Methods for detecting DNA methylation in tumors: From bench to bedside

Feinberg, 2006, The epigenetic progenitor origin of human cancer, Nat. Rev. Genet., 7, 21, 10.1038/nrg1748

Baylin, 2006, Epigenetic gene silencing in cancer - a mechanism for early oncogenic pathway addiction?, Nat. Rev. Cancer, 6, 107, 10.1038/nrc1799

Jones, 2002, The fundamental role of epigenetic events in cancer, Nat. Rev. Genet., 3, 415, 10.1038/nrg816

Jaenisch, 2003, Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals, Nat. Genet., 33, 245, 10.1038/ng1089

Bernstein, 2006, A bivalent chromatin structure marks key developmental genes in embryonic stem cells, Cell, 125, 315, 10.1016/j.cell.2006.02.041

Hong, 2005, Reciprocal binding of CTCF and BORIS to the NY-ESO-1 promoter coincides with derepression of this cancer-testis gene in lung cancer cells, Cancer Res., 65, 7763, 10.1158/0008-5472.CAN-05-0823

Holm, 2005, Global loss of imprinting leads to widespread tumorigenesis in adult mice, Cancer Cell, 8, 275, 10.1016/j.ccr.2005.09.007

Merlo, 1995, 5′ CpG island methylation is associated with transcriptional silencing of the tumour suppressor p16/CDKN2/MTS1 in human cancers, Nat. Med., 1, 686, 10.1038/nm0795-686

Feinberg, 1983, Hypomethylation distinguishes genes of some human cancers from their normal counterparts, Nature, 301, 89, 10.1038/301089a0

Gardiner-Garden, 1987, CpG islands in vertebrate genomes, J. Mol. Biol., 196, 261, 10.1016/0022-2836(87)90689-9

Takai, 2002, Comprehensive analysis of CpG islands in human chromosomes 21 and 22, Proc. Natl. Acad. Sci. USA, 99, 3740, 10.1073/pnas.052410099

Robinson, 2004, Gene-Ontology analysis reveals association of tissue-specific 5′ CpG-island genes with development and embryogenesis, Hum. Mol. Genet., 13, 1969, 10.1093/hmg/ddh207

Bestor, 1992, CpG islands in mammalian gene promoters are inherently resistant to de novo methylation, Genet. Anal. Tech. Appl., 9, 48, 10.1016/1050-3862(92)90030-9

Baylin, 2002, Altered methylation patterns in cancer cell genomes: cause or consequence?, Cancer Cell, 1, 299, 10.1016/S1535-6108(02)00061-2

Bestor, 2003, Unanswered questions about the role of promoter methylation in carcinogenesis, Ann. N. Y. Acad. Sci., 983, 22, 10.1111/j.1749-6632.2003.tb05959.x

Pruitt, 2006, Inhibition of SIRT1 reactivates silenced cancer genes without loss of promoter DNA hypermethylation, PLoS Genet., 2, e40, 10.1371/journal.pgen.0020040

Ayyanathan, 2003, Regulated recruitment of HP1 to a euchromatic gene induces mitotically heritable, epigenetic gene silencing: a mammalian cell culture model of gene variegation, Genes Dev., 17, 1855, 10.1101/gad.1102803

Lee, 2006, Control of developmental regulators by Polycomb in human embryonic stem cells, Cell, 125, 301, 10.1016/j.cell.2006.02.043

Makar, 2003, Active recruitment of DNA methyltransferases regulates interleukin 4 in thymocytes and T cells, Nat. Immunol., 4, 1183, 10.1038/ni1004

Ting, 2006, Differential requirement for DNA methyltransferase 1 in maintaining human cancer cell gene promoter hypermethylation, Cancer Res., 66, 729, 10.1158/0008-5472.CAN-05-1537

Suzuki, 2004, RNA interference-mediated knockdown of DNA methyltransferase 1 leads to promoter demethylation and gene re-expression in human lung and breast cancer cells, Cancer Res., 64, 3137, 10.1158/0008-5472.CAN-03-3046

Robert, 2003, DNMT1 is required to maintain CpG methylation and aberrant gene silencing in human cancer cells, Nat. Genet., 33, 61, 10.1038/ng1068

Jones, 1980, Cellular differentiation, cytidine analogs and DNA methylation, Cell, 20, 85, 10.1016/0092-8674(80)90237-8

Belinsky, 2004, Gene-promoter hypermethylation as a biomarker in lung cancer, Nat. Rev. Cancer, 4, 707, 10.1038/nrc1432

Wistuba, 2006, Lung cancer preneoplasia, Annu. Rev. Pathol. Mech. Dis., 1, 331, 10.1146/annurev.pathol.1.110304.100103

D.S. Shames et al., A genome-wide screen for hypermethylated genes in lung cancer identifies tumor-specific methylation markers for multiple malignancies, PLoS Med. (2006), in press.

Costello, 2000, Aberrant CpG-island methylation has non-random and tumour-type-specific patterns, Nat. Genet., 24, 132, 10.1038/72785

Esteller, 2001, A gene hypermethylation profile of human cancer, Cancer Res., 61, 3225

Issa, 2005, Introduction: emerging role of epigenetic therapy: focus on decitabine, Semin. Hematol., 42, S1, 10.1053/j.seminhematol.2005.05.003

Issa, 2005, Decitabine in chronic leukemias, Semin. Hematol., 42, S43, 10.1053/j.seminhematol.2005.05.005

Weber, 2005, Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells, Nat. Genet., 37, 853, 10.1038/ng1598

Suzuki, 2002, A genomic screen for genes upregulated by demethylation and histone deacetylase inhibition in human colorectal cancer, Nat. Genet., 31, 141, 10.1038/ng892

Karpf, 1999, Inhibition of DNA methyltransferase stimulates the expression of signal transducer and activator of transcription 1, 2, and 3 genes in colon tumor cells, Proc. Natl. Acad. Sci. USA, 96, 14007, 10.1073/pnas.96.24.14007

Kelloff, 2006, Progress in chemoprevention drug development: the promise of molecular biomarkers for prevention of intraepithelial neoplasia and cancer – a plan to move forward, Clin. Cancer Res., 12, 3661, 10.1158/1078-0432.CCR-06-1104

Shivapurkar, 2006, Application of a methylation gene panel by quantitative PCR for lung cancers, Cancer Lett.

Fackler, 2004, Quantitative multiplex methylation-specific PCR assay for the detection of promoter hypermethylation in multiple genes in breast cancer, Cancer Res., 64, 4442, 10.1158/0008-5472.CAN-03-3341

Belinsky, 2006, Promoter hypermethylation of multiple genes in sputum precedes lung cancer incidence in a high-risk cohort, Cancer Res., 66, 3338, 10.1158/0008-5472.CAN-05-3408

Curtis, 2005, DNA methylation analysis in human cancer, Methods Mol. Med., 103, 123

Fraga, 2002, DNA methylation: a profile of methods and applications, Biotechniques, 33, 632, 10.2144/02333rv01

Costello, 2002, Restriction landmark genome scanning, Methods, 27, 144, 10.1016/S1046-2023(02)00067-1

Ehrich, 2005, Quantitative high-throughput analysis of DNA methylation patterns by base-specific cleavage and mass spectrometry, Proc. Natl. Acad. Sci. USA, 102, 15785, 10.1073/pnas.0507816102

Herman, 1996, Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands, Proc. Natl. Acad. Sci. USA, 93, 9821, 10.1073/pnas.93.18.9821

Eads, 2000, MethyLight: a high-throughput assay to measure DNA methylation, Nucleic Acids Res., 28, E32, 10.1093/nar/28.8.e32

Eads, 1999, CpG island hypermethylation in human colorectal tumors is not associated with DNA methyltransferase overexpression, Cancer Res., 59, 2302

Suzuki, 2005, Aberrant methylation profile of human malignant mesotheliomas and its relationship to SV40 infection, Oncogene, 24, 1302, 10.1038/sj.onc.1208263

Shivapurkar, 2004, Presence of simian virus 40 DNA sequences in human lymphoid and hematopoietic malignancies and their relationship to aberrant promoter methylation of multiple genes, Cancer Res., 64, 3757, 10.1158/0008-5472.CAN-03-3307

Shivapurkar, 2005, Novel real-time PCR assay using a universal molecular marker for diagnosis of hematologic cancers, Int. J. Cancer, 116, 656, 10.1002/ijc.21070

Colella, 2003, Sensitive and quantitative universal pyrosequencing methylation analysis of CpG sites, Biotechniques, 35, 146, 10.2144/03351md01

Tost, 2006, Serial pyrosequencing for quantitative DNA methylation analysis, Biotechniques, 40, 721, 10.2144/000112190

Tost, 2003, Analysis and quantification of multiple methylation variable positions in CpG islands by pyrosequencing, Biotechniques, 35, 152, 10.2144/03351md02

Ronaghi, 2001, Pyrosequencing sheds light on DNA sequencing, Genome Res., 11, 3, 10.1101/gr.11.1.3

Uhlmann, 2002, Evaluation of a potential epigenetic biomarker by quantitative methyl-single nucleotide polymorphism analysis, Electrophoresis, 23, 4072, 10.1002/elps.200290023

Dupont, 2004, De novo quantitative bisulfite sequencing using the pyrosequencing technology, Anal. Biochem., 333, 119, 10.1016/j.ab.2004.05.007

Jones, 2005, A blueprint for a human epigenome project: the AACR human epigenome workshop, Cancer Res., 65, 11241, 10.1158/0008-5472.CAN-05-3865

Heisler, 2005, CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome, Nucleic Acids Res., 33, 2952, 10.1093/nar/gki582

Smith, 2006, Epigenetic regulation of the tumor suppressor gene TCF21 on 6q23-q24 in lung and head and neck cancer, Proc. Natl. Acad. Sci. USA, 103, 982, 10.1073/pnas.0510171102

Gius, 2004, Distinct effects on gene expression of chemical and genetic manipulation of the cancer epigenome revealed by a multimodality approach, Cancer Cell, 6, 361, 10.1016/j.ccr.2004.08.029

Sato, 2003, Discovery of novel targets for aberrant methylation in pancreatic carcinoma using high-throughput microarrays, Cancer Res., 63, 3735

Allison, 2006, Microarray data analysis: from disarray to consolidation and consensus, Nat. Rev. Genet., 7, 55, 10.1038/nrg1749

Lodygin, 2005, Functional epigenomics identifies genes frequently silenced in prostate cancer, Cancer Res., 65, 4218, 10.1158/0008-5472.CAN-04-4407

Stresemann, 2006, Functional diversity of DNA methyltransferase inhibitors in human cancer cell lines, Cancer Res., 66, 2794, 10.1158/0008-5472.CAN-05-2821

Smiraglia, 2002, The study of aberrant methylation in cancer via restriction landmark genomic scanning, Oncogene, 21, 5414, 10.1038/sj.onc.1205608

Keshet, 2006, Evidence for an instructive mechanism of de novo methylation in cancer cells, Nat. Genet., 38, 149, 10.1038/ng1719

Fackler, 2006, Quantitative multiplex methylation-specific PCR analysis doubles detection of tumor cells in breast ductal fluid, Clin. Cancer Res., 12, 3306, 10.1158/1078-0432.CCR-05-2733

Goldenberg, 2004, Intraoperative molecular margin analysis in head and neck cancer, Arch. Otolaryngol. Head Neck Surg., 130, 39, 10.1001/archotol.130.1.39

Guo, 2004, Promoter hypermethylation of resected bronchial margins: a field defect of changes?, Clin. Cancer Res., 10, 5131, 10.1158/1078-0432.CCR-03-0763

Matsubayashi, 2006, DNA methylation alterations in the pancreatic juice of patients with suspected pancreatic disease, Cancer Res., 66, 1208, 10.1158/0008-5472.CAN-05-2664

Zochbauer-Muller, 2001, Aberrant promoter methylation of multiple genes in non-small cell lung cancers, Cancer Res., 61, 249