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)