybrid selection with ultra‐long oligonucleotides for massively parallel targeted sequencing. Nature Biotechnology 27(2): 182–189.

Gu TL, Deng X, Huang F et al. (2011) Survey of tyrosine kinase signaling reveals ROS kinase fusions in human cholangiocarcinoma. PLoS One 6(1): e15640.

Han B, Mehra R, Dhanasekaran SM et al. (2008) A fluorescence in situ hybridization screen for E26 transformation‐specific aberrations: identification of DDX5‐ETV4 fusion protein in prostate cancer. Cancer Research 68(18): 7629–7637.

Harbers M and Carninci P (2005) Tag‐based approaches for transcriptome research and genome annotation. Nature Methods 2(7): 495–502.

Helgeson BE, Tomlins SA, Shah N et al. (2008) Characterization of TMPRSS2:ETV5 and SLC45A3:ETV5 gene fusions in prostate cancer. Cancer Research 68(1): 73–80.

Kas K, Voz ML, Roijer E et al. (1997) Promoter swapping between the genes for a novel zinc finger protein and beta‐catenin in pleiomorphic adenomas with t(3;8)(p21;q12) translocations. Nature Genetics 15(2): 170–174.

Kersey JH, Wang D and Oberto M (1998) Resistance of t(4;11) (MLL‐AF4 fusion gene) leukemias to stress‐induced cell death: possible mechanism for extensive extramedullary accumulation of cells and poor prognosis. Leukemia 12(10): 1561–1564.

Kim H, Yoo SB, Choe JY et al. (2011) Detection of ALK gene rearrangement in non‐small cell lung cancer: A comparison of fluorescence in situ hybridization and chromogenic in situ hybridization with correlation of ALK protein expression. Journal of Thoracic Oncology 6(8): 1359–1366.

Kroll TG, Sarraf P, Pecciarini L et al. (2000) PAX8‐PPARgamma1 fusion oncogene in human thyroid carcinoma [corrected]. Science 289(5483): 1357–1360.

Lambros MB, Wilkerson PM, Natrajan R et al. (2011) High‐throughput detection of fusion genes in cancer using the Sequenom MassARRAY platform. Laboratory Investigation. doi:10.1038/labinvest.2011.110.

Levin JZ, Berger MF, Adiconis X et al. (2009) Targeted next‐generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts. Genome Biology 10(10): R115.

Liu ZL, Luo JM, Wang FX et al. (2003) Improved RT‐PCR for detection of PML/RARalpha fusion gene in rapid diagnosis of acute promyelocytic leukemia. Zhongguo Shi Yan Xue Ye Xue Za Zhi 11(6): 587–590.

Maher CA, Kumar‐Sinha C, Cao X et al. (2009a) Transcriptome sequencing to detect gene fusions in cancer. Nature 458(7234): 97–101.

Maher CA, Palanisamy N, Brenner JC et al. (2009b) Chimeric transcript discovery by paired‐end transcriptome sequencing. Proceedings of the National Academy of Sciences of the USA 106(30): 12353–12358.

Maloney K, McGavran L, Murphy J et al. (1999) TEL‐AML1 fusion identifies a subset of children with standard risk acute lymphoblastic leukemia who have an excellent prognosis when treated with therapy that includes a single delayed intensification. Leukemia 13(11): 1708–1712.

Martin‐Zanca D, Hughes SH and Barbacid M (1986) A human oncogene formed by the fusion of truncated tropomyosin and protein tyrosine kinase sequences. Nature 319(6056): 743–748.

Mertes F, Elsharawy A, Sauer S et al. (2011) Targeted enrichment of genomic DNA regions for next‐generation sequencing. Briefings in Functional Genomics 10(6): 374–386.

Mezzelani A, Mariani L, Tamborini E et al. (2001) SYT‐SSX fusion genes and prognosis in synovial sarcoma. British Journal of Cancer 85(10): 1535–1539.

Mitelman F, Johansson B and Mertens F (2004) Fusion genes and rearranged genes as a linear function of chromosome aberrations in cancer. Nature Genetics 36(4): 331–334.

Mitelman F, Johansson B and Mertens F (2007) The impact of translocations and gene fusions on cancer causation. Nature Reviews Cancer 7(4): 233–245.

Mitelman F, Mertens F and Johansson B (2005) Prevalence estimates of recurrent balanced cytogenetic aberrations and gene fusions in unselected patients with neoplastic disorders. Genes, Chromosomes and Cancer 43(4): 350–366.

Motoi T, Kumagai A, Tsuji K, Imamura T and Fukusato T (2010) Diagnostic utility of dual‐color break‐apart chromogenic in situ hybridization for the detection of rearranged SS18 in formalin‐fixed, paraffin‐embedded synovial sarcoma. Human Pathology 41(10): 1397–1404.

Nowell PC and Hungerford DA (1961) Chromosome studies in human leukemia. II. Chronic granulocytic leukemia. Journal of the National Cancer Institute 27: 1013–1035.

Okou DT, Steinberg KM, Middle C et al. (2007) Microarray‐based genomic selection for high‐throughput resequencing. Nature Methods 4(11): 907–909.

Penault‐Llorca F, Bilous M, Dowsett M et al. (2009) Emerging technologies for assessing HER2 amplification. American Journal of Clinical Pathology 132(4): 539–548.

Pierotti MA, Vigneri P and Bongarzone I (1998) Rearrangements of RET and NTRK1 tyrosine kinase receptors in papillary thyroid carcinomas. Recent Results in Cancer Research 154: 237–247.

Rhodes DR, Kalyana‐Sundaram S, Tomlins SA et al. (2007a) Molecular concepts analysis links tumors, pathways, mechanisms, and drugs. Neoplasia 9(5): 443–454.

Rhodes DR, Kalyana‐Sundaram S, Mahavisno V et al. (2007b) Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. Neoplasia 9(2): 166–180.

Rikova K, Guo A, Zeng Q et al. (2007) Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer. Cell 131(6): 1190–1203.

Rostad K, Hellwinkel OJ, Haukaas SA et al. (2009) TMPRSS2:ERG fusion transcripts in urine from prostate cancer patients correlate with a less favorable prognosis. Acta Pathologica, Microbiologica et Immunologica Scandinavica 117(8): 575–582.

Sakarya O, Breu H, Radovich M et al. (2012) RNA‐Seq mapping and detection of gene fusions with a suffix array algorithm. PloS Computational Biology 8(4): e1002464.

Sidhar SK, Clark J, Gill S et al. (1996) The t(X;1)(p11.2;q21.2) translocation in papillary renal cell carcinoma fuses a novel gene PRCC to the TFE3 transcription factor gene. Human Molecular Genetics 5(9): 1333–1338.

Soda M, Choi YL, Enomoto M et al. (2007) Identification of the transforming EML4‐ALK fusion gene in non‐small‐cell lung cancer. Nature 448(7153): 561–566.

Sun Y, Sun BC, Zhao XL et al. (2007) Roles of immunohistochemistry and detection of SYT‐SSX fusion gene in diagnosis of synovial sarcoma. Zhonghua Bing Li Xue Za Zhi 36(7): 480–484.

Tognon C, Knezevich SR, Huntsman D et al. (2002) Expression of the ETV6‐NTRK3 gene fusion as a primary event in human secretory breast carcinoma. Cancer Cell 2(5): 367–376.

Tomlins SA, Laxman B, Dhanasekaran SM et al. (2007) Distinct classes of chromosomal rearrangements create oncogenic ETS gene fusions in prostate cancer. Nature 448(7153): 595–599.

Tomlins SA, Mehra R, Rhodes DR et al. (2006) TMPRSS2:ETV4 gene fusions define a third molecular subtype of prostate cancer. Cancer Research 66(7): 3396–3400.

Tomlins SA, Rhodes DR, Perner S et al. (2005) Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 310(5748): 644–648.

Turner EH, Lee C, Ng SB, Nickerson DA and Shendure J (2009) Massively parallel exon capture and library‐free resequencing across 16 genomes. Nature Methods 6(5): 315–316.

Wang Z, Gerstein M and Snyder M (2009) RNA‐Seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics 10(1): 57–63.

Zuna J, Zaliova M, Muzikova K et al. (2010) Acute leukemias with ETV6/ABL1 (TEL/ABL) fusion: poor prognosis and prenatal origin. Genes Chromosomes and Cancer 49(10): 873–884.

Further Reading

Futreal PA, Coin L, Marshall M et al. (2004) A census of human cancer genes. Nature Reviews Cancer 4(3): 177–183.

Heppner GH and Miller BE (1983) Tumor heterogeneity: biological implications and therapeutic consequences. Cancer and Metastasis Reviews 2(1): 5–23.

Web Links

The Cancer Genome Atlas,

The Mitelman Database of Chromosome Aberrations in Cancer,

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Leow, Pay Chin, Ku, Chee‐Seng, Soo, Ross, and Soong, Richie(Sep 2012) Technological Advances in the Detection of Novel Fusion Genes. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0023916]