Table 1.

The main methodologies used in DNA methylation analysis

Sequence-specific methylation

Quantitative methylation-specific PCR (QMSP)

Methylation-sensitive restriction enzyme analysis

Sensitive restriction-multiplex PCR

Combined bisulfite restriction analysis (COBRA)

Bisulfite sequencing

Pyrosequencing

Multiplex ligation-dependent probe amplification (MLPA)

Mass array analysis

Global methylation

Restriction landmark genomic scanning (RGLS)

Arbitrarily primed methylation-sensitive PCR (AP-MSP)

Methylated CpG island recovery assay (MIRA)

Differential methylation hybridization (DMH)

Analysis of intermethylated sites (AIMS)

Methylated DNA immunoprecipitation (MeDIP)

Whole-genome shotgun bisulfite sequencing (WGSBS)