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Volumn 34, Issue 20, 2006, Pages

MMASS: An optimized array-based method for assessing CpG island methylation

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; BIOINFORMATICS; CELL STRAIN HCT116; CONTROLLED STUDY; CPG ISLAND; DNA HYBRIDIZATION; DNA METHYLATION; DNA REPLICATION; DNA SEQUENCE; GENETIC IDENTIFICATION; GENOME; HIGH THROUGHPUT SCREENING; HUMAN; HUMAN CELL; INTERMETHOD COMPARISON; MICROARRAY ANALYSIS; NONHUMAN; PREDICTION; PRIORITY JOURNAL; SENSITIVITY ANALYSIS; VALIDATION PROCESS; BIOLOGY; CHEMISTRY; DNA MICROARRAY; DNA PROBE; EVALUATION; GENOMICS; METHODOLOGY; TUMOR CELL LINE; TUMOR GENE; VALIDATION STUDY;

EID: 33845643047     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl551     Document Type: Article
Times cited : (45)

References (50)
  • 1
    • 2442684104 scopus 로고    scopus 로고
    • An evaluation of new criteria for CpG islands in the human genome as gene markers
    • Wang,Y. and Leung,F.C.C. (2004) An evaluation of new criteria for CpG islands in the human genome as gene markers. Bioinformatics, 20, 1170-1177.
    • (2004) Bioinformatics , vol.20 , pp. 1170-1177
    • Wang, Y.1    Leung, F.C.C.2
  • 2
    • 0030986103 scopus 로고    scopus 로고
    • Formation of methylation patterns in the mammalian genome
    • Turker,M.S. and Bestor,T.H. (1997) Formation of methylation patterns in the mammalian genome. Mutat. Res., 386, 119-130.
    • (1997) Mutat. Res. , vol.386 , pp. 119-130
    • Turker, M.S.1    Bestor, T.H.2
  • 3
    • 0036144048 scopus 로고    scopus 로고
    • DNA methylation patterns and epigenetic memory
    • Bird,A. (2002) DNA methylation patterns and epigenetic memory. Genes. Dev., 16, 6-21.
    • (2002) Genes. Dev. , vol.16 , pp. 6-21
    • Bird, A.1
  • 4
    • 0032960181 scopus 로고    scopus 로고
    • Cancer epigenetics comes of age
    • Jones,P.A. and Laird,P.W. (1999) Cancer epigenetics comes of age. Nature Genet., 21, 163-167.
    • (1999) Nature Genet. , vol.21 , pp. 163-167
    • Jones, P.A.1    Laird, P.W.2
  • 5
    • 0032731581 scopus 로고    scopus 로고
    • Hypermethylation of tumor suppressor genes in cancer
    • Herman,J.G. (1999) Hypermethylation of tumor suppressor genes in cancer. Semin. Cancer Biol., 9, 359-367.
    • (1999) Semin. Cancer Biol. , vol.9 , pp. 359-367
    • Herman, J.G.1
  • 6
    • 0036274359 scopus 로고    scopus 로고
    • The fundamental role of epigenetic events in cancer
    • Jones,P.A. and Baylin,S.B. (2002) The fundamental role of epigenetic events in cancer. Nature Rev. Genet., 3, 415-428.
    • (2002) Nature Rev. Genet. , vol.3 , pp. 415-428
    • Jones, P.A.1    Baylin, S.B.2
  • 7
    • 0029011539 scopus 로고
    • 5′ CpG island methylation is associated with transcriptional silencing of the tumour suppressor p16/CDKN2/MTS1 in human cancers
    • Merlo,A., Herman,J.G., Mao,L., Lee,DT, Gabrielson,E., Burger,P.C., Baylin,S.B. and Sidransky,D. (1995) 5′ CpG island methylation is associated with transcriptional silencing of the tumour suppressor p16/ CDKN2/MTS1 in human cancers. Nature Med., 1, 686-692.
    • (1995) Nature Med. , vol.1 , pp. 686-692
    • Merlo, A.1    Herman, J.G.2    Mao, L.3    Lee, D.J.4    Gabrielson, E.5    Burger, P.C.6    Baylin, S.B.7    Sidransky, D.8
  • 11
    • 0036154815 scopus 로고    scopus 로고
    • The potential prognostic, predictive, and therapeutic values of DNA methylation in cancer
    • Widschwendter,M. and Jones,P.A. (2002) The potential prognostic, predictive, and therapeutic values of DNA methylation in cancer. Clin. Cancer Res., 8, 17-21.
    • (2002) Clin. Cancer Res. , vol.8 , pp. 17-21
    • Widschwendter, M.1    Jones, P.A.2
  • 12
    • 0033047813 scopus 로고    scopus 로고
    • Methylation profiling of CpG islands in human breast cancer cells
    • Huang,T.H., Perry,M.R. and Laux,D.E. (1999) Methylation profiling of CpG islands in human breast cancer cells. Hum. Mol. Genet., 8, 459-470.
    • (1999) Hum. Mol. Genet. , vol.8 , pp. 459-470
    • Huang, T.H.1    Perry, M.R.2    Laux, D.E.3
  • 13
    • 0035992386 scopus 로고    scopus 로고
    • Methylation microarray analysis of late-stage ovarian carcinomas distinguishes progression-free survival in patients and identifies candidate epigenetic markers
    • Wei,S.H., Chen,C.-M., Strathdee,G., Harnsomburana,J., Shyu,C.-R., Rahmatpanah,F., Shi,H., Ng,S.-W., Yan,P.S., Nephew,K.P. et al. (2002) Methylation microarray analysis of late-stage ovarian carcinomas distinguishes progression-free survival in patients and identifies candidate epigenetic markers. Clin. Cancer Res., 8, 2246-2252.
    • (2002) Clin. Cancer Res. , vol.8 , pp. 2246-2252
    • Wei, S.H.1    Chen, C.-M.2    Strathdee, G.3    Harnsomburana, J.4    Shyu, C.-R.5    Rahmatpanah, F.6    Shi, H.7    Ng, S.-W.8    Yan, P.S.9    Nephew, K.P.10
  • 14
    • 0035577862 scopus 로고    scopus 로고
    • Dissecting complex epigenetic alterations in breast cancer using CpG island microarrays
    • Yan,P.S., Chen,C.M., Shi,H., Rahmatpanah,F., Wei,S.H., Caldwell,C.W. and Huang,T.H. (2001) Dissecting complex epigenetic alterations in breast cancer using CpG island microarrays. Cancer Res., 61, 8375-8380.
    • (2001) Cancer Res. , vol.61 , pp. 8375-8380
    • Yan, P.S.1    Chen, C.M.2    Shi, H.3    Rahmatpanah, F.4    Wei, S.H.5    Caldwell, C.W.6    Huang, T.H.7
  • 15
    • 0034051419 scopus 로고    scopus 로고
    • CpG island arrays: An application toward deciphering epigenetic signatures of breast cancer
    • Yan,P.S., Perry,M.R., Laux,D.E., Asare,A.L., Caldwell,C.W. and Huang,T.H. (2000) CpG island arrays: An application toward deciphering epigenetic signatures of breast cancer. Clin. Cancer Res., 6, 1432-1438.
    • (2000) Clin. Cancer Res. , vol.6 , pp. 1432-1438
    • Yan, P.S.1    Perry, M.R.2    Laux, D.E.3    Asare, A.L.4    Caldwell, C.W.5    Huang, T.H.6
  • 16
    • 0036322489 scopus 로고    scopus 로고
    • Applications of CpG island microarrays for high-throughput analysis of DNA methylation
    • Yan,P.S., Chen,C.-M., Shi,H., Rahmatpanah,F., Wei,S.H. and Huang,T.H.-M. (2002) Applications of CpG island microarrays for high-throughput analysis of DNA methylation. J. Nutr., 132, S2430-S2434.
    • (2002) J. Nutr. , vol.132
    • Yan, P.S.1    Chen, C.-M.2    Shi, H.3    Rahmatpanah, F.4    Wei, S.H.5    Huang, T.H.-M.6
  • 17
    • 0036318071 scopus 로고    scopus 로고
    • Use of CpG island microarrays to identify colorectal tumors with a high degree of concurrent methylation
    • Yan,P.S., Efferth,T., Chen,H.-L., Lin,J., Rodel,F., Fuzesi,L. and Huang,T.H.-M. (2002) Use of CpG island microarrays to identify colorectal tumors with a high degree of concurrent methylation. Methods, 27, 162-169.
    • (2002) Methods , vol.27 , pp. 162-169
    • Yan, P.S.1    Efferth, T.2    Chen, H.-L.3    Lin, J.4    Rodel, F.5    Fuzesi, L.6    Huang, T.H.-M.7
  • 18
    • 0028340280 scopus 로고
    • Purification of CpG islands using a methylated DNA binding column
    • Cross,S.H., Charlton,J.A., Nan,X. and Bird,A.P. (1994) Purification of CpG islands using a methylated DNA binding column. Nature Genet., 6, 236-244.
    • (1994) Nature Genet. , vol.6 , pp. 236-244
    • Cross, S.H.1    Charlton, J.A.2    Nan, X.3    Bird, A.P.4
  • 24
    • 0030825309 scopus 로고    scopus 로고
    • COBRA: A sensitive and quantitative DNA methylation assay
    • Xiong,Z. and Laird,P.W. (1997) COBRA: A sensitive and quantitative DNA methylation assay. Nucleic Acids Res., 25, 2532-2534.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 2532-2534
    • Xiong, Z.1    Laird, P.W.2
  • 25
    • 0030462823 scopus 로고    scopus 로고
    • Rapid analysis of DNA methylation using new restriction enzyme sites created by bisulfite modification
    • Sadri,R. and Hornsby,P.J. (1996) Rapid analysis of DNA methylation using new restriction enzyme sites created by bisulfite modification. Nucleic Acids Res., 24, 5058-5059.
    • (1996) Nucleic Acids Res. , vol.24 , pp. 5058-5059
    • Sadri, R.1    Hornsby, P.J.2
  • 26
    • 4544341015 scopus 로고    scopus 로고
    • Linear models and empirical bayes methods for assessing differential expression in microarray experiments
    • Article 3
    • Smyth,G.K. (2004) Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Star. Appl. Genet. Mol. Biol., 3, Article 3.
    • (2004) Star. Appl. Genet. Mol. Biol. , vol.3
    • Smyth, G.K.1
  • 27
    • 28444445926 scopus 로고    scopus 로고
    • R: A Language and Environment for Statistical Computing
    • R Development Core Team R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0
    • R Development Core Team (2005) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0.
    • (2005)
  • 28
    • 20444458948 scopus 로고    scopus 로고
    • Reproducible statistical research
    • Leisch,F. and Rossini,A.J. (2003) Reproducible statistical research. Chance, 16, 41-45.
    • (2003) Chance , vol.16 , pp. 41-45
    • Leisch, F.1    Rossini, A.J.2
  • 29
    • 0242529706 scopus 로고    scopus 로고
    • Sweave: Dynamic generation of statistical reports using literature data analysis
    • (eds) In Berlin Physika Verlag, Heidelberg, Germany
    • Hardle,W. and Ronz,B. (eds) (2002) Sweave: Dynamic generation of statistical reports using literature data analysis. In Proceedings of the conference on Computational Statistics, Berlin. Physika Verlag, Heidelberg, Germany, pp. 575-580.
    • (2002) Proceedings of the Conference on Computational Statistics , pp. 575-580
    • Hardle, W.1    Ronz, B.2
  • 30
    • 14644411245 scopus 로고    scopus 로고
    • Reproducible research: A bioinformatics case study
    • Gentleman,R. (2004) Reproducible research: A bioinformatics case study. Star. Appl. Genet. Mol. Biol., 3.
    • (2004) Star. Appl. Genet. Mol. Biol. , vol.3
    • Gentleman, R.1
  • 31
    • 0041779528 scopus 로고    scopus 로고
    • Genetic unmasking of epigenetically silenced tumor suppressor genes in colon cancer cells deficient in DNA methyltransferases
    • Paz,M.F., Wei,S., Cigudosa,J.C., Rodriguez-Perales,S., Peinado,M.A., Huang,T.H.-M. and Esteller,M. (2003) Genetic unmasking of epigenetically silenced tumor suppressor genes in colon cancer cells deficient in DNA methyltransferases. Hum. Mol. Genet., 12, 2209-2219.
    • (2003) Hum. Mol. Genet. , vol.12 , pp. 2209-2219
    • Paz, M.F.1    Wei, S.2    Cigudosa, J.C.3    Rodriguez-Perales, S.4    Peinado, M.A.5    Huang, T.H.-M.6    Esteller, M.7
  • 33
    • 0036376993 scopus 로고    scopus 로고
    • Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments
    • Dudoit,S., Yang,Y.H., Callow,M.J. and Speed,T.P. (2002) Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Statistica Sinica, 12, 111-140.
    • (2002) Statistica Sinica , vol.12 , pp. 111-140
    • Dudoit, S.1    Yang, Y.H.2    Callow, M.J.3    Speed, T.P.4
  • 35
    • 0018802805 scopus 로고
    • Mitochondrial DNA from various organisms does not contain internally methylated cytosine in -CCGG- sequences
    • Groot,G.S. and Kroon,A.M. (1979) Mitochondrial DNA from various organisms does not contain internally methylated cytosine in -CCGG- sequences. Biochim. Biophys. Acta, 564, 355-357.
    • (1979) Biochim. Biophys. Acta , vol.564 , pp. 355-357
    • Groot, G.S.1    Kroon, A.M.2
  • 36
    • 3242784855 scopus 로고    scopus 로고
    • Methylation of mitochondrial DNA is not a useful marker for cancer detection
    • Maekawa,M., Taniguchi,T., Higashi,H., Sugimura,H., Sugano,K. and Kanno,T. (2004) Methylation of mitochondrial DNA is not a useful marker for cancer detection. Clin. Chem., 50, 1480-1481.
    • (2004) Clin. Chem. , vol.50 , pp. 1480-1481
    • Maekawa, M.1    Taniguchi, T.2    Higashi, H.3    Sugimura, H.4    Sugano, K.5    Kanno, T.6
  • 37
    • 17644398266 scopus 로고    scopus 로고
    • Hemimethylation and non-CpG methylation levels in a promoter region of human LINE-1 (L1) repeated elements
    • Burden,A.F., Manley,N.C., Clark,A.D., Gartler,S.M., Laird,C.D. and Hansen,R.S. (2005) Hemimethylation and non-CpG methylation levels in a promoter region of human LINE-1 (L1) repeated elements. J. Biol. Chem., 280, 14413-14419.
    • (2005) J. Biol. Chem. , vol.280 , pp. 14413-14419
    • Burden, A.F.1    Manley, N.C.2    Clark, A.D.3    Gartler, S.M.4    Laird, C.D.5    Hansen, R.S.6
  • 38
    • 18944387603 scopus 로고    scopus 로고
    • SFRP, a family of new colorectal tumor suppressor candidate genes
    • Suzuki,H., Toyota,M., Nojima,M., Mori,M. and Imai,K. (2005) SFRP, a family of new colorectal tumor suppressor candidate genes. Nippon Rinsho., 63, 707-719.
    • (2005) Nippon Rinsho. , vol.63 , pp. 707-719
    • Suzuki, H.1    Toyota, M.2    Nojima, M.3    Mori, M.4    Imai, K.5
  • 39
  • 42
    • 0036605995 scopus 로고    scopus 로고
    • Expressed CpG island sequence tag microarray for dual screening of DNA hypermethylation and gene silencing in cancer cells
    • Shi,H., Yan,P.S., Chen,C.-M., Rahmatpanah,F., Lofton-Day,C., Caldwell,C.W. and Huang,T.H.-M. (2002) Expressed CpG island sequence tag microarray for dual screening of DNA hypermethylation and gene silencing in cancer cells. Cancer Res., 62, 3214-3220.
    • (2002) Cancer Res. , vol.62 , pp. 3214-3220
    • Shi, H.1    Yan, P.S.2    Chen, C.-M.3    Rahmatpanah, F.4    Lofton-Day, C.5    Caldwell, C.W.6    Huang, T.H.-M.7
  • 45
    • 0348202422 scopus 로고    scopus 로고
    • Analysis and accurate quantification of CpG methylation by MALDI mass spectrometry
    • Tost,J., Schatz,P., Schuster,M., Berlin,K. and Gut,I.G. (2003) Analysis and accurate quantification of CpG methylation by MALDI mass spectrometry. Nucleic Acids Res., 31, e50.
    • (2003) Nucleic Acids Res. , vol.31
    • Tost, J.1    Schatz, P.2    Schuster, M.3    Berlin, K.4    Gut, I.G.5
  • 46
    • 23044514626 scopus 로고    scopus 로고
    • Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells
    • Weber,M., Davies,J.J., Wittig,D., Oakeley,E.J., Haase,M., Lam,W.L. and Schubeler,D. (2005) Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nature Genet., 37, 853-862.
    • (2005) Nature Genet. , vol.37 , pp. 853-862
    • Weber, M.1    Davies, J.J.2    Wittig, D.3    Oakeley, E.J.4    Haase, M.5    Lam, W.L.6    Schubeler, D.7
  • 50
    • 30144433414 scopus 로고    scopus 로고
    • Hypomethylation-linked activation of PAX2 mediates tamoxifen-stimulated endometrial carcinogenesis
    • Wu,H., Chen,Y., Liang,J., Shi,B., Wu,G., Zhang,Y., Wang,D., Li,R., Yi,X., Zhang,H. et al. (2005) Hypomethylation-linked activation of PAX2 mediates tamoxifen-stimulated endometrial carcinogenesis. Nature, 438, 981-987.
    • (2005) Nature , vol.438 , pp. 981-987
    • Wu, H.1    Chen, Y.2    Liang, J.3    Shi, B.4    Wu, G.5    Zhang, Y.6    Wang, D.7    Li, R.8    Yi, X.9    Zhang, H.10


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