Methylation Analysis technique | Advantages | Limitations | Example | References |
Whole genome bisulfite sequencing (WGBS) | Investigate almost all the CpG sites in the genome | Costly and might cause degradation of DNA after bisulfite treatment | WGBS revealed Breast cancer biomarkers [127] | [128] |
Methylation DNA Immunoprecipitation (MeDIP) | Specific to methylation of cytosine based on the antibody | Cannot identify individual CpG site and mostly biased towards DNA hypermethylation | Methylation analysis using MeDIP technique | [129] |
Comprehensive High Throughput arrays for relative methylation (CHARM) | Examine genome-wide CpG sites regardless of their closeness to the gene or CGIs | Restricted to regions near to recognition sites of enzymes | Altered DNA methylation is found in CGI shore in Colon cancer [130] | [131] |
Illumina Infimium Methylation Assay | A cost-efficient method and require less DNA quantity | Limited because of array designs and degradation of DNA might be possible due to bisulfite treatment | Breast cancer biomarkers identified using microarray [132] | [133] |
TET-assisted Bisulfite Sequencing (TAB) |
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| DNA demethylation levels identified in prenatal germline [134] | [134] |
Reduced Representation Bisulfite Sequencing (RRBS) | High coverage and sensitivity of CGIs | Limited coverage at distal regions and intergenic regions | Liver methylation patterns found [135] | [135] |