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Volumn 14, Issue 1, 2013, Pages

Exploration of the gene fusion landscape of glioblastoma using transcriptome sequencing and copy number data

Author keywords

EGFR fusions; FGFR3 TACC3; Gene fusion; Glioblastoma; Non coding gene fusions; NTRK1; PIK3C2B; RNA seq; ROS1

Indexed keywords

PROTEIN TYROSINE KINASE; TRANSCRIPTOME;

EID: 84887926034     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-818     Document Type: Article
Times cited : (76)

References (50)
  • 1
    • 0015694748 scopus 로고
    • Letter: a new consistent chromosomal abnormality in chronic myelogenous leukaemia identified by quinacrine fluorescence and giemsa staining
    • 10.1038/243290a0, 4126434
    • Rowley JD. Letter: a new consistent chromosomal abnormality in chronic myelogenous leukaemia identified by quinacrine fluorescence and giemsa staining. Nature 1973, 243:290-293. 10.1038/243290a0, 4126434.
    • (1973) Nature , vol.243 , pp. 290-293
    • Rowley, J.D.1
  • 2
    • 33947581390 scopus 로고    scopus 로고
    • The impact of translocations and gene fusions on cancer causation
    • 10.1038/nrc2091, 17361217
    • Mitelman F, Johansson B, Mertens F. The impact of translocations and gene fusions on cancer causation. Nat Rev Cancer 2007, 7:233-245. 10.1038/nrc2091, 17361217.
    • (2007) Nat Rev Cancer , vol.7 , pp. 233-245
    • Mitelman, F.1    Johansson, B.2    Mertens, F.3
  • 4
    • 33750378672 scopus 로고    scopus 로고
    • Evidence of recurrent gene fusions in common epithelial tumors
    • 10.1016/j.molmed.2006.09.005, 17011825
    • Kumar-Sinha C, Tomlins SA, Chinnaiyan AM. Evidence of recurrent gene fusions in common epithelial tumors. Trends Mol Med 2006, 12:529-536. 10.1016/j.molmed.2006.09.005, 17011825.
    • (2006) Trends Mol Med , vol.12 , pp. 529-536
    • Kumar-Sinha, C.1    Tomlins, S.A.2    Chinnaiyan, A.M.3
  • 7
    • 84870748688 scopus 로고    scopus 로고
    • RET fusions define a unique molecular and clinicopathologic subtype of non-small-cell lung cancer
    • 10.1200/JCO.2012.44.1477, 23150706
    • Wang R, Hu H, Pan Y, Li Y, Ye T, Li C, Luo X, Wang L, Li H, Zhang Y, et al. RET fusions define a unique molecular and clinicopathologic subtype of non-small-cell lung cancer. J Clin Oncol 2012, 30:4352-4359. 10.1200/JCO.2012.44.1477, 23150706.
    • (2012) J Clin Oncol , vol.30 , pp. 4352-4359
    • Wang, R.1    Hu, H.2    Pan, Y.3    Li, Y.4    Ye, T.5    Li, C.6    Luo, X.7    Wang, L.8    Li, H.9    Zhang, Y.10
  • 8
    • 45849103492 scopus 로고    scopus 로고
    • Recurrent gene fusions in prostate cancer
    • 10.1038/nrc2402, 2711688, 18563191
    • Kumar-Sinha C, Tomlins SA, Chinnaiyan AM. Recurrent gene fusions in prostate cancer. Nat Rev Cancer 2008, 8:497-511. 10.1038/nrc2402, 2711688, 18563191.
    • (2008) Nat Rev Cancer , vol.8 , pp. 497-511
    • Kumar-Sinha, C.1    Tomlins, S.A.2    Chinnaiyan, A.M.3
  • 11
    • 59149096465 scopus 로고    scopus 로고
    • Secretory breast carcinomas with ETV6-NTRK3 fusion gene belong to the basal-like carcinoma spectrum
    • 10.1038/modpathol.2008.184, 19011601
    • Lae M, Freneaux P, Sastre-Garau X, Chouchane O, Sigal-Zafrani B, Vincent-Salomon A. Secretory breast carcinomas with ETV6-NTRK3 fusion gene belong to the basal-like carcinoma spectrum. Mod Pathol 2009, 22:291-298. 10.1038/modpathol.2008.184, 19011601.
    • (2009) Mod Pathol , vol.22 , pp. 291-298
    • Lae, M.1    Freneaux, P.2    Sastre-Garau, X.3    Chouchane, O.4    Sigal-Zafrani, B.5    Vincent-Salomon, A.6
  • 12
    • 73249115584 scopus 로고    scopus 로고
    • Recurrent fusion of MYB and NFIB transcription factor genes in carcinomas of the breast and head and neck
    • 10.1073/pnas.0909114106, 2773970, 19841262
    • Persson M, Andren Y, Mark J, Horlings HM, Persson F, Stenman G. Recurrent fusion of MYB and NFIB transcription factor genes in carcinomas of the breast and head and neck. Proc Natl Acad Sci USA 2009, 106:18740-18744. 10.1073/pnas.0909114106, 2773970, 19841262.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 18740-18744
    • Persson, M.1    Andren, Y.2    Mark, J.3    Horlings, H.M.4    Persson, F.5    Stenman, G.6
  • 15
    • 84873045850 scopus 로고    scopus 로고
    • Oncogenic FGFR3 gene fusions in bladder cancer
    • 10.1093/hmg/dds486, 3554204, 23175443
    • Williams SV, Hurst CD, Knowles MA. Oncogenic FGFR3 gene fusions in bladder cancer. Hum Mol Genet 2013, 22:795-803. 10.1093/hmg/dds486, 3554204, 23175443.
    • (2013) Hum Mol Genet , vol.22 , pp. 795-803
    • Williams, S.V.1    Hurst, C.D.2    Knowles, M.A.3
  • 16
    • 85081457936 scopus 로고    scopus 로고
    • Crizotinib fact sheet
    • Crizotinib fact sheet. 2012, http://www.pfizer.com/files/news/esmo/xalkori_fact_sheet.pdf.
    • (2012)
  • 17
    • 56749100474 scopus 로고    scopus 로고
    • The 2007 WHO classification of tumors of the central nervous system - what has changed?
    • Rousseau A, Mokhtari K, Duyckaerts C. The 2007 WHO classification of tumors of the central nervous system - what has changed?. Curr Opin Neurol 2007, 2008(21):720-727.
    • (2007) Curr Opin Neurol , vol.2008 , Issue.21 , pp. 720-727
    • Rousseau, A.1    Mokhtari, K.2    Duyckaerts, C.3
  • 18
    • 77956269802 scopus 로고    scopus 로고
    • CBTRUS statistical report: primary brain and central nervous system tumors diagnosed in the United States in 2004-2008
    • CBTRUS statistical report: primary brain and central nervous system tumors diagnosed in the United States in 2004-2008. http://www.cbtrus.org.
  • 19
    • 0037402509 scopus 로고    scopus 로고
    • Fusion of FIG to the receptor tyrosine kinase ROS in a glioblastoma with an interstitial del(6)(q21q21)
    • 10.1002/gcc.10207, 12661006
    • Charest A, Lane K, McMahon K, Park J, Preisinger E, Conroy H, Housman D. Fusion of FIG to the receptor tyrosine kinase ROS in a glioblastoma with an interstitial del(6)(q21q21). Genes Chromosomes Cancer 2003, 37:58-71. 10.1002/gcc.10207, 12661006.
    • (2003) Genes Chromosomes Cancer , vol.37 , pp. 58-71
    • Charest, A.1    Lane, K.2    McMahon, K.3    Park, J.4    Preisinger, E.5    Conroy, H.6    Housman, D.7
  • 25
    • 80051507403 scopus 로고    scopus 로고
    • TopHat-Fusion: an algorithm for discovery of novel fusion transcripts
    • 10.1186/gb-2011-12-8-r72, 3245612, 21835007
    • Kim D, Salzberg SL. TopHat-Fusion: an algorithm for discovery of novel fusion transcripts. Genome Biol 2011, 12:R72. 10.1186/gb-2011-12-8-r72, 3245612, 21835007.
    • (2011) Genome Biol , vol.12
    • Kim, D.1    Salzberg, S.L.2
  • 26
    • 84870815979 scopus 로고    scopus 로고
    • Discovering chimeric transcripts in paired-end RNA-seq data by using EricScript
    • 10.1093/bioinformatics/bts617, 23093608
    • 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, 28:3232-3239. 10.1093/bioinformatics/bts617, 23093608.
    • (2012) Bioinformatics , vol.28 , pp. 3232-3239
    • Benelli, M.1    Pescucci, C.2    Marseglia, G.3    Severgnini, M.4    Torricelli, F.5    Magi, A.6
  • 28
    • 84863009996 scopus 로고    scopus 로고
    • FusionFinder: a software tool to identify expressed gene fusion candidates from RNA-Seq data
    • 10.1371/journal.pone.0039987, 3384600, 22761941
    • Francis RW, Thompson-Wicking K, Carter KW, Anderson D, Kees UR, Beesley AH. FusionFinder: a software tool to identify expressed gene fusion candidates from RNA-Seq data. PLoS One 2012, 7:e39987. 10.1371/journal.pone.0039987, 3384600, 22761941.
    • (2012) PLoS One , vol.7
    • Francis, R.W.1    Thompson-Wicking, K.2    Carter, K.W.3    Anderson, D.4    Kees, U.R.5    Beesley, A.H.6
  • 29
    • 80055071248 scopus 로고    scopus 로고
    • A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines
    • 10.1093/nar/gkr362, 3159479, 21622959
    • Asmann YW, Hossain A, Necela BM, Middha S, Kalari KR, Sun Z, Chai HS, Williamson DW, Radisky D, Schroth GP, 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. 10.1093/nar/gkr362, 3159479, 21622959.
    • (2011) Nucleic Acids Res , vol.39
    • Asmann, Y.W.1    Hossain, A.2    Necela, B.M.3    Middha, S.4    Kalari, K.R.5    Sun, Z.6    Chai, H.S.7    Williamson, D.W.8    Radisky, D.9    Schroth, G.P.10
  • 30
    • 85081454509 scopus 로고    scopus 로고
    • SOLiD™ BioScope™ Software
    • SOLiD™ BioScope™ Software. https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catNavigate2&catID=606802&tab=Overview.
  • 32
    • 0036226603 scopus 로고    scopus 로고
    • BLAT-the BLAST-like alignment tool
    • 187518, 11932250
    • Kent WJ. BLAT-the BLAST-like alignment tool. Genome Res 2002, 12:656-664. 187518, 11932250.
    • (2002) Genome Res , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 33
    • 85081455339 scopus 로고    scopus 로고
    • Cancer Genome Hub - UC Santa Cruz
    • Cancer Genome Hub - UC Santa Cruz. https://cghub.ucsc.edu/.
  • 34
    • 84865214708 scopus 로고    scopus 로고
    • Gene fusions associated with recurrent amplicons represent a class of passenger aberrations in breast cancer
    • 3431177, 22952423
    • Kalyana-Sundaram S, Shankar S, Deroo S, Iyer MK, Palanisamy N, Chinnaiyan AM, Kumar-Sinha C. Gene fusions associated with recurrent amplicons represent a class of passenger aberrations in breast cancer. Neoplasia 2012, 14:702-708. 3431177, 22952423.
    • (2012) Neoplasia , vol.14 , pp. 702-708
    • Kalyana-Sundaram, S.1    Shankar, S.2    Deroo, S.3    Iyer, M.K.4    Palanisamy, N.5    Chinnaiyan, A.M.6    Kumar-Sinha, C.7
  • 35
    • 73649123907 scopus 로고    scopus 로고
    • Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1
    • 10.1016/j.ccr.2009.12.020, 2818769, 20129251
    • Verhaak RG, Hoadley KA, Purdom E, Wang V, Qi Y, Wilkerson MD, Miller CR, Ding L, Golub T, Mesirov JP, et al. Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell 2010, 17:98-110. 10.1016/j.ccr.2009.12.020, 2818769, 20129251.
    • (2010) Cancer Cell , vol.17 , pp. 98-110
    • Verhaak, R.G.1    Hoadley, K.A.2    Purdom, E.3    Wang, V.4    Qi, Y.5    Wilkerson, M.D.6    Miller, C.R.7    Ding, L.8    Golub, T.9    Mesirov, J.P.10
  • 36
    • 84864819611 scopus 로고    scopus 로고
    • The cancer genome atlas - data portal
    • The cancer genome atlas - data portal. https://tcga-data.nci.nih.gov/tcga/.
  • 37
    • 84877113990 scopus 로고    scopus 로고
    • Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms
    • 10.1101/gr.143677.112, 3638133, 23410887
    • Malhotra A, Lindberg M, Faust GG, Leibowitz ML, Clark RA, Layer RM, Quinlan AR, Hall IM. Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms. Genome Res 2013, 23:762-776. 10.1101/gr.143677.112, 3638133, 23410887.
    • (2013) Genome Res , vol.23 , pp. 762-776
    • Malhotra, A.1    Lindberg, M.2    Faust, G.G.3    Leibowitz, M.L.4    Clark, R.A.5    Layer, R.M.6    Quinlan, A.R.7    Hall, I.M.8
  • 40
    • 77950939830 scopus 로고    scopus 로고
    • Rearrangements of NTRK1 gene in papillary thyroid carcinoma
    • 10.1016/j.mce.2009.10.009, 19883730
    • Greco A, Miranda C, Pierotti MA. Rearrangements of NTRK1 gene in papillary thyroid carcinoma. Mol Cell Endocrinol 2010, 321:44-49. 10.1016/j.mce.2009.10.009, 19883730.
    • (2010) Mol Cell Endocrinol , vol.321 , pp. 44-49
    • Greco, A.1    Miranda, C.2    Pierotti, M.A.3
  • 41
    • 84876882782 scopus 로고    scopus 로고
    • Breakpoint analysis of transcriptional and genomic profiles uncovers novel gene fusions spanning multiple human cancer types
    • 10.1371/journal.pgen.1003464, 3636093, 23637631
    • Giacomini CP, Sun S, Varma S, Shain AH, Giacomini MM, Balagtas J, Sweeney RT, Lai E, Del Vecchio CA, Forster AD, et al. Breakpoint analysis of transcriptional and genomic profiles uncovers novel gene fusions spanning multiple human cancer types. PLoS Genet 2013, 9:e1003464. 10.1371/journal.pgen.1003464, 3636093, 23637631.
    • (2013) PLoS Genet , vol.9
    • Giacomini, C.P.1    Sun, S.2    Varma, S.3    Shain, A.H.4    Giacomini, M.M.5    Balagtas, J.6    Sweeney, R.T.7    Lai, E.8    Del Vecchio, C.A.9    Forster, A.D.10
  • 43
    • 84255170397 scopus 로고    scopus 로고
    • Glioblastoma-derived epidermal growth factor receptor carboxyl-terminal deletion mutants are transforming and are sensitive to EGFR-directed therapies
    • 10.1158/0008-5472.CAN-11-0821, 3242822, 22001862
    • Cho J, Pastorino S, Zeng Q, Xu X, Johnson W, Vandenberg S, Verhaak R, Cherniack AD, Watanabe H, Dutt A, et al. Glioblastoma-derived epidermal growth factor receptor carboxyl-terminal deletion mutants are transforming and are sensitive to EGFR-directed therapies. Cancer Res 2011, 71:7587-7596. 10.1158/0008-5472.CAN-11-0821, 3242822, 22001862.
    • (2011) Cancer Res , vol.71 , pp. 7587-7596
    • Cho, J.1    Pastorino, S.2    Zeng, Q.3    Xu, X.4    Johnson, W.5    Vandenberg, S.6    Verhaak, R.7    Cherniack, A.D.8    Watanabe, H.9    Dutt, A.10
  • 45
    • 84878376400 scopus 로고    scopus 로고
    • Long non-coding RNA: a new player in cancer
    • 10.1186/1756-8722-6-37, 3693878, 23725405
    • Zhang H, Chen Z, Wang X, Huang Z, He Z, Chen Y. Long non-coding RNA: a new player in cancer. J Hematol Oncol 2013, 6:37. 10.1186/1756-8722-6-37, 3693878, 23725405.
    • (2013) J Hematol Oncol , vol.6 , pp. 37
    • Zhang, H.1    Chen, Z.2    Wang, X.3    Huang, Z.4    He, Z.5    Chen, Y.6
  • 46
    • 84879764400 scopus 로고    scopus 로고
    • A survey of intragenic breakpoints in glioblastoma identifies a distinct subset associated with poor survival
    • 10.1101/gad.213686.113, 3713427, 23796897
    • Zheng S, Fu J, Vegesna R, Mao Y, Heathcock LE, Torres-Garcia W, Ezhilarasan R, Wang S, McKenna A, Chin L, et al. A survey of intragenic breakpoints in glioblastoma identifies a distinct subset associated with poor survival. Genes Dev 2013, 27:1462-1472. 10.1101/gad.213686.113, 3713427, 23796897.
    • (2013) Genes Dev , vol.27 , pp. 1462-1472
    • Zheng, S.1    Fu, J.2    Vegesna, R.3    Mao, Y.4    Heathcock, L.E.5    Torres-Garcia, W.6    Ezhilarasan, R.7    Wang, S.8    McKenna, A.9    Chin, L.10
  • 47
    • 77955090106 scopus 로고    scopus 로고
    • Subtype-specific genomic alterations define new targets for soft-tissue sarcoma therapy
    • Epub 2010 Jul 4 2010, 10.1038/ng.619, 2911503, 20601955
    • Barretina J, Taylor BS, Banerji S, Ramos AH, Lagos-Quintana M, Decarolis PL, Shah K, Socci ND, Weir BA, Ho A, et al. Subtype-specific genomic alterations define new targets for soft-tissue sarcoma therapy. Nat Genet 2010, 42(8):715-721. Epub 2010 Jul 4 2010, 10.1038/ng.619, 2911503, 20601955.
    • (2010) Nat Genet , vol.42 , Issue.8 , pp. 715-721
    • Barretina, J.1    Taylor, B.S.2    Banerji, S.3    Ramos, A.H.4    Lagos-Quintana, M.5    Decarolis, P.L.6    Shah, K.7    Socci, N.D.8    Weir, B.A.9    Ho, A.10
  • 49
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: a flexible suite of utilities for comparing genomic features
    • 10.1093/bioinformatics/btq033, 2832824, 20110278
    • Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 2010, 26:841-842. 10.1093/bioinformatics/btq033, 2832824, 20110278.
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 50
    • 73949106832 scopus 로고    scopus 로고
    • TFG, a target of chromosome translocations in lymphoma and soft tissue tumors, fuses to GPR128 in healthy individuals
    • 10.3324/haematol.2009.011536, 2805730, 19797732
    • Chase A, Ernst T, Fiebig A, Collins A, Grand F, Erben P, Reiter A, Schreiber S, Cross NC. TFG, a target of chromosome translocations in lymphoma and soft tissue tumors, fuses to GPR128 in healthy individuals. Haematologica 2010, 95:20-26. 10.3324/haematol.2009.011536, 2805730, 19797732.
    • (2010) Haematologica , vol.95 , pp. 20-26
    • Chase, A.1    Ernst, T.2    Fiebig, A.3    Collins, A.4    Grand, F.5    Erben, P.6    Reiter, A.7    Schreiber, S.8    Cross, N.C.9


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