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Volumn 9, Issue 5, 2008, Pages

GeneCount: Genome-wide calculation of absolute tumor DNA copy numbers from array comparative genomic hybridization data

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; DNA;

EID: 47149087914     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2008-9-5-r86     Document Type: Article
Times cited : (10)

References (45)
  • 2
    • 20044375763 scopus 로고    scopus 로고
    • Array comparative genomic hybridization and its applications in cancer
    • 10.1038/ng1569 15920524
    • Pinkel D Albertson DG Array comparative genomic hybridization and its applications in cancer. Nat Genet 2005, 37(Suppl):S11-S17 10.1038/ng1569 15920524
    • (2005) Nat Genet , vol.37 , Issue.SUPPL.
    • Pinkel, D.1    Albertson, D.G.2
  • 3
    • 0042166174 scopus 로고    scopus 로고
    • Chromosome aberrations in solid tumors
    • 10.1038/ng1215 12923544
    • Albertson DG Collins C McCormick F Gray JW Chromosome aberrations in solid tumors. Nat Genet 2003, 34:369-376 10.1038/ng1215 12923544
    • (2003) Nat Genet , vol.34 , pp. 369-376
    • Albertson, D.G.1    Collins, C.2    McCormick, F.3    Gray, J.W.4
  • 4
    • 33746255899 scopus 로고    scopus 로고
    • Gene amplification in cancer
    • 10.1016/j.tig.2006.06.007 16787682
    • Albertson DG Gene amplification in cancer. Trends Genet 2006, 22:447-455 10.1016/j.tig.2006.06.007 16787682
    • (2006) Trends Genet , vol.22 , pp. 447-455
    • Albertson, D.G.1
  • 7
  • 9
    • 12344259648 scopus 로고    scopus 로고
    • Analysis of array CGH data: From signal ratio to gain and loss of DNA regions
    • 10.1093/bioinformatics/bth418 15381628
    • Hupe P Stransky N Thiery JP Radvanyi F Barillot E Analysis of array CGH data: From signal ratio to gain and loss of DNA regions. Bioinformatics 2004, 20:3413-3422 10.1093/bioinformatics/bth418 15381628
    • (2004) Bioinformatics , vol.20 , pp. 3413-3422
    • Hupe, P.1    Stransky, N.2    Thiery, J.P.3    Radvanyi, F.4    Barillot, E.5
  • 10
    • 9444223586 scopus 로고    scopus 로고
    • Breakpoint identification and smoothing of array comparative genomic hybridization data
    • 10.1093/bioinformatics/bth355 15201182
    • Jong K Marchiori E Meijer G Vaart AV Ylstra B Breakpoint identification and smoothing of array comparative genomic hybridization data. Bioinformatics 2004, 20:3636-3637 10.1093/bioinformatics/bth355 15201182
    • (2004) Bioinformatics , vol.20 , pp. 3636-3637
    • Jong, K.1    Marchiori, E.2    Meijer, G.3    Vaart, A.V.4    Ylstra, B.5
  • 12
    • 3543105225 scopus 로고    scopus 로고
    • Circular binary segmentation for the analysis of array-based DNA copy number data
    • 10.1093/biostatistics/kxh008 15475419
    • Olshen AB Venkatraman ES Lucito R Wigler M Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 2004, 5:557-572 10.1093/biostatistics/kxh008 15475419
    • (2004) Biostatistics , vol.5 , pp. 557-572
    • Olshen, A.B.1    Venkatraman, E.S.2    Lucito, R.3    Wigler, M.4
  • 13
    • 1842287971 scopus 로고    scopus 로고
    • Comparative genomic hybridization in hypotriploid/hyperdiploid tumors
    • 10.1002/(SICI)1097-0320(19971001)29:2<113::AID-CYTO3>3.0.CO;2-E 9332817
    • Rosenberg C Schut TB Mostert MC Tanke HJ Raap AK Oosterhuis JW Looijenga LH Comparative genomic hybridization in hypotriploid/hyperdiploid tumors. Cytometry 1997, 29:113-121 10.1002/ (SICI)1097-0320(19971001)29:2<113::AID-CYTO3>3.0.CO;2-E 9332817
    • (1997) Cytometry , vol.29 , pp. 113-121
    • Rosenberg, C.1    Schut, T.B.2    Mostert, M.C.3    Tanke, H.J.4    Raap, A.K.5    Oosterhuis, J.W.6    Looijenga, L.H.7
  • 15
    • 0032532078 scopus 로고    scopus 로고
    • Intratumoral cytogenetic heterogeneity detected by comparative genomic hybridization and laser scanning cytometry in human gliomas
    • 9788624
    • Harada K Nishizaki T Ozaki S Kubota H Ito H Sasaki K Intratumoral cytogenetic heterogeneity detected by comparative genomic hybridization and laser scanning cytometry in human gliomas. Cancer Res 1998, 58:4694-4700 9788624
    • (1998) Cancer Res , vol.58 , pp. 4694-4700
    • Harada, K.1    Nishizaki, T.2    Ozaki, S.3    Kubota, H.4    Ito, H.5    Sasaki, K.6
  • 16
    • 0036468868 scopus 로고    scopus 로고
    • Interglandular cytogenetic heterogeneity detected by comparative genomic hybridization in pancreatic cancer
    • 11830540
    • Harada T Okita K Shiraishi K Kusano N Kondoh S Sasaki K Interglandular cytogenetic heterogeneity detected by comparative genomic hybridization in pancreatic cancer. Cancer Res 2002, 62:835-839 11830540
    • (2002) Cancer Res , vol.62 , pp. 835-839
    • Harada, T.1    Okita, K.2    Shiraishi, K.3    Kusano, N.4    Kondoh, S.5    Sasaki, K.6
  • 19
    • 0030690049 scopus 로고    scopus 로고
    • Analyses of brain tumor cell lines confirm a simple model of relationships among fluorescence in situ hybridization, DNA index, and comparative genomic hybridization
    • 10.1002/(SICI)1098-2264(199712)20:4<311::AID-GCC1>3.0.CO;2-4 9408746
    • Mohapatra G Moore DH Kim DH Grewal L Hyun WC Waldman FM Pinkel D Feuerstein BG Analyses of brain tumor cell lines confirm a simple model of relationships among fluorescence in situ hybridization, DNA index, and comparative genomic hybridization. Genes Chromosomes Cancer 1997, 20:311-319 10.1002/ (SICI)1098-2264(199712)20:4<311::AID-GCC1>3.0.CO;2-4 9408746
    • (1997) Genes Chromosomes Cancer , vol.20 , pp. 311-319
    • Mohapatra, G.1    Moore, D.H.2    Kim, D.H.3    Grewal, L.4    Hyun, W.C.5    Waldman, F.M.6    Pinkel, D.7    Feuerstein, B.G.8
  • 20
    • 0033560838 scopus 로고    scopus 로고
    • c-MYC, RB-1, TP53, and centromere 8 and 17 copy number in B-cell non-Hodgkin's lymphomas assessed by dual-color fluorescence in situ hybridization
    • 10.1002/(SICI)1097-0320(19990415)38:2<53::AID-CYTO2>3.0.CO;2-0 10323217
    • Galteland E Holte H Stokke T c-MYC, RB-1, TP53, and centromere 8 and 17 copy number in B-cell non-Hodgkin's lymphomas assessed by dual-color fluorescence in situ hybridization. Cytometry 1999, 38:53-60 10.1002/ (SICI)1097-0320(19990415)38:2<53::AID-CYTO2>3.0.CO;2-0 10323217
    • (1999) Cytometry , vol.38 , pp. 53-60
    • Galteland, E.1    Holte, H.2    Stokke, T.3
  • 21
    • 0036046646 scopus 로고    scopus 로고
    • Proliferation-dependent expression and phosphorylation of pRB in B cell non-Hodgkin's lymphomas: Dependence on RB1 copy number
    • 10.1038/sj.leu.2402644 12145697
    • Galteland E Smedshammer L Suo Z DeAngelis P Stokke T Proliferation-dependent expression and phosphorylation of pRB in B cell non-Hodgkin's lymphomas: Dependence on RB1 copy number. Leukemia 2002, 16:1549-1555 10.1038/sj.leu.2402644 12145697
    • (2002) Leukemia , vol.16 , pp. 1549-1555
    • Galteland, E.1    Smedshammer, L.2    Suo, Z.3    DeAngelis, P.4    Stokke, T.5
  • 23
    • 33644515323 scopus 로고    scopus 로고
    • Gain of chromosome 6p is an infrequent cause of increased PIM1 expression in B-cell non-Hodgkin's lymphomas
    • 10.1038/sj.leu.2404094 16437153
    • Sivertsen EA Galteland E Mu D Holte H Meza-Zepeda L Myklebost O Patzke S Smeland EB Stokke T Gain of chromosome 6p is an infrequent cause of increased PIM1 expression in B-cell non-Hodgkin's lymphomas. Leukemia 2006, 20:539-542 10.1038/sj.leu.2404094 16437153
    • (2006) Leukemia , vol.20 , pp. 539-542
    • Sivertsen, E.A.1    Galteland, E.2    Mu, D.3    Holte, H.4    Meza-Zepeda, L.5    Myklebost, O.6    Patzke, S.7    Smeland, E.B.8    Stokke, T.9
  • 24
    • 0034691549 scopus 로고    scopus 로고
    • Oncogenic aberrations in the p53 pathway are associated with a high S phase fraction and poor patient survival in B-cell Non-Hodgkin's lymphoma
    • 10.1002/1097-0215(20000720)89:4<313::AID-IJC1>3.0.CO;2-D 10956404
    • Stokke T Galteland E Holte H Smedshammer L Suo Z Smeland EB Borresen-Dale AL DeAngelis P Steen HB Oncogenic aberrations in the p53 pathway are associated with a high S phase fraction and poor patient survival in B-cell Non-Hodgkin's lymphoma. Int J Cancer 2000, 89:313-324 10.1002/1097-0215(20000720)89:4<313::AID-IJC1>3.0.CO;2-D 10956404
    • (2000) Int J Cancer , vol.89 , pp. 313-324
    • Stokke, T.1    Galteland, E.2    Holte, H.3    Smedshammer, L.4    Suo, Z.5    Smeland, E.B.6    Borresen-Dale, A.L.7    DeAngelis, P.8    Steen, H.B.9
  • 25
    • 0035556305 scopus 로고    scopus 로고
    • Loss of chromosome 11q21-23.1 and 17p and gain of chromosome 6p are independent prognostic indicators in B-cell non-Hodgkin's lymphoma
    • 10.1054/bjoc.2001.2164 11747333
    • Stokke T DeAngelis P Smedshammer L Galteland E Steen HB Smeland EB Delabie J Holte H Loss of chromosome 11q21-23.1 and 17p and gain of chromosome 6p are independent prognostic indicators in B-cell non-Hodgkin's lymphoma. Br J Cancer 2001, 85:1900-1913 10.1054/ bjoc.2001.2164 11747333
    • (2001) Br J Cancer , vol.85 , pp. 1900-1913
    • Stokke, T.1    DeAngelis, P.2    Smedshammer, L.3    Galteland, E.4    Steen, H.B.5    Smeland, E.B.6    Delabie, J.7    Holte, H.8
  • 26
    • 0037099005 scopus 로고    scopus 로고
    • BioArray Software Environment (BASE): A platform for comprehensive management and analysis of microarray data
    • SOFTWARE0003 139402 12186655 10.1186/gb-2002-3-8-software0003
    • Saal LH Troein C Vallon-Christersson J Gruvberger S Borg A Peterson C BioArray Software Environment (BASE): A platform for comprehensive management and analysis of microarray data. Genome Biol 2002, 3 SOFTWARE0003 139402 12186655 10.1186/gb-2002-3-8-software0003
    • (2002) Genome Biol , vol.3
    • Saal, L.H.1    Troein, C.2    Vallon-Christersson, J.3    Gruvberger, S.4    Borg, A.5    Peterson, C.6
  • 28
    • 23444459574 scopus 로고    scopus 로고
    • Array CGH technologies and their applications to cancer genomes
    • 10.1007/s10577-005-2168-x 15868418
    • Davies JJ Wilson IM Lam WL Array CGH technologies and their applications to cancer genomes. Chromosome Res 2005, 13:237-248 10.1007/ s10577-005-2168-x 15868418
    • (2005) Chromosome Res , vol.13 , pp. 237-248
    • Davies, J.J.1    Wilson, I.M.2    Lam, W.L.3
  • 29
    • 0027966172 scopus 로고
    • Optimizing comparative genomic hybridization for analysis of DNA sequence copy number changes in solid tumors
    • 10.1002/gcc.2870100403 7522536
    • Kallioniemi OP Kallioniemi A Piper J Isola J Waldman FM Gray JW Pinkel D Optimizing comparative genomic hybridization for analysis of DNA sequence copy number changes in solid tumors. Genes Chromosomes Cancer 1994, 10:231-243 10.1002/gcc.2870100403 7522536
    • (1994) Genes Chromosomes Cancer , vol.10 , pp. 231-243
    • Kallioniemi, O.P.1    Kallioniemi, A.2    Piper, J.3    Isola, J.4    Waldman, F.M.5    Gray, J.W.6    Pinkel, D.7
  • 30
    • 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
  • 31
    • 33751092268 scopus 로고    scopus 로고
    • Analysis of chromosomal changes in serous ovarian carcinoma using high-resolution array comparative genomic hybridization: Potential predictive markers of chemoresistant disease
    • 10.1002/gcc.20384 17044060
    • Kim SW Kim JW Kim YT Kim JH Kim S Yoon BS Nam EJ Kim HY Analysis of chromosomal changes in serous ovarian carcinoma using high-resolution array comparative genomic hybridization: Potential predictive markers of chemoresistant disease. Genes Chromosomes Cancer 2007, 46:1-9 10.1002/ gcc.20384 17044060
    • (2007) Genes Chromosomes Cancer , vol.46 , pp. 1-9
    • Kim, S.W.1    Kim, J.W.2    Kim, Y.T.3    Kim, J.H.4    Kim, S.5    Yoon, B.S.6    Nam, E.J.7    Kim, H.Y.8
  • 34
    • 33749629724 scopus 로고    scopus 로고
    • Identification of novel candidate target genes in amplicons of Glioblastoma multiforme tumors detected by expression and CGH microarray profiling
    • 1592108 17002787 10.1186/1476-4598-5-39
    • Ruano Y Mollejo M Ribalta T Fiano C Camacho FI Gomez E de Lope AR Hernandez-Moneo JL Martinez P Melendez B Identification of novel candidate target genes in amplicons of Glioblastoma multiforme tumors detected by expression and CGH microarray profiling. Mol Cancer 2006, 5:39 1592108 17002787 10.1186/1476-4598-5-39
    • (2006) Mol Cancer , vol.5 , pp. 39
    • Ruano, Y.1    Mollejo, M.2    Ribalta, T.3    Fiano, C.4    Camacho, F.I.5    Gomez, E.6    de Lope, A.R.7    Hernandez-Moneo, J.L.8    Martinez, P.9    Melendez, B.10
  • 35
    • 33747860911 scopus 로고    scopus 로고
    • ACE-it: A tool for genome-wide integration of gene dosage and RNA expression data
    • 10.1093/bioinformatics/btl269 16731696
    • van Wieringen WN Belien JA Vosse SJ Achame EM Ylstra B ACE-it: A tool for genome-wide integration of gene dosage and RNA expression data. Bioinformatics 2006, 22:1919-1920 10.1093/bioinformatics/btl269 16731696
    • (2006) Bioinformatics , vol.22 , pp. 1919-1920
    • van Wieringen, W.N.1    Belien, J.A.2    Vosse, S.J.3    Achame, E.M.4    Ylstra, B.5
  • 37
    • 0033119762 scopus 로고    scopus 로고
    • Intratumor heterogeneity of chromosome 1, 7, 17, and 18 aneusomies obtained by FISH and association with flow cytometric DNA index in human colorectal adenocarcinomas
    • 10.1002/(SICI)1097-0320(19990401)35:4<369::AID-CYTO10>3.0.CO;2-6 10213203
    • Di VA Infusini E Peveri C Sciutto A Orecchia R Geido E Monaco R Giaretti W Intratumor heterogeneity of chromosome 1, 7, 17, and 18 aneusomies obtained by FISH and association with flow cytometric DNA index in human colorectal adenocarcinomas. Cytometry 1999, 35:369-375 10.1002/ (SICI)1097-0320(19990401)35:4<369::AID-CYTO10>3.0.CO;2-6 10213203
    • (1999) Cytometry , vol.35 , pp. 369-375
    • Di, V.A.1    Infusini, E.2    Peveri, C.3    Sciutto, A.4    Orecchia, R.5    Geido, E.6    Monaco, R.7    Giaretti, W.8
  • 38
    • 0031059179 scopus 로고    scopus 로고
    • Detection of c-myc oncogene amplification and chromosomal anomalies in metastatic prostatic carcinoma by fluorescence in situ hybridization
    • 9012485
    • Jenkins RB Qian J Lieber MM Bostwick DG Detection of c-myc oncogene amplification and chromosomal anomalies in metastatic prostatic carcinoma by fluorescence in situ hybridization. Cancer Res 1997, 57:524-531 9012485
    • (1997) Cancer Res , vol.57 , pp. 524-531
    • Jenkins, R.B.1    Qian, J.2    Lieber, M.M.3    Bostwick, D.G.4
  • 39
    • 0032542364 scopus 로고    scopus 로고
    • Genetic instabilities in human cancers
    • 10.1038/25292 9872311
    • Lengauer C Kinzler KW Vogelstein B Genetic instabilities in human cancers. Nature 1998, 396:643-649 10.1038/25292 9872311
    • (1998) Nature , vol.396 , pp. 643-649
    • Lengauer, C.1    Kinzler, K.W.2    Vogelstein, B.3
  • 41
    • 0020530724 scopus 로고
    • A detergent-trypsin method for the preparation of nuclei for flow cytometric DNA analysis
    • 10.1002/cyto.990030503 6188586
    • Vindelov LL Christensen IJ Nissen NI A detergent-trypsin method for the preparation of nuclei for flow cytometric DNA analysis. Cytometry 1983, 3:323-327 10.1002/cyto.990030503 6188586
    • (1983) Cytometry , vol.3 , pp. 323-327
    • Vindelov, L.L.1    Christensen, I.J.2    Nissen, N.I.3
  • 42
    • 33749499031 scopus 로고    scopus 로고
    • Array comparative genomic hybridization reveals distinct DNA copy number differences between gastrointestinal stromal tumors and leiomyosarcomas
    • 10.1158/0008-5472.CAN-06-1972 16982739
    • Meza-Zepeda LA Kresse SH Barragan-Polania AH Bjerkehagen B Ohnstad HO Namlos HM Wang J Kristiansen BE Myklebost O Array comparative genomic hybridization reveals distinct DNA copy number differences between gastrointestinal stromal tumors and leiomyosarcomas. Cancer Res 2006, 66:8984-8993 10.1158/0008-5472.CAN-06-1972 16982739
    • (2006) Cancer Res , vol.66 , pp. 8984-8993
    • Meza-Zepeda, L.A.1    Kresse, S.H.2    Barragan-Polania, A.H.3    Bjerkehagen, B.4    Ohnstad, H.O.5    Namlos, H.M.6    Wang, J.7    Kristiansen, B.E.8    Myklebost, O.9
  • 43
    • 47149099916 scopus 로고    scopus 로고
    • Ensembl http://www.ensembl.org/Homo_sapiens/searchview
    • Ensembl
  • 44
    • 0032903791 scopus 로고    scopus 로고
    • Chromosomal gains and losses in primary colorectal carcinomas detected by CGH and their associations with tumour DNA ploidy, genotypes and phenotypes
    • 10.1038/sj.bjc.6690388 10408863
    • De Angelis PM Clausen OP Schjolberg A Stokke T Chromosomal gains and losses in primary colorectal carcinomas detected by CGH and their associations with tumour DNA ploidy, genotypes and phenotypes. Br J Cancer 1999, 80:526-535 10.1038/sj.bjc.6690388 10408863
    • (1999) Br J Cancer , vol.80 , pp. 526-535
    • De Angelis, P.M.1    Clausen, O.P.2    Schjolberg, A.3    Stokke, T.4


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