메뉴 건너뛰기




Volumn 11, Issue 12, 2016, Pages

InFusion: Advancing discovery of fusion genes and chimeric transcripts from deep RNA-sequencing data

Author keywords

[No Author keywords available]

Indexed keywords

DIAGNOSTIC TEST ACCURACY STUDY; DNA STRAND; DNA TRANSCRIPTION; GENE FUSION; HUMAN; HUMAN CELL; IN VITRO STUDY; INFUSION; PROSTATE CANCER CELL LINE; RNA SEQUENCE; SENSITIVITY AND SPECIFICITY; ALGORITHM; BIOLOGY; GENETICS; HIGH THROUGHPUT SEQUENCING; ISOLATION AND PURIFICATION; NEOPLASM; PROCEDURES; SEQUENCE ANALYSIS; SOFTWARE;

EID: 85000702198     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0167417     Document Type: Article
Times cited : (42)

References (52)
  • 1
    • 0025348013 scopus 로고
    • Tyrosine kinase activity and transformation potency of bcr-abl oncogene products
    • Epub 1990/03/02. PMID: 2408149
    • Lugo TG, Pendergast AM, Muller AJ, Witte ON. Tyrosine kinase activity and transformation potency of bcr-abl oncogene products. Science. 1990; 247(4946):1079-82. Epub 1990/03/02. PMID: 2408149
    • (1990) Science. , vol.247 , Issue.4946 , pp. 1079-1082
    • Lugo, T.G.1    Pendergast, A.M.2    Muller, A.J.3    Witte, O.N.4
  • 2
    • 33947581390 scopus 로고    scopus 로고
    • The impact of translocations and gene fusions on cancer causation
    • Epub 2007/03/16. PMID: 17361217
    • Mitelman F, Johansson B, Mertens F. The impact of translocations and gene fusions on cancer causation. Nat Rev Cancer. 2007; 7(4):233-45. Epub 2007/03/16. doi: 10.1038/nrc2091 PMID: 17361217
    • (2007) Nat Rev Cancer. , vol.7 , Issue.4 , pp. 233-245
    • Mitelman, F.1    Johansson, B.2    Mertens, F.3
  • 3
    • 27344451557 scopus 로고    scopus 로고
    • Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer
    • Epub 2005/10/29. PMID: 16254181
    • Tomlins SA, Rhodes DR, Perner S, Dhanasekaran SM, Mehra R, Sun XW, et al. Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science. 2005; 310(5748):644-8. Epub 2005/10/29. doi: 10.1126/science.1117679 PMID: 16254181
    • (2005) Science. , vol.310 , Issue.5748 , pp. 644-648
    • Tomlins, S.A.1    Rhodes, D.R.2    Perner, S.3    Dhanasekaran, S.M.4    Mehra, R.5    Sun, X.W.6
  • 4
    • 0035289271 scopus 로고    scopus 로고
    • Congenitalinfantile fibrosarcoma. A clinicopathologic study of 10 cases and molecular detection of the ETV6-NTRK3 fusion transcripts using paraffin-embedded tissues
    • Epub 2001/03/13. PMID: 11242790
    • Sheng WQ, Hisaoka M, Okamoto S, Tanaka A, Meis-Kindblom JM, Kindblom LG, et al. Congenitalinfantile fibrosarcoma. A clinicopathologic study of 10 cases and molecular detection of the ETV6-NTRK3 fusion transcripts using paraffin-embedded tissues. Am J Clin Pathol. 2001; 115(3):348-55. Epub 2001/03/13. doi: 10.1309/3H24-E7T7-V37G-AKKQ PMID: 11242790
    • (2001) Am J Clin Pathol. , vol.115 , Issue.3 , pp. 348-355
    • Sheng, W.Q.1    Hisaoka, M.2    Okamoto, S.3    Tanaka, A.4    Meis-Kindblom, J.M.5    Kindblom, L.G.6
  • 5
    • 0031738824 scopus 로고    scopus 로고
    • Congenital mesoblastic nephroma t(12;15) is associated with ETV6-NTRK3 gene fusion: Cytogenetic and molecular relationship to congenital (infantile) fibrosarcoma
    • Epub 1998/11/12. PMID: 9811336
    • Rubin BP, Chen CJ, Morgan TW, Xiao S, Grier HE, Kozakewich HP, et al. Congenital mesoblastic nephroma t(12;15) is associated with ETV6-NTRK3 gene fusion: cytogenetic and molecular relationship to congenital (infantile) fibrosarcoma. Am J Pathol. 1998; 153(5):1451-8. Epub 1998/11/12. doi: 10. 1016/S0002-9440(10)65732-X PMID: 9811336
    • (1998) Am J Pathol. , vol.153 , Issue.5 , pp. 1451-1458
    • Rubin, B.P.1    Chen, C.J.2    Morgan, T.W.3    Xiao, S.4    Grier, H.E.5    Kozakewich, H.P.6
  • 6
    • 19044391610 scopus 로고    scopus 로고
    • Expression of the ETV6-NTRK3 gene fusion as a primary event in human secretory breast carcinoma
    • Epub 2002/11/27. PMID: 12450792
    • Tognon C, Knezevich SR, Huntsman D, Roskelley CD, Melnyk N, Mathers JA, et al. Expression of the ETV6-NTRK3 gene fusion as a primary event in human secretory breast carcinoma. Cancer Cell. 2002; 2(5):367-76. Epub 2002/11/27. PMID: 12450792
    • (2002) Cancer Cell. , vol.2 , Issue.5 , pp. 367-376
    • Tognon, C.1    Knezevich, S.R.2    Huntsman, D.3    Roskelley, C.D.4    Melnyk, N.5    Mathers, J.A.6
  • 7
    • 30044445670 scopus 로고    scopus 로고
    • Tandem chimerism as a means to increase protein complexity in the human genome
    • Epub 2005/12/14. PMID: 16344564
    • Parra G, Reymond A, Dabbouseh N, Dermitzakis ET, Castelo R, Thomson TM, et al. Tandem chimerism as a means to increase protein complexity in the human genome. Genome Res. 2006; 16(1):37-44. Epub 2005/12/14. doi: 10.1101/gr.4145906 PMID: 16344564
    • (2006) Genome Res. , vol.16 , Issue.1 , pp. 37-44
    • Parra, G.1    Reymond, A.2    Dabbouseh, N.3    Dermitzakis, E.T.4    Castelo, R.5    Thomson, T.M.6
  • 8
    • 59849091728 scopus 로고    scopus 로고
    • Short homologous sequences are strongly associated with the generation of chimeric RNAs in eukaryotes
    • Epub 2008/12/18. PMID: 19089307
    • Li X, Zhao L, Jiang H, Wang W. Short homologous sequences are strongly associated with the generation of chimeric RNAs in eukaryotes. J Mol Evol. 2009; 68(1):56-65. Epub 2008/12/18. doi: 10.1007/s00239-008-9187-0 PMID: 19089307
    • (2009) J Mol Evol. , vol.68 , Issue.1 , pp. 56-65
    • Li, X.1    Zhao, L.2    Jiang, H.3    Wang, W.4
  • 9
    • 30044431810 scopus 로고    scopus 로고
    • Transcription-mediated gene fusion in the human genome
    • Epub 2005/12/14. PMID: 16344562
    • Akiva P, Toporik A, Edelheit S, Peretz Y, Diber A, Shemesh R, et al. Transcription-mediated gene fusion in the human genome. Genome Res. 2006; 16(1):30-6. Epub 2005/12/14. doi: 10.1101/gr.4137606 PMID: 16344562
    • (2006) Genome Res. , vol.16 , Issue.1 , pp. 30-36
    • Akiva, P.1    Toporik, A.2    Edelheit, S.3    Peretz, Y.4    Diber, A.5    Shemesh, R.6
  • 10
    • 84863541698 scopus 로고    scopus 로고
    • Chimeras taking shape: Potential functions of proteins encoded by chimeric RNA transcripts
    • Epub 2012/05/17. PMID: 22588898
    • Frenkel-Morgenstern M, Lacroix V, Ezkurdia I, Levin Y, Gabashvili A, Prilusky J, et al. Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts. Genome Res. 2012; 22 (7):1231-42. Epub 2012/05/17. doi: 10.1101/gr.130062.111 PMID: 22588898
    • (2012) Genome Res. , vol.22 , Issue.7 , pp. 1231-1242
    • Frenkel-Morgenstern, M.1    Lacroix, V.2    Ezkurdia, I.3    Levin, Y.4    Gabashvili, A.5    Prilusky, J.6
  • 11
    • 46249106990 scopus 로고    scopus 로고
    • Mapping and quantifying mammalian transcriptomes by RNA-Seq
    • Epub 2008/06/03. PMID: 18516045
    • Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008; 5(7):621-8. Epub 2008/06/03. doi: 10.1038/nmeth.1226 PMID: 18516045
    • (2008) Nat Methods. , vol.5 , Issue.7 , pp. 621-628
    • Mortazavi, A.1    Williams, B.A.2    McCue, K.3    Schaeffer, L.4    Wold, B.5
  • 12
    • 84878234942 scopus 로고    scopus 로고
    • Characterizing and measuring bias in sequence data
    • Epub 2013/05/31. PMID: 23718773
    • Ross MG, Russ C, Costello M, Hollinger A, Lennon NJ, Hegarty R, et al. Characterizing and measuring bias in sequence data. Genome Biol. 2013; 14(5):R51. Epub 2013/05/31. doi: 10.1186/gb-2013-14-5-r51 PMID: 23718773
    • (2013) Genome Biol. , vol.14 , Issue.5 , pp. R51
    • Ross, M.G.1    Russ, C.2    Costello, M.3    Hollinger, A.4    Lennon, N.J.5    Hegarty, R.6
  • 13
    • 83055192078 scopus 로고    scopus 로고
    • Differential expression in RNA-seq: A matter of depth
    • Epub 2011/09/10. PMID: 21903743
    • Tarazona S, Garcia-Alcalde F, Dopazo J, Ferrer A, Conesa A. Differential expression in RNA-seq: A matter of depth. Genome Res. 2011; 21(12):2213-23. Epub 2011/09/10. doi: 10.1101/gr.124321.111 PMID: 21903743
    • (2011) Genome Res. , vol.21 , Issue.12 , pp. 2213-2223
    • Tarazona, S.1    Garcia-Alcalde, F.2    Dopazo, J.3    Ferrer, A.4    Conesa, A.5
  • 14
    • 33746683274 scopus 로고    scopus 로고
    • Reverse transcriptase template switching and false alternative transcripts
    • Epub 2006/02/07. PMID: 16457984
    • Cocquet J, Chong A, Zhang G, Veitia RA. Reverse transcriptase template switching and false alternative transcripts. Genomics. 2006; 88(1):127-31. Epub 2006/02/07. doi: 10.1016/j.ygeno.2005.12.013 PMID: 16457984
    • (2006) Genomics. , vol.88 , Issue.1 , pp. 127-131
    • Cocquet, J.1    Chong, A.2    Zhang, G.3    Veitia, R.A.4
  • 15
    • 84861743958 scopus 로고    scopus 로고
    • RNA-SeQC: RNA-seq metrics for quality control and process optimization
    • Epub 2012/04/28. PMID: 22539670
    • DeLuca DS, Levin JZ, Sivachenko A, Fennell T, Nazaire MD, Williams C, et al. RNA-SeQC: RNA-seq metrics for quality control and process optimization. Bioinformatics. 2012; 28(11):1530-2. Epub 2012/04/28. doi: 10.1093/bioinformatics/bts196 PMID: 22539670
    • (2012) Bioinformatics. , vol.28 , Issue.11 , pp. 1530-1532
    • DeLuca, D.S.1    Levin, J.Z.2    Sivachenko, A.3    Fennell, T.4    Nazaire, M.D.5    Williams, C.6
  • 16
    • 79957842166 scopus 로고    scopus 로고
    • Computational methods for transcriptome annotation and quantification using RNA-seq
    • Epub 2011/05/31. PMID: 21623353
    • Garber M, Grabherr MG, Guttman M, Trapnell C. Computational methods for transcriptome annotation and quantification using RNA-seq. Nat Methods. 2011; 8(6):469-77. Epub 2011/05/31. doi: 10.1038/nmeth.1613 PMID: 21623353
    • (2011) Nat Methods. , vol.8 , Issue.6 , pp. 469-477
    • Garber, M.1    Grabherr, M.G.2    Guttman, M.3    Trapnell, C.4
  • 17
    • 84870422798 scopus 로고    scopus 로고
    • Qualimap: Evaluating next-generation sequencing alignment data
    • Epub 2012/08/24. PMID: 22914218
    • Garcia-Alcalde F, Okonechnikov K, Carbonell J, Cruz LM, Gotz S, Tarazona S, et al. Qualimap: evaluating next-generation sequencing alignment data. Bioinformatics. 2012; 28(20):2678-9. Epub 2012/08/24. doi: 10.1093/bioinformatics/bts503 PMID: 22914218
    • (2012) Bioinformatics. , vol.28 , Issue.20 , pp. 2678-2679
    • Garcia-Alcalde, F.1    Okonechnikov, K.2    Carbonell, J.3    Cruz, L.M.4    Gotz, S.5    Tarazona, S.6
  • 18
    • 68149176840 scopus 로고    scopus 로고
    • Chimeric transcript discovery by paired-end transcriptome sequencing
    • Epub 2009/07/14. PMID: 19592507
    • Maher CA, Palanisamy N, Brenner JC, Cao X, Kalyana-Sundaram S, Luo S, et al. Chimeric transcript discovery by paired-end transcriptome sequencing. Proc Natl Acad Sci U S A. 2009; 106(30):12353-8. Epub 2009/07/14. doi: 10.1073/pnas.0904720106 PMID: 19592507
    • (2009) Proc Natl Acad Sci U S A. , vol.106 , Issue.30 , pp. 12353-12358
    • Maher, C.A.1    Palanisamy, N.2    Brenner, J.C.3    Cao, X.4    Kalyana-Sundaram, S.5    Luo, S.6
  • 19
    • 77958040520 scopus 로고    scopus 로고
    • FusionSeq: A modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data
    • Epub 2010/10/23. PMID: 20964841
    • Sboner A, Habegger L, Pflueger D, Terry S, Chen DZ, Rozowsky JS, et al. FusionSeq: A modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data. Genome Biol. 2010; 11 (10):R104. Epub 2010/10/23. doi: 10.1186/gb-2010-11-10-r104 PMID: 20964841
    • (2010) Genome Biol. , vol.11 , Issue.10 , pp. R104
    • Sboner, A.1    Habegger, L.2    Pflueger, D.3    Terry, S.4    Chen, D.Z.5    Rozowsky, J.S.6
  • 20
    • 79958172285 scopus 로고    scopus 로고
    • FusionHunter: Identifying fusion transcripts in cancer using paired-end RNA-seq
    • Epub 2011/05/07. PMID: 21546395
    • Li Y, Chien J, Smith DI, Ma J. FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq. Bioinformatics. 2011; 27(12):1708-10. Epub 2011/05/07. doi: 10.1093/bioinformatics/btr265 PMID: 21546395
    • (2011) Bioinformatics. , vol.27 , Issue.12 , pp. 1708-1710
    • Li, Y.1    Chien, J.2    Smith, D.I.3    Ma, J.4
  • 21
    • 80051507403 scopus 로고    scopus 로고
    • TopHat-Fusion: An algorithm for discovery of novel fusion transcripts
    • Epub 2011/08/13. PMID: 21835007
    • Kim D, Salzberg SL. TopHat-Fusion: an algorithm for discovery of novel fusion transcripts. Genome Biol. 2011; 12(8):R72. Epub 2011/08/13. doi: 10.1186/gb-2011-12-8-r72 PMID: 21835007
    • (2011) Genome Biol. , vol.12 , Issue.8 , pp. R72
    • Kim, D.1    Salzberg, S.L.2
  • 22
    • 80054003528 scopus 로고    scopus 로고
    • ChimeraScan: A tool for identifying chimeric transcription in sequencing data
    • Epub 2011/08/16. PMID: 21840877
    • Iyer MK, Chinnaiyan AM, Maher CA. ChimeraScan: A tool for identifying chimeric transcription in sequencing data. Bioinformatics. 2011; 27(20):2903-4. Epub 2011/08/16. doi: 10.1093/bioinformatics/btr467 PMID: 21840877
    • (2011) Bioinformatics. , vol.27 , Issue.20 , pp. 2903-2904
    • Iyer, M.K.1    Chinnaiyan, A.M.2    Maher, C.A.3
  • 23
    • 79957829805 scopus 로고    scopus 로고
    • DeFuse: An algorithm for gene fusion discovery in tumor RNA-Seq data
    • Epub 2011/06/01. PMID: 21625565
    • McPherson A, Hormozdiari F, Zayed A, Giuliany R, Ha G, Sun MG, et al. deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data. PLoS Comput Biol. 2011; 7(5):e1001138. Epub 2011/06/01. doi: 10.1371/journal.pcbi.1001138 PMID: 21625565
    • (2011) PLoS Comput Biol. , vol.7 , Issue.5 , pp. e1001138
    • McPherson, A.1    Hormozdiari, F.2    Zayed, A.3    Giuliany, R.4    Ha, G.5    Sun, M.G.6
  • 24
    • 84873606413 scopus 로고    scopus 로고
    • SOAPfuse: An algorithm for identifying fusion transcripts from paired-end RNA-Seq data
    • Epub 2013/02/16. PMID: 23409703
    • Jia W, Qiu K, He M, Song P, Zhou Q, Zhou F, et al. SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data. Genome Biol. 2013; 14(2):R12. Epub 2013/02/16. doi: 10.1186/gb-2013-14-2-r12 PMID: 23409703
    • (2013) Genome Biol. , vol.14 , Issue.2 , pp. R12
    • Jia, W.1    Qiu, K.2    He, M.3    Song, P.4    Zhou, Q.5    Zhou, F.6
  • 26
    • 84864143346 scopus 로고    scopus 로고
    • BreakFusion: Targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data
    • Epub 2012/05/09. PMID: 22563071
    • Chen K, Wallis JW, Kandoth C, Kalicki-Veizer JM, Mungall KL, Mungall AJ, et al. BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data. Bioinformatics. 2012; 28(14):1923-4. Epub 2012/05/09. doi: 10.1093/bioinformatics/bts272 PMID: 22563071
    • (2012) Bioinformatics. , vol.28 , Issue.14 , pp. 1923-1924
    • Chen, K.1    Wallis, J.W.2    Kandoth, C.3    Kalicki-Veizer, J.M.4    Mungall, K.L.5    Mungall, A.J.6
  • 27
    • 84939129092 scopus 로고    scopus 로고
    • Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data
    • Epub 2015/02/05. PMID: 25650807
    • Fernandez-Cuesta L, Sun R, Menon R, George J, Lorenz S, Meza-Zepeda LA, et al. Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data. Genome Biol. 2015; 16:7. Epub 2015/02/05. doi: 10.1186/s13059-014-0558-0 PMID: 25650807
    • (2015) Genome Biol. , vol.16 , pp. 7
    • Fernandez-Cuesta, L.1    Sun, R.2    Menon, R.3    George, J.4    Lorenz, S.5    Meza-Zepeda, L.A.6
  • 28
    • 84929858006 scopus 로고    scopus 로고
    • The emerging complexity of gene fusions in cancer
    • Epub 2015/05/23. PMID: 25998716
    • Mertens F, Johansson B, Fioretos T, Mitelman F. The emerging complexity of gene fusions in cancer. Nat Rev Cancer. 2015; 15(6):371-81. Epub 2015/05/23. doi: 10.1038/nrc3947 PMID: 25998716
    • (2015) Nat Rev Cancer. , vol.15 , Issue.6 , pp. 371-381
    • Mertens, F.1    Johansson, B.2    Fioretos, T.3    Mitelman, F.4
  • 29
    • 44349107231 scopus 로고    scopus 로고
    • Cis-and trans-splicing of mRNAs mediated by tRNA sequences in eukaryotic cells
    • Epub 2008/05/07. PMID: 18458335
    • Di Segni G, Gastaldi S, Tocchini-Valentini GP. Cis-and trans-splicing of mRNAs mediated by tRNA sequences in eukaryotic cells. Proc Natl Acad Sci U S A. 2008; 105(19):6864-9. Epub 2008/05/07. doi: 10.1073/pnas.0800420105 PMID: 18458335
    • (2008) Proc Natl Acad Sci U S A. , vol.105 , Issue.19 , pp. 6864-6869
    • Di Segni, G.1    Gastaldi, S.2    Tocchini-Valentini, G.P.3
  • 30
    • 84874867981 scopus 로고    scopus 로고
    • State-of-The-art fusion-finder algorithms sensitivity and specificity
    • Epub 2013/04/05. PMID: 23555082
    • Carrara M, Beccuti M, Lazzarato F, Cavallo F, Cordero F, Donatelli S, et al. State-of-The-art fusion-finder algorithms sensitivity and specificity. Biomed Res Int. 2013; 2013:340620. Epub 2013/04/05. doi: 10. 1155/2013/340620 PMID: 23555082
    • (2013) Biomed Res Int. , vol.2013 , pp. 340620
    • Carrara, M.1    Beccuti, M.2    Lazzarato, F.3    Cavallo, F.4    Cordero, F.5    Donatelli, S.6
  • 32
    • 84873096886 scopus 로고    scopus 로고
    • Identification of recurrent NAB2-STAT6 gene fusions in solitary fibrous tumor by integrative sequencing
    • Epub 2013/01/15. PMID: 23313952
    • Robinson DR, Wu YM, Kalyana-Sundaram S, Cao X, Lonigro RJ, Sung YS, et al. Identification of recurrent NAB2-STAT6 gene fusions in solitary fibrous tumor by integrative sequencing. Nat Genet. 2013; 45 (2):180-5. Epub 2013/01/15. doi: 10.1038/ng.2509 PMID: 23313952
    • (2013) Nat Genet. , vol.45 , Issue.2 , pp. 180-185
    • Robinson, D.R.1    Wu, Y.M.2    Kalyana-Sundaram, S.3    Cao, X.4    Lonigro, R.J.5    Sung, Y.S.6
  • 33
    • 84887926034 scopus 로고    scopus 로고
    • Exploration of the gene fusion landscape of glioblastoma using transcriptome sequencing and copy number data
    • Epub 2013/11/23. PMID: 24261984
    • Shah N, Lankerovich M, Lee H, Yoon JG, Schroeder B, Foltz G. Exploration of the gene fusion landscape of glioblastoma using transcriptome sequencing and copy number data. BMC Genomics. 2013; 14:818. Epub 2013/11/23. doi: 10.1186/1471-2164-14-818 PMID: 24261984
    • (2013) BMC Genomics. , vol.14 , pp. 818
    • Shah, N.1    Lankerovich, M.2    Lee, H.3    Yoon, J.G.4    Schroeder, B.5    Foltz, G.6
  • 34
    • 84868295073 scopus 로고    scopus 로고
    • Reanalysis of RNAsequencing data reveals several additional fusion genes with multiple isoforms
    • Epub 2012/11/03. PMID: 23119097
    • Kangaspeska S, Hultsch S, Edgren H, Nicorici D, Murumagi A, Kallioniemi O. Reanalysis of RNAsequencing data reveals several additional fusion genes with multiple isoforms. PLoS One. 2012; 7(10): e48745. Epub 2012/11/03. doi: 10.1371/journal.pone.0048745 PMID: 23119097
    • (2012) PLoS One. , vol.7 , Issue.10 , pp. e48745
    • Kangaspeska, S.1    Hultsch, S.2    Edgren, H.3    Nicorici, D.4    Murumagi, A.5    Kallioniemi, O.6
  • 35
    • 79952816655 scopus 로고    scopus 로고
    • MHC class II transactivator CIITA is a recurrent gene fusion partner in lymphoid cancers
    • Epub 2011/03/04. PMID: 21368758
    • Steidl C, Shah SP, Woolcock BW, Rui L, Kawahara M, Farinha P, et al. MHC class II transactivator CIITA is a recurrent gene fusion partner in lymphoid cancers. Nature. 2011; 471(7338):377-81. Epub 2011/03/04. doi: 10.1038/nature09754 PMID: 21368758
    • (2011) Nature. , vol.471 , Issue.7338 , pp. 377-381
    • Steidl, C.1    Shah, S.P.2    Woolcock, B.W.3    Rui, L.4    Kawahara, M.5    Farinha, P.6
  • 36
    • 84891369303 scopus 로고    scopus 로고
    • Fusion of TTYH1 with the C19MC microRNA cluster drives expression of a brain-specific DNMT3B isoform in the embryonal brain tumor ETMR
    • Epub 2013/12/10. PMID: 24316981
    • Kleinman CL, Gerges N, Papillon-Cavanagh S, Sin-Chan P, Pramatarova A, Quang DA, et al. Fusion of TTYH1 with the C19MC microRNA cluster drives expression of a brain-specific DNMT3B isoform in the embryonal brain tumor ETMR. Nat Genet. 2014; 46(1):39-44. Epub 2013/12/10. doi: 10.1038/ng.2849 PMID: 24316981
    • (2014) Nat Genet. , vol.46 , Issue.1 , pp. 39-44
    • Kleinman, C.L.1    Gerges, N.2    Papillon-Cavanagh, S.3    Sin-Chan, P.4    Pramatarova, A.5    Quang, D.A.6
  • 37
    • 84887506884 scopus 로고    scopus 로고
    • Novel fusion transcripts in human gastric cancer revealed by transcriptome analysis
    • PMID: 24240688
    • Kim HP, Cho GA, Han SW, Shin JY, Jeong EG, Song SH, et al. Novel fusion transcripts in human gastric cancer revealed by transcriptome analysis. Oncogene. 2014; 33(47):5434-41. doi: 10.1038/onc. 2013.490 PMID: 24240688
    • (2014) Oncogene. , vol.33 , Issue.47 , pp. 5434-5441
    • Kim, H.P.1    Cho, G.A.2    Han, S.W.3    Shin, J.Y.4    Jeong, E.G.5    Song, S.H.6
  • 38
    • 84877898479 scopus 로고    scopus 로고
    • Fusion of the ZC3H7B and BCOR genes in endometrial stromal sarcomas carrying an X;22-translocation
    • Epub 2013/04/13. PMID: 23580382
    • Panagopoulos I, Thorsen J, Gorunova L, Haugom L, Bjerkehagen B, Davidson B, et al. Fusion of the ZC3H7B and BCOR genes in endometrial stromal sarcomas carrying an X;22-translocation. Genes Chromosomes Cancer. 2013; 52(7):610-8. Epub 2013/04/13. doi: 10.1002/gcc.22057 PMID: 23580382
    • (2013) Genes Chromosomes Cancer. , vol.52 , Issue.7 , pp. 610-618
    • Panagopoulos, I.1    Thorsen, J.2    Gorunova, L.3    Haugom, L.4    Bjerkehagen, B.5    Davidson, B.6
  • 39
    • 39549090389 scopus 로고    scopus 로고
    • SeqAn an efficient, generic C++ library for sequence analysis
    • Epub 2008/01/11. PMID: 18184432
    • Doring A, Weese D, Rausch T, Reinert K. SeqAn an efficient, generic C++ library for sequence analysis. BMC Bioinformatics. 2008; 9:11. Epub 2008/01/11. doi: 10.1186/1471-2105-9-11 PMID: 18184432
    • (2008) BMC Bioinformatics. , vol.9 , pp. 11
    • Doring, A.1    Weese, D.2    Rausch, T.3    Reinert, K.4
  • 40
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Epub 2012/03/06. PMID: 22388286
    • Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012; 9(4):357-9. Epub 2012/03/06. doi: 10.1038/nmeth.1923 PMID: 22388286
    • (2012) Nat Methods. , vol.9 , Issue.4 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 41
    • 79959709133 scopus 로고    scopus 로고
    • Digital Equipment Corporation, Institut fur Mathematik und Informatik, Freie Universitat Berlin. Tech. Rep. TB-B-10-06
    • Holtgrewe M. Mason-A read simulator for second generation sequencing data. Digital Equipment Corporation, Institut fur Mathematik und Informatik, Freie Universitat Berlin. 2010;Tech. Rep. TB-B-10-06.
    • (2010) Mason-A Read Simulator for Second Generation Sequencing Data
    • Holtgrewe, M.1
  • 42
    • 78651486046 scopus 로고    scopus 로고
    • Identification of fusion genes in breast cancer by paired-end RNA-sequencing
    • Epub 2008/06/14. PMID: 21247443
    • Edgren H, Murumagi A, Kangaspeska S, Nicorici D, Hongisto V, Kleivi K, et al. Identification of fusion genes in breast cancer by paired-end RNA-sequencing. Genome Biol. 2011; 12(1):R6. Epub 2008/06/14. doi: 10.1186/gb-2011-12-1-r6 PMID: 21247443
    • (2011) Genome Biol. , vol.12 , Issue.1 , pp. R6
    • Edgren, H.1    Murumagi, A.2    Kangaspeska, S.3    Nicorici, D.4    Hongisto, V.5    Kleivi, K.6
  • 43
    • 77950633122 scopus 로고    scopus 로고
    • Integrative analysis of the melanoma transcriptome
    • Epub 2010/02/25. PMID: 20179022
    • Berger MF, Levin JZ, Vijayendran K, Sivachenko A, Adiconis X, Maguire J, et al. Integrative analysis of the melanoma transcriptome. Genome Res. 2010; 20(4):413-27. Epub 2010/02/25. doi: 10.1101/gr. 103697.109 PMID: 20179022
    • (2010) Genome Res. , vol.20 , Issue.4 , pp. 413-427
    • Berger, M.F.1    Levin, J.Z.2    Vijayendran, K.3    Sivachenko, A.4    Adiconis, X.5    Maguire, J.6
  • 44
    • 84867233415 scopus 로고    scopus 로고
    • Poly-gene fusion transcripts and chromothripsis in prostate cancer
    • Epub 2011/01/21 2012/08/29. PMID: 22927308
    • Wu C, Wyatt AW, McPherson A, Lin D, McConeghy BJ, Mo F, et al. Poly-gene fusion transcripts and chromothripsis in prostate cancer. Genes Chromosomes Cancer. 2012; 51(12):1144-53. Epub 2011/01/21 2012/08/29. doi: 10.1002/gcc.21999 PMID: 22927308
    • (2012) Genes Chromosomes Cancer. , vol.51 , Issue.12 , pp. 1144-1153
    • Wu, C.1    Wyatt, A.W.2    McPherson, A.3    Lin, D.4    McConeghy, B.J.5    Mo, F.6
  • 45
    • 84963877141 scopus 로고    scopus 로고
    • Comprehensive evaluation of fusion transcript detection algorithms and a meta-caller to combine top performing methods in paired-end RNA-seq data
    • Epub 2015/11/20
    • Liu S, Tsai WH, Ding Y, Chen R, Fang Z, Huo Z, et al. Comprehensive evaluation of fusion transcript detection algorithms and a meta-caller to combine top performing methods in paired-end RNA-seq data. Nucleic Acids Res. 2015. Epub 2015/11/20.
    • (2015) Nucleic Acids Res.
    • Liu, S.1    Tsai, W.H.2    Ding, Y.3    Chen, R.4    Fang, Z.5    Huo, Z.6
  • 46
    • 84879488128 scopus 로고    scopus 로고
    • Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene
    • Epub 2013/07/03. PMID: 23815980
    • Gonzalez-Porta M, Frankish A, Rung J, Harrow J, Brazma A. Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene. Genome Biol. 2013; 14(7):R70. Epub 2013/07/03. doi: 10.1186/gb-2013-14-7-r70 PMID: 23815980
    • (2013) Genome Biol. , vol.14 , Issue.7 , pp. R70
    • Gonzalez-Porta, M.1    Frankish, A.2    Rung, J.3    Harrow, J.4    Brazma, A.5
  • 47
    • 84892728434 scopus 로고    scopus 로고
    • Sequencing depth and coverage: Key considerations in genomic analyses
    • Epub 2014/01/18. PMID: 24434847
    • Sims D, Sudbery I, Ilott NE, Heger A, Ponting CP. Sequencing depth and coverage: key considerations in genomic analyses. Nat Rev Genet. 2014; 15(2):121-32. Epub 2014/01/18. doi: 10.1038/nrg3642 PMID: 24434847
    • (2014) Nat Rev Genet. , vol.15 , Issue.2 , pp. 121-132
    • Sims, D.1    Sudbery, I.2    Ilott, N.E.3    Heger, A.4    Ponting, C.P.5
  • 48
    • 84878637612 scopus 로고    scopus 로고
    • Strand-specific RNA-seq provides greater resolution of transcriptome profiling
    • Epub 2013/11/02. PMID: 24179440
    • Mills JD, Kawahara Y, Janitz M. Strand-Specific RNA-Seq Provides Greater Resolution of Transcriptome Profiling. Curr Genomics. 2013; 14(3):173-81. Epub 2013/11/02. doi: 10.2174/1389202911314030003 PMID: 24179440
    • (2013) Curr Genomics. , vol.14 , Issue.3 , pp. 173-181
    • Mills, J.D.1    Kawahara, Y.2    Janitz, M.3
  • 49
    • 79961123152 scopus 로고    scopus 로고
    • RSEM: Accurate transcript quantification from RNA-Seq data with or without a reference genome
    • Epub 2011/08/06. PMID: 21816040
    • Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 2011; 12:323. Epub 2011/08/06. doi: 10.1186/1471-2105-12-323 PMID: 21816040
    • (2011) BMC Bioinformatics. , vol.12 , pp. 323
    • Li, B.1    Dewey, C.N.2
  • 50
    • 84983741971 scopus 로고    scopus 로고
    • Characterization of fusion genes and the significantly expressed fusion isoforms in breast cancer by hybrid sequencing
    • Epub 2015/06/05
    • Weirather JL, Afshar PT, Clark TA, Tseng E, Powers LS, Underwood JG, et al. Characterization of fusion genes and the significantly expressed fusion isoforms in breast cancer by hybrid sequencing. Nucleic Acids Res. 2015. Epub 2015/06/05.
    • (2015) Nucleic Acids Res.
    • Weirather, J.L.1    Afshar, P.T.2    Clark, T.A.3    Tseng, E.4    Powers, L.S.5    Underwood, J.G.6
  • 51
    • 84868332770 scopus 로고    scopus 로고
    • NFuse: Discovery of complex genomic rearrangements in cancer using high-throughput sequencing
    • Epub 2012/06/30. PMID: 22745232
    • McPherson A, Wu C, Wyatt AW, Shah S, Collins C, Sahinalp SC. nFuse: discovery of complex genomic rearrangements in cancer using high-throughput sequencing. Genome Res. 2012; 22(11):2250-61. Epub 2012/06/30. doi: 10.1101/gr.136572.111 PMID: 22745232
    • (2012) Genome Res. , vol.22 , Issue.11 , pp. 2250-2261
    • McPherson, A.1    Wu, C.2    Wyatt, A.W.3    Shah, S.4    Collins, C.5    Sahinalp, S.C.6
  • 52
    • 84907959171 scopus 로고    scopus 로고
    • Chimeric RNAs generated by intergenic splicing in normal and cancer cells
    • Epub 2014/08/19. PMID: 25131334
    • Jividen K, Li H. Chimeric RNAs generated by intergenic splicing in normal and cancer cells. Genes Chromosomes Cancer. 2014; 53(12):963-71. Epub 2014/08/19. doi: 10.1002/gcc.22207 PMID: 25131334
    • (2014) Genes Chromosomes Cancer. , vol.53 , Issue.12 , pp. 963-971
    • Jividen, K.1    Li, H.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.