Comprehensive high-throughput arrays for relative methylation (CHARM)

Genome Research

Volumn 18, Issue 5, 2008, Pages 780-790

  Irizarry, Rafael A ^a   Ladd Acosta, Christine ^b   Carvalho, Benilton ^a   Wu, Hao ^a   Brandenburg, Sheri A ^b   Jeddeloh, Jeffrey A ^c,d   Wen, Bo ^b   Feinberg, Andrew P ^b  

^a JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH   (United States)

^b JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c Orion Genomics   (United States)

^d NimbeleGen Systems Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CPG ISLAND; DNA METHYLATION; EPIGENETICS; FRACTIONATION; GENE AMPLIFICATION; GENE LOCATION; GENE LOCUS; GENOMICS; HIGH THROUGHPUT SCREENING; HUMAN; HUMAN CELL; IMMUNOPRECIPITATION; METHYLATION; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PYROSEQUENCING; QUANTITATIVE ANALYSIS; SENSITIVITY AND SENSIBILITY; STATISTICAL ANALYSIS; VALIDATION PROCESS;

BIAS (EPIDEMIOLOGY); CPG ISLANDS; DNA METHYLATION; GENOME, HUMAN; GENOMICS; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REFERENCE STANDARDS; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY;

EID: 43149098062     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.7301508     Document Type: Article

References (35)

1. Allinen, M., Beroukhim, R., Cai, L., Brennan, C., Lahti-Domenici, J., Huang, H., Porter, D., Hu, M., Chin, L., Richardson, A., et al. 2004. Molecular characterization of the tumor microenvironment in breast cancer. Cancer Cell 6: 17-32.
2. Allison, D.B., Cui, X., Page, G.P., and Sabripour, M. 2006. Microarray data analysis: From disarray to consolidation and consensus. Nat. Rev. Genet. 7: 55-65.
3. Bibikova, M., Lin, Z., Zhou, L., Chudin, E., Garcia, E.W., Wu, B., Doucet, D., Thomas, N.J., Wang, Y., Vollmer, E., et al. 2006. High-throughput DNA methylation profiling using universal bead arrays. Genome Res. 16: 383-393.
4. Bird, A.P., Taggart, M.H., Nicholls, R.D., and Higgs, D.R. 1987. Non-methylated CpG-rich islands at the human alpha-globin locus: Implications for evolution of the alpha-globin pseudogene. EMBO J. 6: 999-1004.
5. Bolstad, B.M., Irizarry, R.A., Astrand, M., and Speed, T.P. 2003. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185-193.
6. Callinan, P.A. and Feinberg, A.P. 2006. The emerging science of epigenomics. Hum. Mol. Genet. 15: R95-R101. doi: 10.1093/hmg/ddl095.
7. Dupont, J.M., Tost, J., Jammes, H., and Gut, I.G. 2004. De novo quantitative bisulfite sequencing using the pyrosequencing technology. Anal. Biochem. 333: 119-127.
8. Eads, C.A., Danenberg, K.D., Kawakami, K., Saltz, L.B., Blake, C., Shibata, D., Danenberg, P.V., and Laird, P.W. 2000. MethyLight: A high-throughput assay to measure DNA methylation. Nucleic Acids Res. 28: e32. doi: 10.1093/nar/28.8.e32.
9. Eckhardt, F., Lewin, J., Cortese, R., Rakyan, V.K., Attwood, J., Burger, M., Burton, J., Cox, T.V., Davies, R., Down, T.A., et al. 2006. DNA methylation profiling of human chromosomes 6, 20 and 22. Nat. Genet. 38: 1378-1385.
10. Esteller, M. 2006. Epigenetics provides a new generation of oncogenes and tumour-suppressor genes. Br. J. Cancer 94: 179-183.
11. Feinberg, A.P. 2001. Methylation meets genomics. Nat. Genet. 27: 9-10.
12. Gitan, R.S., Shi, H., Chen, C.M., Yan, P.S., and Huang, T.H. 2002. Methylation-specific oligonucleotide microarray: A new potential for high-throughput methylation analysis. Genome Res. 12: 158-164.
13. Hardle, W. and Steiger, W. 1995. Algorithm AS 296: Optimal median smoothing. Appl. Stat. 44: 258-264.
14. Irizarry, R.A., Wu, Z., and Jaffee, H.A. 2006. Comparison of Affymetrix GeneChip expression measures. Bioinformatics 22: 789-794.
15. Jiang, G., Yang, F., Sanchez, C., and Ehrlich, M. 2004. Histone modification in constitutive heterochromatin versus unexpressed euchromatin in human cells. J. Cell. Biochem. 93: 286-300.
16. Jones, P.A. and Baylin, S.B. 2007. The epigenomics of cancer. Cell 128: 683-692.
17. Kerr, M.K. and Churchill, G.A. 2001. Experimental design for gene expression microarrays. Biostatistics 2: 183-201.
18. Khulan, B., Thompson, R.F., Ye, K., Fazzari, M.J., Suzuki, M., Stasiek, E., Figueroa, M.E., Glass, J.L., Chen, Q., Montagna, C., et al. 2006. Comparative isoschizomer profiling of cytosine methylation: The HELP assay. Genome Res. 16: 1046-1055.
19. Ladd-Acosta, C.P.J., Sabunciyan, S., Yolken, R., Webster, M., Dinkins, T., Callinan, P.A., Fan, J.-B., Potash, J.B., and Feinberg, A.P. 2007. DNA methylation signatures within the human brain. Am. J. Hum. Genet. 81: 1304-1315.
20. Lippman, Z., Gendrel, A.V., Black, M., Vaughn, M.W., Dedhia, N., McCombie, W.R., Lavine, K., Mittal, V., May, B., Kasschau, K.D., et al. 2004. Role of transposable elements in heterochromatin and epigenetic control. Nature 430: 471-476.
21. Martienssen, R.A., Doerge, R.W., and Colot, V. 2005. Epigenomic mapping in Arabidopsis using tiling microarrays. Chromosome Res. 13: 299-308.
22. Mikkelsen, T.S., Ku, M., Jaffe, D.B., Issac, B., Lieberman, E., Giannoukos, G., Alvarez, P., Brockman, W., Kim, T.K., Koche, R.P., et al. 2007. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448: 553-560.
23. Onyango, P., Miller, W., Lehoczky, J., Leung, C.T., Birren, B., Wheelan, S., Dewar, K., and Feinberg, A.P. 2000. Sequence and comparative analysis of the mouse 1-megabase region orthologous to the human 11p15 imprinted domain. Genome Res. 10: 1697-1710.
24. Ordway, J.M., Bedell, J.A., Citek, R.W., Nunberg, A., Garrido, A., Kendall, R., Stevens, J.R., Cao, D., Doerge, R.W., Korshunova, Y., et al. 2006. Comprehensive DNA methylation profiling in a human cancer genome identifies novel epigenetic targets. Carcinogenesis 27: 2409-2423.
25. Rakyan, V.K., Hildmann, T., Novik, K.L., Lewin, J., Tost, J., Cox, A.V., Andrews, T.D., Howe, K.L., Otto, T., Olek, A., et al. 2004. DNA methylation profiling of the human major histocompatibility complex: A pilot study for the human epigenome project. PLoS Biol. 2: e405. doi: 10.1371/journal.pbio.0020405.
26. Reinhold, W.C., Reimers, M.A., Maunakea, A.K., Kim, S., Lababidi, S., Scherf, U., Shankavaram, U.T., Ziegler, M.S., Stewart, C., Kouros-Mehr, H., et al. 2007. Detailed DNA methylation profiles of the E-cadherin promoter in the NCI-60 cancer cells. Mol. Cancer Ther. 6: 391-403.
27. Rhee, I., Bachman, K.E., Park, B.H., Jair, K.W., Yen, R.W., Schuebel, K.E., Cui, H., Feinberg, A.P., Lengauer, C., Kinzler, K.W., et al. 2002. DNMT1 and DNMT3b cooperate to silence genes in human cancer cells. Nature 416: 552-556.
28. Rosa, A.L., Wu, Y.Q., Kwabi-Addo, B., Coveler, K.J., Reid Sutton, V., and Shaffer, L.G. 2005. Allele-specific methylation of a functional CTCF binding site upstream of MEG3 in the human imprinted domain of 14q32. Chromosome Res. 13: 809-818.
29. Selzer, R.R., Richmond, T.A., Pofahl, N.J., Green, R.D., Eis, P.S., Nair, P., Brothman, A.R., and Stallings, R.L. 2005. Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.
30. Sutherland, E., Coe, L., and Raleigh, E.A. 1992. McrBC: A multisubunit GTP-dependent restriction endonuclease. J. Mol. Biol. 225: 327-348.
31. Tukey, J. 1977. Exploratory data analysis. Addison-Wesley, Reading, MA.
32. 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. Nat. Genet. 37: 853-862.
33. Wu, Z. and Irizarry, R.A. 2005. Stochastic models inspired by hybridization theory for short oligonucleotide arrays. J. Comput. Biol. 12: 882-893.
34. Xiong, Z. and Laird, P.W. 1997. COBRA: A sensitive and quantitative DNA methylation assay. Nucleic Acids Res. 25: 2532-2534.
35. Yang, Y.H., Dudoit, S., Luu, P., Lin, D.M., Peng, V., Ngai, J., and Speed, T.P. 2002. Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 30: e15. doi: 10.1093/nar/30.4.e15. 791-801