메뉴 건너뛰기




Volumn 526, Issue 7573, 2015, Pages 453-457

Alternative transcription initiation leads to expression of a novel ALK isoform in cancer

(32)  Wiesner, Thomas a,b   Lee, William a   Obenauf, Anna C a   Ran, Leili a   Murali, Rajmohan a   Zhang, Qi Fan a   Wong, Elissa W P a   Hu, Wenhuo a   Scott, Sasinya N a   Shah, Ronak H a   Landa, Iñigo a   Button, Julia a,g   Lailler, Nathalie a   Sboner, Andrea c   Gao, Dong a   Murphy, Devan A a   Cao, Zhen a   Shukla, Shipra a   Hollmann, Travis J a   Wang, Lu a   more..


Author keywords

[No Author keywords available]

Indexed keywords

ANAPLASTIC LYMPHOMA KINASE; CRIZOTINIB; PHOSPHOTRANSFERASE; RNA POLYMERASE II; HISTONE; ISOENZYME; LYSINE; MESSENGER RNA; PROTEIN TYROSINE KINASE;

EID: 84944342787     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature15258     Document Type: Article
Times cited : (188)

References (39)
  • 1
    • 33847076849 scopus 로고    scopus 로고
    • Chromatin modifications and their function
    • Kouzarides, T. Chromatin modifications and their function. Cell 128, 693-705 (2007).
    • (2007) Cell , vol.128 , pp. 693-705
    • Kouzarides, T.1
  • 2
    • 84865527768 scopus 로고    scopus 로고
    • Detecting differential usage of exons from RNAseq data
    • Anders, S., Reyes, A. & Huber, W. Detecting differential usage of exons from RNAseq data. Genome Res. 22, 2008-2017 (2012).
    • (2012) Genome Res. , vol.22 , pp. 2008-2017
    • Anders, S.1    Reyes, A.2    Huber, W.3
  • 3
    • 84878682420 scopus 로고    scopus 로고
    • The Genotype-Tissue Expression (GTEx) project
    • GTEx Consortium. The Genotype-Tissue Expression (GTEx) project. Nature Genet. 45, 580-585 (2013).
    • (2013) Nature Genet. , vol.45 , pp. 580-585
    • GTEx Consortium.1
  • 4
    • 79955674240 scopus 로고    scopus 로고
    • mRNA transcript quantification in archival samples using multiplexed, color-coded probes
    • Reis, P. P. et al. mRNA transcript quantification in archival samples using multiplexed, color-coded probes. BMC Biotechnol. 11, 46 (2011).
    • (2011) BMC Biotechnol. , vol.11 , pp. 46
    • Reis, P.P.1
  • 5
    • 84904816744 scopus 로고    scopus 로고
    • Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma
    • Northcott, P. A. et al. Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma. Nature 511, 428-434 (2014).
    • (2014) Nature , vol.511 , pp. 428-434
    • Northcott, P.A.1
  • 6
    • 84879611157 scopus 로고    scopus 로고
    • DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape
    • Xie, M. et al. DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape. Nature Genet. 45, 836-841 (2013).
    • (2013) Nature Genet. , vol.45 , pp. 836-841
    • Xie, M.1
  • 7
    • 84876836223 scopus 로고    scopus 로고
    • Modification of enhancer chromatin: What, how, and why?
    • Calo, E. & Wysocka, J. Modification of enhancer chromatin: what, how, and why? Mol. Cell 49, 825-837 (2013).
    • (2013) Mol. Cell , vol.49 , pp. 825-837
    • Calo, E.1    Wysocka, J.2
  • 8
    • 79953300078 scopus 로고    scopus 로고
    • FIMO: Scanning for occurrences of a given motif
    • Grant, C. E., Bailey, T. L. & Noble, W. S. FIMO: scanning for occurrences of a given motif. Bioinformatics 27, 1017-1018 (2011).
    • (2011) Bioinformatics , vol.27 , pp. 1017-1018
    • Grant, C.E.1    Bailey, T.L.2    Noble, W.S.3
  • 9
    • 34547638047 scopus 로고    scopus 로고
    • Identification of the transforming EML4-ALK fusion gene in nonsmall-cell lung cancer
    • Soda, M. et al. Identification of the transforming EML4-ALK fusion gene in nonsmall-cell lung cancer. Nature 448, 561-566 (2007).
    • (2007) Nature , vol.448 , pp. 561-566
    • Soda, M.1
  • 10
    • 77953896432 scopus 로고    scopus 로고
    • Cell signaling by receptor tyrosine kinases
    • Lemmon, M. A. & Schlessinger, J. Cell signaling by receptor tyrosine kinases. Cell 141, 1117-1134 (2010).
    • (2010) Cell , vol.141 , pp. 1117-1134
    • Lemmon, M.A.1    Schlessinger, J.2
  • 11
    • 81055126433 scopus 로고    scopus 로고
    • Differential inhibitor sensitivity of anaplastic lymphoma kinase variants found in neuroblastoma
    • Bresler, S. C. et al. Differential inhibitor sensitivity of anaplastic lymphoma kinase variants found in neuroblastoma. Sci. Transl. Med. 3, 108ra114 (2011).
    • (2011) Sci. Transl. Med. , vol.3 , pp. 108ra114
    • Bresler, S.C.1
  • 12
    • 54049094708 scopus 로고    scopus 로고
    • Identification of ALK as a major familial neuroblastoma predisposition gene
    • Mossé, Y. P. et al. Identification of ALK as a major familial neuroblastoma predisposition gene. Nature 455, 930-935 (2008).
    • (2008) Nature , vol.455 , pp. 930-935
    • Mossé, Y.P.1
  • 13
    • 54049149961 scopus 로고    scopus 로고
    • Somatic and germline activating mutations of the ALK kinase receptor in neuroblastoma
    • Janoueix-Lerosey, I. et al. Somatic and germline activating mutations of the ALK kinase receptor in neuroblastoma. Nature 455, 967-970 (2008).
    • (2008) Nature , vol.455 , pp. 967-970
    • Janoueix-Lerosey, I.1
  • 14
    • 70349733112 scopus 로고    scopus 로고
    • Mutation-independent anaplastic lymphoma kinase overexpression in poor prognosis neuroblastoma patients
    • Passoni, L. et al. Mutation-independent anaplastic lymphoma kinase overexpression in poor prognosis neuroblastoma patients. Cancer Res. 69, 7338-7346 (2009).
    • (2009) Cancer Res. , vol.69 , pp. 7338-7346
    • Passoni, L.1
  • 15
    • 84905086382 scopus 로고    scopus 로고
    • Wild-type ALK and activating ALK-R1275Q and ALK-F1174L mutations upregulate Myc and initiate tumor formation in murine neural crest progenitor cells
    • Montavon, G. et al. Wild-type ALK and activating ALK-R1275Q and ALK-F1174L mutations upregulate Myc and initiate tumor formation in murine neural crest progenitor cells. Oncotarget 5, 4452-4466 (2014).
    • (2014) Oncotarget , vol.5 , pp. 4452-4466
    • Montavon, G.1
  • 16
    • 79961002472 scopus 로고    scopus 로고
    • High ALK receptor tyrosine kinase expression supersedes ALK mutation as a determining factor of an unfavorable phenotype in primary neuroblastoma
    • Schulte, J. H. et al. High ALK receptor tyrosine kinase expression supersedes ALK mutation as a determining factor of an unfavorable phenotype in primary neuroblastoma. Clin. Cancer Res. 17, 5082-5092 (2011).
    • (2011) Clin. Cancer Res. , vol.17 , pp. 5082-5092
    • Schulte, J.H.1
  • 17
    • 84928105158 scopus 로고    scopus 로고
    • Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT): A hybridization capture-based nextgeneration sequencing clinical assay for solid tumor molecular oncology
    • Cheng, D. T. et al. Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT): A hybridization capture-based nextgeneration sequencing clinical assay for solid tumor molecular oncology. J. Mol. Diagn. 17, 251-264 (2015).
    • (2015) J. Mol. Diagn. , vol.17 , pp. 251-264
    • Cheng, D.T.1
  • 18
    • 68549104404 scopus 로고    scopus 로고
    • The sequence alignment/map format and SAMtools
    • Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1
  • 19
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: Discovering splice junctions with RNA-Seq
    • Trapnell, C., Pachter, L. & Salzberg, S. L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105-1111 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 20
    • 77956295988 scopus 로고    scopus 로고
    • The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
    • McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297-1303 (2010).
    • (2010) Genome Res. , vol.20 , pp. 1297-1303
    • McKenna, A.1
  • 21
    • 78651271733 scopus 로고    scopus 로고
    • Integrative genomics viewer
    • Robinson, J. T. et al. Integrative genomics viewer. Nature Biotechnol. 29, 24-26 (2011).
    • (2011) Nature Biotechnol. , vol.29 , pp. 24-26
    • Robinson, J.T.1
  • 22
    • 58349111875 scopus 로고    scopus 로고
    • AmiGO: Online access to ontology and annotation data
    • Carbon, S. et al. AmiGO: online access to ontology and annotation data. Bioinformatics 25, 288-289 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 288-289
    • Carbon, S.1
  • 23
    • 84891808382 scopus 로고    scopus 로고
    • JASPAR 2014: An extensively expanded and updated openaccess database of transcription factor binding profiles
    • Mathelier, A. et al. JASPAR 2014: an extensively expanded and updated openaccess database of transcription factor binding profiles. Nucleic Acids Res. 42, D142-D147 (2014).
    • (2014) Nucleic Acids Res. , vol.42 , pp. D142-D147
    • Mathelier, A.1
  • 24
    • 77957943127 scopus 로고    scopus 로고
    • ETV1 is a lineage survival factor that cooperates with KIT in gastrointestinal stromal tumours
    • Chi, P. et al. ETV1 is a lineage survival factor that cooperates with KIT in gastrointestinal stromal tumours. Nature 467, 849-853 (2010).
    • (2010) Nature , vol.467 , pp. 849-853
    • Chi, P.1
  • 25
    • 53849146020 scopus 로고    scopus 로고
    • Model-based analysis of ChIP-Seq (MACS)
    • Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).
    • (2008) Genome Biol. , vol.9 , pp. R137
    • Zhang, Y.1
  • 26
    • 84886812425 scopus 로고    scopus 로고
    • Detecting somatic genetic alterations in tumor specimens by exon capture and massively parallel sequencing
    • Won,H.H., Scott, S. N., Brannon, A. R., Shah, R. H.& Berger, M. F. Detecting somatic genetic alterations in tumor specimens by exon capture and massively parallel sequencing. J. Vis. Exp. e50710 (2013).
    • (2013) J. Vis. Exp.
    • Won, H.H.1    Scott, S.N.2    Brannon, A.R.3    Shah, R.H.4    Berger, M.F.5
  • 27
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 28
    • 79955483667 scopus 로고    scopus 로고
    • A framework for variation discovery and genotyping using next-generation DNA sequencing data
    • DePristo, M. A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genet. 43, 491-498 (2011).
    • (2011) Nature Genet. , vol.43 , pp. 491-498
    • DePristo, M.A.1
  • 29
    • 84874025843 scopus 로고    scopus 로고
    • Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples
    • Cibulskis, K. et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nature Biotechnol. 31, 213-219 (2013).
    • (2013) Nature Biotechnol. , vol.31 , pp. 213-219
    • Cibulskis, K.1
  • 30
    • 84866440781 scopus 로고    scopus 로고
    • DELLY: Structural variant discovery by integrated paired-end and split-read analysis
    • Rausch, T. et al. DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics 28, i333-i339 (2012).
    • (2012) Bioinformatics , vol.28 , pp. i333-i339
    • Rausch, T.1
  • 31
    • 79957868920 scopus 로고    scopus 로고
    • Bismark: A flexible aligner and methylation caller for Bisulfite-Seq applications
    • Krueger, F. & Andrews, S. R. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27, 1571-1572 (2011).
    • (2011) Bioinformatics , vol.27 , pp. 1571-1572
    • Krueger, F.1    Andrews, S.R.2
  • 32
    • 78651430230 scopus 로고    scopus 로고
    • Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization
    • Boeva, V. et al. Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization. Bioinformatics 27, 268-269 (2011).
    • (2011) Bioinformatics , vol.27 , pp. 268-269
    • Boeva, V.1
  • 33
    • 79961007031 scopus 로고    scopus 로고
    • CREST maps somatic structural variation in cancer genomes with base-pair resolution
    • Wang, J. et al. CREST maps somatic structural variation in cancer genomes with base-pair resolution. Nature Methods 8, 652-654 (2011).
    • (2011) Nature Methods , vol.8 , pp. 652-654
    • Wang, J.1
  • 34
    • 77955405475 scopus 로고    scopus 로고
    • Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor
    • McLaren, W. et al. Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics 26, 2069-2070 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 2069-2070
    • McLaren, W.1
  • 35
    • 69649109364 scopus 로고    scopus 로고
    • Circos: An information aesthetic for comparative genomics
    • Krzywinski, M. et al. Circos: an information aesthetic for comparative genomics. Genome Res. 19, 1639-1645 (2009).
    • (2009) Genome Res. , vol.19 , pp. 1639-1645
    • Krzywinski, M.1
  • 36
    • 40449100030 scopus 로고    scopus 로고
    • Direct multiplexed measurement of gene expression with colorcoded probe pairs
    • Geiss, G. K. et al. Direct multiplexed measurement of gene expression with colorcoded probe pairs. Nature Biotechnol. 26, 317-325 (2008).
    • (2008) Nature Biotechnol. , vol.26 , pp. 317-325
    • Geiss, G.K.1
  • 37
    • 0023145290 scopus 로고
    • A line of non-tumorigenic mouse melanocytes, syngeneic with the B16 melanoma and requiring a tumour promoter for growth
    • Bennett, D. C., Cooper, P. J. & Hart, I. R. A line of non-tumorigenic mouse melanocytes, syngeneic with the B16 melanoma and requiring a tumour promoter for growth. Int. J. Cancer 39, 414-418 (1987).
    • (1987) Int. J. Cancer , vol.39 , pp. 414-418
    • Bennett, D.C.1    Cooper, P.J.2    Hart, I.R.3
  • 38
    • 0037037582 scopus 로고    scopus 로고
    • Interferongamma is required for activation-induced death of T lymphocytes
    • Refaeli, Y., Van Parijs, L., Alexander, S. I.&Abbas, A. K. Interferongamma is required for activation-induced death of T lymphocytes. J. Exp. Med. 196, 999-1005 (2002).
    • (2002) J. Exp. Med. , vol.196 , pp. 999-1005
    • Refaeli, Y.1    Van Parijs, L.2    Alexander, S.I.3    Abbas, A.K.4
  • 39
    • 2442562277 scopus 로고    scopus 로고
    • A novel triple-modality reporter gene for whole-body fluorescent, bioluminescent, and nuclear noninvasive imaging
    • Ponomarev, V. et al. A novel triple-modality reporter gene for whole-body fluorescent, bioluminescent, and nuclear noninvasive imaging. Eur. J. Nucl. Med. Mol. Imaging 31, 740-751 (2004).
    • (2004) Eur. J. Nucl. Med. Mol. Imaging , vol.31 , pp. 740-751
    • Ponomarev, V.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.