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)

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]