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Volumn 6, Issue 6, 2011, Pages 692-702

Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome

Author keywords

Colon cancer; CpG sites; DNA methylation; DNA methyltransferase; Epigenetics; Microarray; Validation

Indexed keywords

CYTOSINE; DNA METHYLTRANSFERASE; GENOMIC DNA; NUCLEOTIDE;

EID: 79958754527     PISSN: 15592294     EISSN: 15592308     Source Type: Journal    
DOI: 10.4161/epi.6.6.16196     Document Type: Article
Times cited : (828)

References (51)
  • 1
    • 33847065486 scopus 로고    scopus 로고
    • The epigenomics of cancer
    • Jones PA, Baylin SB. The epigenomics of cancer. Cell 2007; 128:683-6892.
    • (2007) Cell , vol.128 , pp. 683-6892
    • Jones, P.A.1    Baylin, S.B.2
  • 2
    • 78149478781 scopus 로고    scopus 로고
    • Aberrant epigenetic landscape in cancer: How cellular identity goes awry
    • Berdasco M, Esteller M. Aberrant epigenetic landscape in cancer: how cellular identity goes awry. Dev Cell 2010; 19:698-711.
    • (2010) Dev Cell , vol.19 , pp. 698-711
    • Berdasco, M.1    Esteller, M.2
  • 3
    • 79952384705 scopus 로고    scopus 로고
    • Cancer epigenetics reaches mainstream oncology
    • Rodríguez-Paredes M, Esteller M. Cancer epigenetics reaches mainstream oncology. Nat Med 2011; 17:330-339.
    • (2011) Nat Med , vol.17 , pp. 330-339
    • Rodríguez-Paredes, M.1    Esteller, M.2
  • 4
    • 77957970301 scopus 로고    scopus 로고
    • Epigenetic modifications and human disease
    • Portela A, Esteller M. Epigenetic modifications and human disease. Nat Biotechnol 2010; 28:1057-1068.
    • (2010) Nat Biotechnol , vol.28 , pp. 1057-1068
    • Portela, A.1    Esteller, M.2
  • 5
    • 77957965145 scopus 로고    scopus 로고
    • Epigenomics reveals a functional genome anatomy and a new approach to common disease
    • Feinberg AP. Epigenomics reveals a functional genome anatomy and a new approach to common disease. Nat Biotechnol 2010; 28:1049-1052.
    • (2010) Nat Biotechnol , vol.28 , pp. 1049-1052
    • Feinberg, A.P.1
  • 6
    • 70449725209 scopus 로고    scopus 로고
    • Epigenetic mechanisms in neurological diseases: Genes, syndromes and therapies
    • Urdinguio RG, Sanchez-Mut JV, Esteller M. Epigenetic mechanisms in neurological diseases: genes, syndromes and therapies. Lancet Neurol 2009; 8:1056-1072.
    • (2009) Lancet Neurol , vol.8 , pp. 1056-1072
    • Urdinguio, R.G.1    Sanchez-Mut, J.V.2    Esteller, M.3
  • 7
    • 77956058729 scopus 로고    scopus 로고
    • Epigenetics and cardiovascular disease
    • Ordovás JM, Smith CE. Epigenetics and cardiovascular disease. Nat Rev Cardiol 2010; 7:510-519.
    • (2010) Nat Rev Cardiol , vol.7 , pp. 510-519
    • Ordovás, J.M.1    Smith, C.E.2
  • 8
    • 23744484912 scopus 로고    scopus 로고
    • Profiling DNA methylation patterns using genomic tiling microarrays
    • Lippman Z, Gendrel AV, Colot V, Martienssen R. Profiling DNA methylation patterns using genomic tiling microarrays. Nat Methods 2005; 2:219-224.
    • (2005) Nat Methods , vol.2 , pp. 219-224
    • Lippman, Z.1    Gendrel, A.V.2    Colot, V.3    Martienssen, R.4
  • 10
    • 59149084538 scopus 로고    scopus 로고
    • The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores
    • Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, Onyango P, et al. The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet 2009; 41:178-186.
    • (2009) Nat Genet , vol.41 , pp. 178-186
    • Irizarry, R.A.1    Ladd-Acosta, C.2    Wen, B.3    Wu, Z.4    Montano, C.5    Onyango, P.6
  • 11
    • 0348134871 scopus 로고    scopus 로고
    • Methyl-CpG binding proteins identify novel sites of epigenetic inactivation in human cancer
    • Ballestar E, Paz MF, Valle L, Wei S, Fraga MF, Espada J, et al. Methyl-CpG binding proteins identify novel sites of epigenetic inactivation in human cancer. EMBO J 2003; 22:6335-6345.
    • (2003) EMBO J , vol.22 , pp. 6335-6345
    • Ballestar, E.1    Paz, M.F.2    Valle, L.3    Wei, S.4    Fraga, M.F.5    Espada, J.6
  • 13
    • 23044514626 scopus 로고    scopus 로고
    • Chromosome-wide and promoterspecific analyses identify sites of differential DNA methylation in normal and transformed human cells
    • Weber M, Davies JJ, Wittig D, Oakeley EJ, Haase M, Lam WL, et al. Chromosome-wide and promoterspecific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 2005; 37:853-862.
    • (2005) Nat 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
  • 14
    • 31744433660 scopus 로고    scopus 로고
    • Evidence for an instructive mechanism of de novo methylation in cancer cells
    • Keshet I, Schlesinger Y, Farkash S, Rand E, Hecht M, Segal E, et al. Evidence for an instructive mechanism of de novo methylation in cancer cells. Nat Genet 2006; 38:149-153.
    • (2006) Nat Genet , vol.38 , pp. 149-153
    • Keshet, I.1    Schlesinger, Y.2    Farkash, S.3    Rand, E.4    Hecht, M.5    Segal, E.6
  • 15
    • 34047116826 scopus 로고    scopus 로고
    • Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome
    • Weber M, Hellmann I, Stadler MB, Ramos L, Paabo S, Rebhan M, et al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 2007; 39:457-466.
    • (2007) Nat Genet , vol.39 , pp. 457-466
    • Weber, M.1    Hellmann, I.2    Stadler, M.B.3    Ramos, L.4    Paabo, S.5    Rebhan, M.6
  • 16
    • 46949098742 scopus 로고    scopus 로고
    • A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis
    • Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, et al. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol 2008; 26:779-785.
    • (2008) Nat Biotechnol , vol.26 , pp. 779-785
    • Down, T.A.1    Rakyan, V.K.2    Turner, D.J.3    Flicek, P.4    Li, H.5    Kulesha, E.6
  • 17
    • 49649125042 scopus 로고    scopus 로고
    • Genome-scale DNA methylation maps of pluripotent and differentiated cells
    • Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A, et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 2008; 454:766-770.
    • (2008) Nature , vol.454 , pp. 766-770
    • Meissner, A.1    Mikkelsen, T.S.2    Gu, H.3    Wernig, M.4    Hanna, J.5    Sivachenko, A.6
  • 19
    • 78649969065 scopus 로고    scopus 로고
    • The DNA methylome of human peripheral blood mononuclear cells
    • Li Y, Zhu J, Tian G, Li N, Li Q, Ye M, et al. The DNA methylome of human peripheral blood mononuclear cells. PLoS Biol 2010; 8:1000533.
    • (2010) PLoS Biol , vol.8 , pp. 1000533
    • Li, Y.1    Zhu, J.2    Tian, G.3    Li, N.4    Li, Q.5    Ye, M.6
  • 20
    • 33644649616 scopus 로고    scopus 로고
    • High-throughput DNA methylation profiling using universal bead arrays
    • Bibikova M, Lin Z, Zhou L, Chudin E, Garcia EW, Wu B, et al. High-throughput DNA methylation profiling using universal bead arrays. Genome Res 2006; 16:383-393.
    • (2006) Genome Res , vol.16 , pp. 383-393
    • Bibikova, M.1    Lin, Z.2    Zhou, L.3    Chudin, E.4    Garcia, E.W.5    Wu, B.6
  • 21
    • 70149099610 scopus 로고    scopus 로고
    • Aging and environmental exposures alter tissue-specific DNA methylation dependent upon CpG island context
    • Christensen BC, Houseman EA, Marsit CJ, Zheng S, Wrensch MR, Wiemels JL, et al. Aging and environmental exposures alter tissue-specific DNA methylation dependent upon CpG island context. PLoS Genet 2009; 5:1000602.
    • (2009) PLoS Genet , vol.5 , pp. 1000602
    • Christensen, B.C.1    Houseman, E.A.2    Marsit, C.J.3    Zheng, S.4    Wrensch, M.R.5    Wiemels, J.L.6
  • 22
    • 70450169678 scopus 로고    scopus 로고
    • Epigenetic profiling of somatic tissues from human autopsy specimens identifies tissue- and individual-specific DNA methylation patterns
    • Byun HM, Siegmund KD, Pan F, Weisenberger DJ, Kanel G, Laird PW, et al. Epigenetic profiling of somatic tissues from human autopsy specimens identifies tissue- and individual-specific DNA methylation patterns. Hum Mol Genet 2009; 18:4808-4817.
    • (2009) Hum Mol Genet , vol.18 , pp. 4808-4817
    • Byun, H.M.1    Siegmund, K.D.2    Pan, F.3    Weisenberger, D.J.4    Kanel, G.5    Laird, P.W.6
  • 24
    • 75649133610 scopus 로고    scopus 로고
    • Differential genome-wide array-based methylation profiles in prognostic subsets of chronic lymphocytic leukemia
    • Kanduri M, Cahill N, Göransson H, Enström C, Ryan F, Isaksson A, et al. Differential genome-wide array-based methylation profiles in prognostic subsets of chronic lymphocytic leukemia. Blood 2010; 115:296-305.
    • (2010) Blood , vol.115 , pp. 296-305
    • Kanduri, M.1    Cahill, N.2    Göransson, H.3    Enström, C.4    Ryan, F.5    Isaksson, A.6
  • 25
    • 76249107254 scopus 로고    scopus 로고
    • DNA methylation pattern changes upon long-term culture and aging of human mesenchymal stromal cells
    • Bork S, Pfister S, Witt H, Horn P, Korn B, Ho AD, et al. DNA methylation pattern changes upon long-term culture and aging of human mesenchymal stromal cells. Aging Cell 2010; 9:54-63.
    • (2010) Aging Cell , vol.9 , pp. 54-63
    • Bork, S.1    Pfister, S.2    Witt, H.3    Horn, P.4    Korn, B.5    Ho, A.D.6
  • 27
    • 77950657253 scopus 로고    scopus 로고
    • Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains
    • Rakyan VK, Down TA, Maslau S, Andrew T, Yang TP, Beyan H, et al. Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains. Genome Res 2010; 20:434-439.
    • (2010) Genome Res , vol.20 , pp. 434-439
    • Rakyan, V.K.1    Down, T.A.2    Maslau, S.3    Andrew, T.4    Yang, T.P.5    Beyan, H.6
  • 28
  • 30
    • 0036613250 scopus 로고    scopus 로고
    • A genomic screen for genes upregulated by demethylation and histone deacetylase inhibition in human colorectal cancer
    • Suzuki H, Gabrielson E, Chen W, Anbazhagan R, van Engeland M, Weijenberg MP, et al. A genomic screen for genes upregulated by demethylation and histone deacetylase inhibition in human colorectal cancer. Nat Genet 2002; 31:141-149.
    • (2002) Nat Genet , vol.31 , pp. 141-149
    • Suzuki, H.1    Gabrielson, E.2    Chen, W.3    Anbazhagan, R.4    van Engeland, M.5    Weijenberg, M.P.6
  • 31
    • 0041779528 scopus 로고    scopus 로고
    • Genetic unmasking of epigenetically silenced tumor suppressor genes in colon cancer cells deficient in DNA methyltransferases
    • Paz MF, Wei S, Cigudosa JC, Rodriguez-Perales S, Peinado MA, Huang TH, et al. Genetic unmasking of epigenetically silenced tumor suppressor genes in colon cancer cells deficient in DNA methyltransferases. Hum Mol Genet 2003; 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.6
  • 32
    • 37549066863 scopus 로고    scopus 로고
    • Discovery of epigenetically silenced genes by methylated DNA immunoprecipitation in colon cancer cells
    • 11481-1146
    • Jacinto FV, Ballestar E, Ropero S, Esteller M. Discovery of epigenetically silenced genes by methylated DNA immunoprecipitation in colon cancer cells. Cancer Res 2007; 67:11481-1146.
    • (2007) Cancer Res , vol.67
    • Jacinto, F.V.1    Ballestar, E.2    Ropero, S.3    Esteller, M.4
  • 33
    • 33847763576 scopus 로고    scopus 로고
    • Genetic unmasking of an epigenetically silenced microRNA in human cancer cells
    • Lujambio A, Ropero S, Ballestar E, Fraga MF, Cerrato C, Setién F, et al. Genetic unmasking of an epigenetically silenced microRNA in human cancer cells. Cancer Res 2007; 67:1424-1429.
    • (2007) Cancer Res , vol.67 , pp. 1424-1429
    • Lujambio, A.1    Ropero, S.2    Ballestar, E.3    Fraga, M.F.4    Cerrato, C.5    Setién, F.6
  • 34
    • 34848918829 scopus 로고    scopus 로고
    • Comparing the DNA hypermethylome with gene mutations in human colorectal cancer
    • Schuebel KE, Chen W, Cope L, Glöckner SC, Suzuki H, Yi JM, et al. Comparing the DNA hypermethylome with gene mutations in human colorectal cancer. PLoS Genet 2007; 3:1709-1723.
    • (2007) PLoS Genet , vol.3 , pp. 1709-1723
    • Schuebel, K.E.1    Chen, W.2    Cope, L.3    Glöckner, S.C.4    Suzuki, H.5    Yi, J.M.6
  • 35
    • 78649881517 scopus 로고    scopus 로고
    • CpG island hypermethylation-associated silencing of non-coding RNAs transcribed from ultraconserved regions in human cancer
    • Lujambio A, Portela A, Liz J, Melo SA, Rossi S, Spizzo R, et al. CpG island hypermethylation-associated silencing of non-coding RNAs transcribed from ultraconserved regions in human cancer. Oncogene 2010; 29:6390-6401.
    • (2010) Oncogene , vol.29 , pp. 6390-6401
    • Lujambio, A.1    Portela, A.2    Liz, J.3    Melo, S.A.4    Rossi, S.5    Spizzo, R.6
  • 37
    • 0242552587 scopus 로고    scopus 로고
    • GATA-4 and GATA-5 transcription factor genes and potential downstream antitumor target genes are epigenetically silenced in colorectal and gastric cancer
    • Akiyama Y, Watkins N, Suzuki H, Jair KW, van Engeland M, Esteller M, et al. GATA-4 and GATA-5 transcription factor genes and potential downstream antitumor target genes are epigenetically silenced in colorectal and gastric cancer. Mol Cell Biol 2003; 23:8429-8439.
    • (2003) Mol Cell Biol , vol.23 , pp. 8429-8439
    • Akiyama, Y.1    Watkins, N.2    Suzuki, H.3    Jair, K.W.4    van Engeland, M.5    Esteller, M.6
  • 38
    • 34248531606 scopus 로고    scopus 로고
    • Methylation patterns of IGFBP7 in colon cancer cell lines are associated with levels of gene expression
    • Lin J, Lai M, Huang Q, Ma Y, Cui J, Ruan W. Methylation patterns of IGFBP7 in colon cancer cell lines are associated with levels of gene expression. J Pathol 2007; 212:83-90.
    • (2007) J Pathol , vol.212 , pp. 83-90
    • Lin, J.1    Lai, M.2    Huang, Q.3    Ma, Y.4    Cui, J.5    Ruan, W.6
  • 39
    • 0035890771 scopus 로고    scopus 로고
    • Hypermethylation in human cancers of the RIZ1 tumor suppressor gene, a member of a histone/protein methyltransferase superfamily
    • Du Y, Carling T, Fang W, Piao Z, Sheu JC, Huang S. Hypermethylation in human cancers of the RIZ1 tumor suppressor gene, a member of a histone/protein methyltransferase superfamily. Cancer Res 2001; 61:8094-8099.
    • (2001) Cancer Res , vol.61 , pp. 8094-8099
    • Du, Y.1    Carling, T.2    Fang, W.3    Piao, Z.4    Sheu, J.C.5    Huang, S.6
  • 40
    • 49149121975 scopus 로고    scopus 로고
    • PCDH8, the human homolog of PAPC, is a candidate tumor suppressor of breast cancer
    • Yu JS, Koujak S, Nagase S, Li CM, Su T, Wang X, et al. PCDH8, the human homolog of PAPC, is a candidate tumor suppressor of breast cancer. Oncogene 2008; 27:4657-4665.
    • (2008) Oncogene , vol.27 , pp. 4657-4665
    • Yu, J.S.1    Koujak, S.2    Nagase, S.3    Li, C.M.4    Su, T.5    Wang, X.6
  • 42
    • 49249121155 scopus 로고    scopus 로고
    • Epigenetic silencing of microRNA-34b/c and B-cell translocation gene 4 is associated with CpG island methylation in colorectal cancer
    • Toyota M, Suzuki H, Sasaki Y, Maruyama R, Imai K, Shinomura Y, et al. Epigenetic silencing of microRNA-34b/c and B-cell translocation gene 4 is associated with CpG island methylation in colorectal cancer. Cancer Res 2008; 68:4123-4132.
    • (2008) Cancer Res , vol.68 , pp. 4123-4132
    • Toyota, M.1    Suzuki, H.2    Sasaki, Y.3    Maruyama, R.4    Imai, K.5    Shinomura, Y.6
  • 43
    • 71549121035 scopus 로고    scopus 로고
    • Epigenetic repression of microRNA-129-2 leads to overexpression of SOX4 oncogene in endometrial cancer
    • Huang YW, Liu JC, Deatherage DE, Luo J, Mutch DG, Goodfellow PJ, et al. Epigenetic repression of microRNA-129-2 leads to overexpression of SOX4 oncogene in endometrial cancer. Cancer Res 2009; 69:9038-9046.
    • (2009) Cancer Res , vol.69 , pp. 9038-9046
    • Huang, Y.W.1    Liu, J.C.2    Deatherage, D.E.3    Luo, J.4    Mutch, D.G.5    Goodfellow, P.J.6
  • 45
    • 77952299722 scopus 로고    scopus 로고
    • miR-124 and miR-203 are epigenetically silenced tumor-suppressive microRNAs in hepatocellular carcinoma
    • Furuta M, Kozaki KI, Tanaka S, Arii S, Imoto I, Inazawa J. miR-124 and miR-203 are epigenetically silenced tumor-suppressive microRNAs in hepatocellular carcinoma. Carcinogenesis 2010; 31:766-776.
    • (2010) Carcinogenesis , vol.31 , pp. 766-776
    • Furuta, M.1    Kozaki, K.I.2    Tanaka, S.3    Arii, S.4    Imoto, I.5    Inazawa, J.6
  • 46
    • 77955365635 scopus 로고    scopus 로고
    • Deciphering the cancer imprintome
    • Monk D. Deciphering the cancer imprintome. Brief Funct Genomics 2010; 9:329-339.
    • (2010) Brief Funct Genomics , vol.9 , pp. 329-339
    • Monk, D.1
  • 47
    • 40949121440 scopus 로고    scopus 로고
    • Cancer testis antigens in human melanoma stem cells: Expression, distribution and methylation status
    • Sigalotti L, Covre A, Zabierowski S, Himes B, Colizzi F, Natali PG, et al. Cancer testis antigens in human melanoma stem cells: expression, distribution and methylation status. J Cell Physiol 2008; 215:287-291.
    • (2008) J Cell Physiol , vol.215 , pp. 287-291
    • Sigalotti, L.1    Covre, A.2    Zabierowski, S.3    Himes, B.4    Colizzi, F.5    Natali, P.G.6
  • 48
    • 0037224722 scopus 로고    scopus 로고
    • DNMT1 is required to maintain CpG methylation and aberrant gene silencing in human cancer cells
    • Robert MF, Morin S, Beaulieu N, Gauthier F, Chute IC, Barsalou A, et al. DNMT1 is required to maintain CpG methylation and aberrant gene silencing in human cancer cells. Nat Genet 2003; 33:61-65.
    • (2003) Nat Genet , vol.33 , pp. 61-65
    • Robert, M.F.1    Morin, S.2    Beaulieu, N.3    Gauthier, F.4    Chute, I.C.5    Barsalou, A.6
  • 49
    • 33847293264 scopus 로고    scopus 로고
    • Complete inactivation of DNMT1 leads to mitotic catastrophe in human cancer cells
    • Chen T, Hevi S, Gay F, Tsujimoto N, He T, Zhang B, et al. Complete inactivation of DNMT1 leads to mitotic catastrophe in human cancer cells. Nat Genet 2007; 39:391-396.
    • (2007) Nat Genet , vol.39 , pp. 391-396
    • Chen, T.1    Hevi, S.2    Gay, F.3    Tsujimoto, N.4    He, T.5    Zhang, B.6
  • 50
    • 9744251005 scopus 로고    scopus 로고
    • Biochemistry and biology of mammalian DNA methyltransferases
    • Hermann A, Gowher H, Jeltsch A. Biochemistry and biology of mammalian DNA methyltransferases. Cell Mol Life Sci 2004; 61:2571-2587.
    • (2004) Cell Mol Life Sci , vol.61 , pp. 2571-2587
    • Hermann, A.1    Gowher, H.2    Jeltsch, A.3


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