메뉴 건너뛰기




Volumn 7, Issue 10, 2012, Pages

Reanalysis of RNA-Sequencing Data Reveals Several Additional Fusion Genes with Multiple Isoforms

Author keywords

[No Author keywords available]

Indexed keywords

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ACSF2 GENE; AHCTF1 GENE; ARTICLE; BCAS3 GENE; BIOINFORMATICS; BREAST CANCER; CARM1 GENE; CONTROLLED STUDY; FUSION GENE; GCN1L1 GENE; GENE ACTIVITY; GENE AMPLIFICATION; GENE DOSAGE; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE FUSION; GENE REARRANGEMENT; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; HUMAN; HUMAN CELL; MED1 GENE; MED13 GENE; MRPL45 GENE; MSI1 GENE; NAAA GENE; NUCLEOTIDE SEQUENCE; PIP4K2B GENE; RAD51C GENE; RAE1 GENE; RNA SEQUENCE; SEQUENCE ANALYSIS; SMARCA4 GENE; STX16 GENE; STXBP4 GENE; SYNRG GENE; THRA GENE; TMEM49 GENE; TOB1 GENE; TRPC4AP GENE; USP32 GENE;

EID: 84868295073     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0048745     Document Type: Article
Times cited : (66)

References (41)
  • 1
    • 0015694748 scopus 로고
    • Letter: A new consistent chromosomal abnormality in chronic myelogenous leukaemia identified by quinacrine fluorescence and Giemsa staining
    • Rowley JD, (1973) Letter: A new consistent chromosomal abnormality in chronic myelogenous leukaemia identified by quinacrine fluorescence and Giemsa staining. Nature 243: 290-293.
    • (1973) Nature , vol.243 , pp. 290-293
    • Rowley, J.D.1
  • 2
    • 0020333906 scopus 로고
    • A cellular oncogene is translocated to the Philadelphia chromosome in chronic myelocytic leukaemia
    • de Klein A, van Kessel AG, Grosveld G, Bartram CR, Hagemeijer A, et al. (1982) A cellular oncogene is translocated to the Philadelphia chromosome in chronic myelocytic leukaemia. Nature 300: 765-767.
    • (1982) Nature , vol.300 , pp. 765-767
    • de Klein, A.1    van Kessel, A.G.2    Grosveld, G.3    Bartram, C.R.4    Hagemeijer, A.5
  • 4
    • 33947581390 scopus 로고    scopus 로고
    • The impact of translocations and gene fusions on cancer causation
    • Mitelman F, Johansson B, Mertens F, (2007) The impact of translocations and gene fusions on cancer causation. Nat Rev Cancer 7: 233-245.
    • (2007) Nat Rev Cancer , vol.7 , pp. 233-245
    • Mitelman, F.1    Johansson, B.2    Mertens, F.3
  • 5
    • 34547638047 scopus 로고    scopus 로고
    • Identification of the transforming EML4-ALK fusion gene in non-small-cell lung cancer
    • Soda M, Choi YL, Enomoto M, Takada S, Yamashita Y, et al. (2007) Identification of the transforming EML4-ALK fusion gene in non-small-cell lung cancer. Nature 448: 561-566.
    • (2007) Nature , vol.448 , pp. 561-566
    • Soda, M.1    Choi, Y.L.2    Enomoto, M.3    Takada, S.4    Yamashita, Y.5
  • 6
    • 34547642493 scopus 로고    scopus 로고
    • Distinct classes of chromosomal rearrangements create oncogenic ETS gene fusions in prostate cancer
    • Tomlins SA, Laxman B, Dhanasekaran SM, Helgeson BE, Cao X, et al. (2007) Distinct classes of chromosomal rearrangements create oncogenic ETS gene fusions in prostate cancer. Nature 448: 595-599.
    • (2007) Nature , vol.448 , pp. 595-599
    • Tomlins, S.A.1    Laxman, B.2    Dhanasekaran, S.M.3    Helgeson, B.E.4    Cao, X.5
  • 7
    • 27344451557 scopus 로고    scopus 로고
    • Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer
    • Tomlins SA, Rhodes DR, Perner S, Dhanasekaran SM, Mehra R, et al. (2005) Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 310: 644-648.
    • (2005) Science , vol.310 , pp. 644-648
    • Tomlins, S.A.1    Rhodes, D.R.2    Perner, S.3    Dhanasekaran, S.M.4    Mehra, R.5
  • 8
    • 19044391610 scopus 로고    scopus 로고
    • Expression of the ETV6-NTRK3 gene fusion as a primary event in human secretory breast carcinoma
    • Tognon C, Knezevich SR, Huntsman D, Roskelley CD, Melnyk N, et al. (2002) Expression of the ETV6-NTRK3 gene fusion as a primary event in human secretory breast carcinoma. Cancer Cell 2: 367-376.
    • (2002) Cancer Cell , vol.2 , pp. 367-376
    • Tognon, C.1    Knezevich, S.R.2    Huntsman, D.3    Roskelley, C.D.4    Melnyk, N.5
  • 9
    • 73249115584 scopus 로고    scopus 로고
    • Recurrent fusion of MYB and NFIB transcription factor genes in carcinomas of the breast and head and neck
    • Persson M, Andren Y, Mark J, Horlings HM, Persson F, et al. (2009) Recurrent fusion of MYB and NFIB transcription factor genes in carcinomas of the breast and head and neck. Proc Natl Acad Sci U S A 106: 18740-18744.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 18740-18744
    • Persson, M.1    Andren, Y.2    Mark, J.3    Horlings, H.M.4    Persson, F.5
  • 10
    • 84856091317 scopus 로고    scopus 로고
    • Functionally recurrent rearrangements of the MAST kinase and Notch gene families in breast cancer
    • Robinson DR, Kalyana-Sundaram S, Wu YM, Shankar S, Cao X, et al. (2011) Functionally recurrent rearrangements of the MAST kinase and Notch gene families in breast cancer. Nat Med.
    • (2011) Nat Med.
    • Robinson, D.R.1    Kalyana-Sundaram, S.2    Wu, Y.M.3    Shankar, S.4    Cao, X.5
  • 11
    • 72849144434 scopus 로고    scopus 로고
    • Sequencing technologies - the next generation
    • Metzker ML, (2010) Sequencing technologies- the next generation. Nat Rev Genet 11: 31-46.
    • (2010) Nat Rev Genet , vol.11 , pp. 31-46
    • Metzker, M.L.1
  • 14
    • 60549092281 scopus 로고    scopus 로고
    • Transcriptome-guided characterization of genomic rearrangements in a breast cancer cell line
    • Zhao Q, Caballero OL, Levy S, Stevenson BJ, Iseli C, et al. (2009) Transcriptome-guided characterization of genomic rearrangements in a breast cancer cell line. Proc Natl Acad Sci U S A 106: 1886-1891.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 1886-1891
    • Zhao, Q.1    Caballero, O.L.2    Levy, S.3    Stevenson, B.J.4    Iseli, C.5
  • 15
    • 65549155761 scopus 로고    scopus 로고
    • A transcriptional sketch of a primary human breast cancer by 454 deep sequencing
    • Guffanti A, Iacono M, Pelucchi P, Kim N, Solda G, et al. (2009) A transcriptional sketch of a primary human breast cancer by 454 deep sequencing. BMC Genomics 10: 163.
    • (2009) BMC Genomics , vol.10 , pp. 163
    • Guffanti, A.1    Iacono, M.2    Pelucchi, P.3    Kim, N.4    Solda, G.5
  • 16
    • 79955560249 scopus 로고    scopus 로고
    • Transcriptional consequences of genomic structural aberrations in breast cancer
    • Inaki K, Hillmer AM, Ukil L, Yao F, Woo XY, et al. (2011) Transcriptional consequences of genomic structural aberrations in breast cancer. Genome Res 21: 676-687.
    • (2011) Genome Res , vol.21 , pp. 676-687
    • Inaki, K.1    Hillmer, A.M.2    Ukil, L.3    Yao, F.4    Woo, X.Y.5
  • 17
    • 80055071248 scopus 로고    scopus 로고
    • A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines
    • Asmann YW, Hossain A, Necela BM, Middha S, Kalari KR, et al. (2011) A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines. Nucleic Acids Res 39: e100.
    • (2011) Nucleic Acids Res , vol.39
    • Asmann, Y.W.1    Hossain, A.2    Necela, B.M.3    Middha, S.4    Kalari, K.R.5
  • 18
    • 80051507403 scopus 로고    scopus 로고
    • TopHat-Fusion: an algorithm for discovery of novel fusion transcripts
    • Kim D, Salzberg SL, (2011) TopHat-Fusion: an algorithm for discovery of novel fusion transcripts. Genome Biol 12: R72.
    • (2011) Genome Biol , vol.12
    • Kim, D.1    Salzberg, S.L.2
  • 20
    • 0028266213 scopus 로고
    • Mutation analysis of the THRA1 gene in breast cancer: deletion/fusion of the gene to a novel sequence on 17q in the BT474 cell line
    • Futreal PA, Cochran C, Marks JR, Iglehart JD, Zimmerman W, et al. (1994) Mutation analysis of the THRA1 gene in breast cancer: deletion/fusion of the gene to a novel sequence on 17q in the BT474 cell line. Cancer Res 54: 1791-1794.
    • (1994) Cancer Res , vol.54 , pp. 1791-1794
    • Futreal, P.A.1    Cochran, C.2    Marks, J.R.3    Iglehart, J.D.4    Zimmerman, W.5
  • 21
    • 51149114001 scopus 로고    scopus 로고
    • A neoplastic gene fusion mimics trans-splicing of RNAs in normal human cells
    • Li H, Wang J, Mor G, Sklar J, (2008) A neoplastic gene fusion mimics trans-splicing of RNAs in normal human cells. Science 321: 1357-1361.
    • (2008) Science , vol.321 , pp. 1357-1361
    • Li, H.1    Wang, J.2    Mor, G.3    Sklar, J.4
  • 22
    • 72949119310 scopus 로고    scopus 로고
    • Complex landscapes of somatic rearrangement in human breast cancer genomes
    • Stephens PJ, McBride DJ, Lin ML, Varela I, Pleasance ED, et al. (2009) Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature 462: 1005-1010.
    • (2009) Nature , vol.462 , pp. 1005-1010
    • Stephens, P.J.1    McBride, D.J.2    Lin, M.L.3    Varela, I.4    Pleasance, E.D.5
  • 23
    • 44349191457 scopus 로고    scopus 로고
    • Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing
    • Campbell PJ, Stephens PJ, Pleasance ED, O'Meara S, Li H, et al. (2008) Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet 40: 722-729.
    • (2008) Nat Genet , vol.40 , pp. 722-729
    • Campbell, P.J.1    Stephens, P.J.2    Pleasance, E.D.3    O'Meara, S.4    Li, H.5
  • 24
    • 77954526989 scopus 로고    scopus 로고
    • Rearrangements of the RAF kinase pathway in prostate cancer, gastric cancer and melanoma
    • Palanisamy N, Ateeq B, Kalyana-Sundaram S, Pflueger D, Ramnarayanan K, et al. (2010) Rearrangements of the RAF kinase pathway in prostate cancer, gastric cancer and melanoma. Nat Med 16: 793-798.
    • (2010) Nat Med , vol.16 , pp. 793-798
    • Palanisamy, N.1    Ateeq, B.2    Kalyana-Sundaram, S.3    Pflueger, D.4    Ramnarayanan, K.5
  • 26
    • 70449375354 scopus 로고    scopus 로고
    • An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer
    • Wang XS, Prensner JR, Chen G, Cao Q, Han B, et al. (2009) An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer. Nat Biotechnol 27: 1005-1011.
    • (2009) Nat Biotechnol , vol.27 , pp. 1005-1011
    • Wang, X.S.1    Prensner, J.R.2    Chen, G.3    Cao, Q.4    Han, B.5
  • 27
    • 70349969478 scopus 로고    scopus 로고
    • Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution
    • Shah SP, Morin RD, Khattra J, Prentice L, Pugh T, et al. (2009) Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature 461: 809-813.
    • (2009) Nature , vol.461 , pp. 809-813
    • Shah, S.P.1    Morin, R.D.2    Khattra, J.3    Prentice, L.4    Pugh, T.5
  • 28
    • 77958040520 scopus 로고    scopus 로고
    • FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data
    • Sboner A, Habegger L, Pflueger D, Terry S, Chen DZ, et al. (2010) FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data. Genome Biol 11: R104.
    • (2010) Genome Biol , vol.11
    • Sboner, A.1    Habegger, L.2    Pflueger, D.3    Terry, S.4    Chen, D.Z.5
  • 30
    • 33751260934 scopus 로고    scopus 로고
    • TMPRSS2 fusions with oncogenic ETS factors in prostate cancer involve unbalanced genomic rearrangements and are associated with HDAC1 and epigenetic reprogramming
    • Iljin K, Wolf M, Edgren H, Gupta S, Kilpinen S, et al. (2006) TMPRSS2 fusions with oncogenic ETS factors in prostate cancer involve unbalanced genomic rearrangements and are associated with HDAC1 and epigenetic reprogramming. Cancer Res 66: 10242-10246.
    • (2006) Cancer Res , vol.66 , pp. 10242-10246
    • Iljin, K.1    Wolf, M.2    Edgren, H.3    Gupta, S.4    Kilpinen, S.5
  • 31
    • 65249144557 scopus 로고    scopus 로고
    • Commonality but diversity in cancer gene fusions
    • Rabbitts TH, (2009) Commonality but diversity in cancer gene fusions. Cell 137: 391-395.
    • (2009) Cell , vol.137 , pp. 391-395
    • Rabbitts, T.H.1
  • 32
    • 0034596364 scopus 로고    scopus 로고
    • Detecting activation of ribosomal protein S6 kinase by complementary DNA and tissue microarray analysis
    • Barlund M, Forozan F, Kononen J, Bubendorf L, Chen Y, et al. (2000) Detecting activation of ribosomal protein S6 kinase by complementary DNA and tissue microarray analysis. J Natl Cancer Inst 92: 1252-1259.
    • (2000) J Natl Cancer Inst , vol.92 , pp. 1252-1259
    • Barlund, M.1    Forozan, F.2    Kononen, J.3    Bubendorf, L.4    Chen, Y.5
  • 33
    • 80054698731 scopus 로고    scopus 로고
    • Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer
    • Kloosterman WP, Hoogstraat M, Paling O, Tavakoli-Yaraki M, Renkens I, et al. (2011) Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer. Genome Biol 12: R103.
    • (2011) Genome Biol , vol.12
    • Kloosterman, W.P.1    Hoogstraat, M.2    Paling, O.3    Tavakoli-Yaraki, M.4    Renkens, I.5
  • 35
    • 78651476339 scopus 로고    scopus 로고
    • Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing
    • Pflueger D, Terry S, Sboner A, Habegger L, Esgueva R, et al. (2011) Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing. Genome Res 21: 56-67.
    • (2011) Genome Res , vol.21 , pp. 56-67
    • Pflueger, D.1    Terry, S.2    Sboner, A.3    Habegger, L.4    Esgueva, R.5
  • 36
    • 64549133889 scopus 로고    scopus 로고
    • Resistance to paclitaxel therapy is related with Bcl-2 expression through an estrogen receptor mediated pathway in breast cancer
    • Tabuchi Y, Matsuoka J, Gunduz M, Imada T, Ono R, et al. (2009) Resistance to paclitaxel therapy is related with Bcl-2 expression through an estrogen receptor mediated pathway in breast cancer. Int J Oncol 34: 313-319.
    • (2009) Int J Oncol , vol.34 , pp. 313-319
    • Tabuchi, Y.1    Matsuoka, J.2    Gunduz, M.3    Imada, T.4    Ono, R.5
  • 37
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead B, Trapnell C, Pop M, Salzberg SL, (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25.
    • (2009) Genome Biol , vol.10
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 38
    • 84864742748 scopus 로고    scopus 로고
    • SMART 7: recent updates to the protein domain annotation resource
    • Letunic I, Doerks T, Bork P (2011) SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Res.
    • (2011) Nucleic Acids Res.
    • Letunic, I.1    Doerks, T.2    Bork, P.3
  • 39
    • 0032568655 scopus 로고    scopus 로고
    • SMART, a simple modular architecture research tool: identification of signaling domains
    • Schultz J, Milpetz F, Bork P, Ponting CP, (1998) SMART, a simple modular architecture research tool: identification of signaling domains. Proc Natl Acad Sci U S A 95: 5857-5864.
    • (1998) Proc Natl Acad Sci U S A , vol.95 , pp. 5857-5864
    • Schultz, J.1    Milpetz, F.2    Bork, P.3    Ponting, C.P.4
  • 41
    • 0036226603 scopus 로고    scopus 로고
    • BLAT-the BLAST-like alignment tool
    • Kent WJ, (2002) BLAT-the BLAST-like alignment tool. Genome Res 12: 656-664.
    • (2002) Genome Res , vol.12 , pp. 656-664
    • Kent, W.J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.