Table 2.
Genome-wide DNA methylation studies in various cancer types
| Cancer type | Technique used | Notable findings | Reference |
|---|---|---|---|
| Acute myeloid leukemia | Bisulfite Illumina bead array | Genome-wide promoter associated hypermethylation associated with improved patient survival | (Deneberg et al., 2010) |
| Brain cancer | Bisulfite lllumina bead array | Genes hypermethylated in glioblastoma were highly enriched for targets of PRC2 in embryonic stem cells | (Martinez et al., 2009) |
| Brain cancer | MIRA | Hypermethylation of neuronal differentiation genes in astrocytomas | (Wu et al., 2010) |
| Breast cancer | MIRA | Methylation of homeobox and other developmental genes regulated by the Polycomb complex | (Tommasi et al., 2009) |
| Breast cancer | MeDIP | Agglomerative epigenetic aberrations are frequent events in human breast cancer | (Novak et al., 2008) |
| Breast cancer | MeDIP | Interdependence between DNA methylome alterations and morphological changes | (Ruike et al., 2010) |
| Chronic lymphocytic leukemia | MCA | Methylation of LINE and APP was associated with shorter overall survival | (Kuang et al., 2008) |
| Chronic lymphocytic leukemia | Bisulfite Illumina bead array | Possible mechanism for pathogenesis | (Kanduri et al., 2010) |
| Colorectal cancer | MeDIP | Three different methylation epigenotypes exist in colorectal cancer | (Yagi et al., 2010) |
| Esophageal squamous cell carcinoma | HELP | Influence of genetic background on DNA methylation | (Yang et al., 2010) |
| Follicular lymphoma | MCA | Extensive hypermethylation in promoters of Polycomb target genes | (Bennett et al., 2008) |
| Haematological malignancies | MIRA | Methylation status of TFAP2A and EBF2 genes associated with advanced disease in CML | (Dunwell et al., 2010) |
| Head and neck cancer | RLGS | Methylation of genes involved in the transforming growth factor beta signaling pathway | (Bennett et al., 2008) |
| Hematologic neoplasms | Bisulfite Illumina bead array | Methylation of DBC1, DIO3, FZD9, HS3ST2, MOS, and MYOD1 and their role in development of different hematologic neoplasms | (Martin-Subero et al., 2009) |
| Hepatocellular carcinomas | MCA | DNA methylation status was correlated with the cancer-free and overall survival rates of patients | (Arai et al., 2009) |
| Lung cancer | MIRA | Biomarkers for early detection of lung cancer and extensive hypomethylation of repetitive sequences in tumors | (Rauch et al., 2008) |
| Lung cancer | MCA | Differential methylation between mesothelioma and adenocarcinoma | (Goto et al., 2009) |
| Mantle cell lymphoma | HELP | Methylation-based drug targeting | (Leshchenko et al., 2010) |
| Ovarian cancer | Bisulfite Illumina bead array | Diagnostic or risk-prediction of ovarian cancer by blood methylation profiling | (Teschendorff et al., 2009) |
| Pancreatic cancer | MCA | Identification of aberrantly methylated genes in pancreatic cancers | (Omura et al., 2008) |
| Prostate cancer | DMH | Methylation of homeobox or T-box genes | (Kron et al., 2009) |
| Skin cancer | MeDIP | Moderate increases of methylation in early and significantly in advanced-stage melanomas | (Koga et al., 2009) |
| Testicular germ cell tumors | MeDIP | Function of intergenic and intronic DMRs in the regulation of ncRNAs | (Cheung et al., 2010) |
| Urothelial cancer | MCA | DNA methylation as indicator for carcinogenetic risk estimation | (Nishiyama et al., 2010) |