메뉴 건너뛰기




Volumn 7, Issue 7, 2012, Pages

TAGCNA: A method to identify significant consensus events of copy number alterations in cancer

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIN DEPENDENT KINASE 4; CYCLIN DEPENDENT KINASE INHIBITOR 2A; CYCLIN DEPENDENT KINASE INHIBITOR 2B; EPIDERMAL GROWTH FACTOR RECEPTOR;

EID: 84864020010     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0041082     Document Type: Article
Times cited : (5)

References (34)
  • 1
    • 77249119762 scopus 로고    scopus 로고
    • The landscape of somatic copy-number alteration across human cancers
    • Beroukhim R, Mermel CH, Porter D, Wei G, Raychaudhuri S, et al. (2010) The landscape of somatic copy-number alteration across human cancers. Nature 463: 899-905.
    • (2010) Nature , vol.463 , pp. 899-905
    • Beroukhim, R.1    Mermel, C.H.2    Porter, D.3    Wei, G.4    Raychaudhuri, S.5
  • 2
    • 79953158399 scopus 로고    scopus 로고
    • Exploring the genomes of cancer cells: progress and promise
    • Stratton MR, (2011) Exploring the genomes of cancer cells: progress and promise. Science 331: 1553-1558.
    • (2011) Science , vol.331 , pp. 1553-1558
    • Stratton, M.R.1
  • 3
    • 38049100456 scopus 로고    scopus 로고
    • Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma
    • Beroukhim R, Getz G, Nghiemphu L, Barretina J, Hsueh T, et al. (2007) Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc Natl Acad Sci U S A 104: 20007-20012.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 20007-20012
    • Beroukhim, R.1    Getz, G.2    Nghiemphu, L.3    Barretina, J.4    Hsueh, T.5
  • 4
    • 34547844126 scopus 로고    scopus 로고
    • Modeling recurrent DNA copy number alterations in array CGH data
    • Shah SP, Lam WL, Ng RT, Murphy KP, (2007) Modeling recurrent DNA copy number alterations in array CGH data. Bioinformatics 23: i450-458.
    • (2007) Bioinformatics , vol.23
    • Shah, S.P.1    Lam, W.L.2    Ng, R.T.3    Murphy, K.P.4
  • 5
    • 33748276243 scopus 로고    scopus 로고
    • STAC: A method for testing the significance of DNA copy number aberrations across multiple array-CGH experiments
    • Diskin SJ, Eck T, Greshock J, Mosse YP, Naylor T, et al. (2006) STAC: A method for testing the significance of DNA copy number aberrations across multiple array-CGH experiments. Genome Res 16: 1149-1158.
    • (2006) Genome Res , vol.16 , pp. 1149-1158
    • Diskin, S.J.1    Eck, T.2    Greshock, J.3    Mosse, Y.P.4    Naylor, T.5
  • 6
    • 65949104847 scopus 로고    scopus 로고
    • Analysis of DNA copy number alterations in ovarian serous tumors identifies new molecular genetic changes in low-grade and high-grade carcinomas
    • Kuo KT, Guan B, Feng Y, Mao TL, Chen X, et al. (2009) Analysis of DNA copy number alterations in ovarian serous tumors identifies new molecular genetic changes in low-grade and high-grade carcinomas. Cancer Res 69: 4036-4042.
    • (2009) Cancer Res , vol.69 , pp. 4036-4042
    • Kuo, K.T.1    Guan, B.2    Feng, Y.3    Mao, T.L.4    Chen, X.5
  • 7
    • 84864017237 scopus 로고    scopus 로고
    • Finding Recurrent Copy Number Alteration Regions: A Review of Methods Current Bioinformatics
    • Rueda OM, Diaz-Uriarte R, (2010) Finding Recurrent Copy Number Alteration Regions: A Review of Methods Current Bioinformatics 5: 17.
    • (2010) , vol.5 , pp. 17
    • Rueda, O.M.1    Diaz-Uriarte, R.2
  • 8
    • 79955166265 scopus 로고    scopus 로고
    • GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers
    • Mermel CH, Schumacher SE, Hill B, Meyerson ML, Beroukhim R, et al. (2011) GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol 12: R41.
    • (2011) Genome Biol , vol.12
    • Mermel, C.H.1    Schumacher, S.E.2    Hill, B.3    Meyerson, M.L.4    Beroukhim, R.5
  • 9
    • 79951998794 scopus 로고    scopus 로고
    • DiNAMIC: a method to identify recurrent DNA copy number aberrations in tumors
    • Walter V, Nobel AB, Wright FA, (2011) DiNAMIC: a method to identify recurrent DNA copy number aberrations in tumors. Bioinformatics 27: 678-685.
    • (2011) Bioinformatics , vol.27 , pp. 678-685
    • Walter, V.1    Nobel, A.B.2    Wright, F.A.3
  • 10
    • 34147104969 scopus 로고    scopus 로고
    • A faster circular binary segmentation algorithm for the analysis of array CGH data
    • Venkatraman ES, Olshen AB, (2007) A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 23: 657-663.
    • (2007) Bioinformatics , vol.23 , pp. 657-663
    • Venkatraman, E.S.1    Olshen, A.B.2
  • 11
    • 12344259648 scopus 로고    scopus 로고
    • Analysis of array CGH data: from signal ratio to gain and loss of DNA regions
    • Hupe P, Stransky N, Thiery JP, Radvanyi F, Barillot E, (2004) Analysis of array CGH data: from signal ratio to gain and loss of DNA regions. Bioinformatics 20: 3413-3422.
    • (2004) Bioinformatics , vol.20 , pp. 3413-3422
    • Hupe, P.1    Stransky, N.2    Thiery, J.P.3    Radvanyi, F.4    Barillot, E.5
  • 12
    • 39149107114 scopus 로고    scopus 로고
    • Identification of cancer genes using a statistical framework for multiexperiment analysis of nondiscretized array CGH data
    • Klijn C, Holstege H, de Ridder J, Liu X, Reinders M, et al. (2008) Identification of cancer genes using a statistical framework for multiexperiment analysis of nondiscretized array CGH data. Nucleic Acids Res 36: e13.
    • (2008) Nucleic Acids Res , vol.36
    • Klijn, C.1    Holstege, H.2    de Ridder, J.3    Liu, X.4    Reinders, M.5
  • 13
    • 77949501694 scopus 로고    scopus 로고
    • CMDS: a population-based method for identifying recurrent DNA copy number aberrations in cancer from high-resolution data
    • Zhang Q, Ding L, Larson DE, Koboldt DC, McLellan MD, et al. (2010) CMDS: a population-based method for identifying recurrent DNA copy number aberrations in cancer from high-resolution data. Bioinformatics 26: 464-469.
    • (2010) Bioinformatics , vol.26 , pp. 464-469
    • Zhang, Q.1    Ding, L.2    Larson, D.E.3    Koboldt, D.C.4    McLellan, M.D.5
  • 14
    • 62549158266 scopus 로고    scopus 로고
    • Computational methods for identification of recurrent copy number alteration patterns by array CGH
    • Shah SP, (2008) Computational methods for identification of recurrent copy number alteration patterns by array CGH. Cytogenet Genome Res 123: 343-351.
    • (2008) Cytogenet Genome Res , vol.123 , pp. 343-351
    • Shah, S.P.1
  • 15
    • 77249099315 scopus 로고    scopus 로고
    • A double-layered mixture model for the joint analysis of DNA copy number and gene expression data
    • Choi H, Qin ZS, Ghosh D, (2010) A double-layered mixture model for the joint analysis of DNA copy number and gene expression data. J Comput Biol 17: 121-137.
    • (2010) J Comput Biol , vol.17 , pp. 121-137
    • Choi, H.1    Qin, Z.S.2    Ghosh, D.3
  • 17
    • 3543105225 scopus 로고    scopus 로고
    • Circular binary segmentation for the analysis of array-based DNA copy number data
    • Olshen AB, Venkatraman ES, Lucito R, Wigler M, (2004) Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 5: 557-572.
    • (2004) Biostatistics , vol.5 , pp. 557-572
    • Olshen, A.B.1    Venkatraman, E.S.2    Lucito, R.3    Wigler, M.4
  • 18
    • 27944455289 scopus 로고    scopus 로고
    • A comparison study: applying segmentation to array CGH data for downstream analyses
    • Willenbrock H, Fridlyand J, (2005) A comparison study: applying segmentation to array CGH data for downstream analyses. Bioinformatics 21: 4084-4091.
    • (2005) Bioinformatics , vol.21 , pp. 4084-4091
    • Willenbrock, H.1    Fridlyand, J.2
  • 19
    • 36248980204 scopus 로고    scopus 로고
    • Characterizing the cancer genome in lung adenocarcinoma
    • Weir BA, Woo MS, Getz G, Perner S, Ding L, et al. (2007) Characterizing the cancer genome in lung adenocarcinoma. Nature 450: 893-898.
    • (2007) Nature , vol.450 , pp. 893-898
    • Weir, B.A.1    Woo, M.S.2    Getz, G.3    Perner, S.4    Ding, L.5
  • 20
    • 2342471392 scopus 로고    scopus 로고
    • Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib
    • Lynch TJ, Bell DW, Sordella R, Gurubhagavatula S, Okimoto RA, et al. (2004) Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib. N Engl J Med 350: 2129-2139.
    • (2004) N Engl J Med , vol.350 , pp. 2129-2139
    • Lynch, T.J.1    Bell, D.W.2    Sordella, R.3    Gurubhagavatula, S.4    Okimoto, R.A.5
  • 21
    • 0036176041 scopus 로고    scopus 로고
    • Mutations in the TMPRSS3 gene are a rare cause of childhood nonsyndromic deafness in Caucasian patients
    • Wattenhofer M, Di Iorio MV, Rabionet R, Dougherty L, Pampanos A, et al. (2002) Mutations in the TMPRSS3 gene are a rare cause of childhood nonsyndromic deafness in Caucasian patients. J Mol Med (Berl) 80: 124-131.
    • (2002) J Mol Med (Berl) , vol.80 , pp. 124-131
    • Wattenhofer, M.1    Di Iorio, M.V.2    Rabionet, R.3    Dougherty, L.4    Pampanos, A.5
  • 22
    • 4644309151 scopus 로고    scopus 로고
    • The transmembrane protease serine (TMPRSS3/TADG-12) D variant: a potential candidate for diagnosis and therapeutic intervention in ovarian cancer
    • Sawasaki T, Shigemasa K, Gu L, Beard JB, O'Brien TJ, (2004) The transmembrane protease serine (TMPRSS3/TADG-12) D variant: a potential candidate for diagnosis and therapeutic intervention in ovarian cancer. Tumour Biol 25: 141-148.
    • (2004) Tumour Biol , vol.25 , pp. 141-148
    • Sawasaki, T.1    Shigemasa, K.2    Gu, L.3    Beard, J.B.4    O'Brien, T.J.5
  • 23
    • 84863996691 scopus 로고    scopus 로고
    • Gene copy number alterations in prostate cancer
    • Outi S, (2006) Gene copy number alterations in prostate cancer. Tampere University Press.
    • (2006) Tampere University Press
    • Outi, S.1
  • 24
    • 3242672465 scopus 로고    scopus 로고
    • Whole genome scanning identifies genotypes associated with recurrence and metastasis in prostate tumors
    • Paris PL, Andaya A, Fridlyand J, Jain AN, Weinberg V, et al. (2004) Whole genome scanning identifies genotypes associated with recurrence and metastasis in prostate tumors. Hum Mol Genet 13: 1303-1313.
    • (2004) Hum Mol Genet , vol.13 , pp. 1303-1313
    • Paris, P.L.1    Andaya, A.2    Fridlyand, J.3    Jain, A.N.4    Weinberg, V.5
  • 25
    • 2442637585 scopus 로고    scopus 로고
    • High-resolution analysis of gene copy number alterations in human prostate cancer using CGH on cDNA microarrays: impact of copy number on gene expression
    • Wolf M, Mousses S, Hautaniemi S, Karhu R, Huusko P, et al. (2004) High-resolution analysis of gene copy number alterations in human prostate cancer using CGH on cDNA microarrays: impact of copy number on gene expression. Neoplasia 6: 240-247.
    • (2004) Neoplasia , vol.6 , pp. 240-247
    • Wolf, M.1    Mousses, S.2    Hautaniemi, S.3    Karhu, R.4    Huusko, P.5
  • 26
    • 84863999558 scopus 로고    scopus 로고
    • Characterization of Copy Number Aberrations and Epigenetic Modifications in Prostate Cancer
    • Kim JH, (2010) Characterization of Copy Number Aberrations and Epigenetic Modifications in Prostate Cancer. Dissertations and Theses.
    • (2010) Dissertations and Theses
    • Kim, J.H.1
  • 27
    • 77954810283 scopus 로고    scopus 로고
    • Copy number and gene expression differences between African American and Caucasian American prostate cancer
    • Rose AE, Satagopan JM, Oddoux C, Zhou Q, Xu R, et al. (2010) Copy number and gene expression differences between African American and Caucasian American prostate cancer. J Transl Med 8: 70.
    • (2010) J Transl Med , vol.8 , pp. 70
    • Rose, A.E.1    Satagopan, J.M.2    Oddoux, C.3    Zhou, Q.4    Xu, R.5
  • 28
    • 9344222738 scopus 로고    scopus 로고
    • Analysis of 99 microdissected prostate carcinomas reveals a high frequency of allelic loss on chromosome 8p12-21
    • Vocke CD, Pozzatti RO, Bostwick DG, Florence CD, Jennings SB, et al. (1996) Analysis of 99 microdissected prostate carcinomas reveals a high frequency of allelic loss on chromosome 8p12-21. Cancer Res 56: 2411-2416.
    • (1996) Cancer Res , vol.56 , pp. 2411-2416
    • Vocke, C.D.1    Pozzatti, R.O.2    Bostwick, D.G.3    Florence, C.D.4    Jennings, S.B.5
  • 29
    • 61849087866 scopus 로고    scopus 로고
    • A novel Frabin (FGD4) nonsense mutation p.R275X associated with phenotypic variability in CMT4H
    • Houlden H, Hammans S, Katifi H, Reilly MM, (2009) A novel Frabin (FGD4) nonsense mutation p.R275X associated with phenotypic variability in CMT4H. Neurology 72: 617-620.
    • (2009) Neurology , vol.72 , pp. 617-620
    • Houlden, H.1    Hammans, S.2    Katifi, H.3    Reilly, M.M.4
  • 30
    • 34548453724 scopus 로고    scopus 로고
    • Point mutation in the HCN4 cardiac ion channel pore affecting synthesis, trafficking, and functional expression is associated with familial asymptomatic sinus bradycardia
    • Nof E, Luria D, Brass D, Marek D, Lahat H, et al. (2007) Point mutation in the HCN4 cardiac ion channel pore affecting synthesis, trafficking, and functional expression is associated with familial asymptomatic sinus bradycardia. Circulation 116: 463-470.
    • (2007) Circulation , vol.116 , pp. 463-470
    • Nof, E.1    Luria, D.2    Brass, D.3    Marek, D.4    Lahat, H.5
  • 31
    • 67349172925 scopus 로고    scopus 로고
    • Dissection of phenotype reveals possible association between schizophrenia and Glutamate Receptor Delta 1 (GRID1) gene promoter
    • Treutlein J, Muhleisen TW, Frank J, Mattheisen M, Herms S, et al. (2009) Dissection of phenotype reveals possible association between schizophrenia and Glutamate Receptor Delta 1 (GRID1) gene promoter. Schizophr Res 111: 123-130.
    • (2009) Schizophr Res , vol.111 , pp. 123-130
    • Treutlein, J.1    Muhleisen, T.W.2    Frank, J.3    Mattheisen, M.4    Herms, S.5
  • 32
    • 34548452229 scopus 로고    scopus 로고
    • Assessing the significance of conserved genomic aberrations using high resolution genomic microarrays
    • Guttman M, Mies C, Dudycz-Sulicz K, Diskin SJ, Baldwin DA, et al. (2007) Assessing the significance of conserved genomic aberrations using high resolution genomic microarrays. PLoS Genet 3: e143.
    • (2007) PLoS Genet , vol.3
    • Guttman, M.1    Mies, C.2    Dudycz-Sulicz, K.3    Diskin, S.J.4    Baldwin, D.A.5
  • 33
    • 79957859881 scopus 로고    scopus 로고
    • BACOM: in silico detection of genomic deletion types and correction of normal cell contamination in copy number data
    • Yu G, Zhang B, Bova GS, Xu J, Shih Ie M, et al. (2011) BACOM: in silico detection of genomic deletion types and correction of normal cell contamination in copy number data. Bioinformatics 27: 1473-1480.
    • (2011) Bioinformatics , vol.27 , pp. 1473-1480
    • Yu, G.1    Zhang, B.2    Bova, G.S.3    Xu, J.4    Shih Ie, M.5
  • 34
    • 67649458202 scopus 로고    scopus 로고
    • Quantification of normal cell fraction and copy number neutral LOH in clinical lung cancer samples using SNP array data
    • Goransson H, Edlund K, Rydaker M, Rasmussen M, Winquist J, et al. (2009) Quantification of normal cell fraction and copy number neutral LOH in clinical lung cancer samples using SNP array data. PLoS One 4: e6057.
    • (2009) PLoS One , vol.4
    • Goransson, H.1    Edlund, K.2    Rydaker, M.3    Rasmussen, M.4    Winquist, J.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.