Table 2.

Summary of some major methods for profiling DNA methylation.

Methodology	Examples	Advantages	Major limitations	Ref.
DNA microarray based on methylation-sensitive restriction	DMH	The first isoschizomers-based (BstUI and HpaII) microarray for analysis of hypermethylated CGIs in cancer genome	BstUI restriction sites mainly distribute in CGIs with a poor coverage for CpG sites in other genomic regions	[22,32–34]
	HELP	Less bias toward CGIs; better coverage on genomic regions with low CpG density	Not for detection of DNA hypermethylation in genome	[37]
	McrBC	Higher restriction sensitivity than that of other methylation-sensitive enzymes; preferentially digests densely methylated genomic regions, such as CGIs and repetitive sequences	Compromised annotation for the genomic locations in data analysis	[38]
	CHARM (based on McrBC)	With the improvement of statistical procedures and array design algorithm; less bias toward CGI; better location annotation and highly quantitative.	Relatively lower resolution than that in sequencing-based technology	[39,40]
Allele-specific methylation on microarray	MSNP	Detection of allele-specific DNA methylation at imprinted and nonimprinted loci; measurement of copy number aberrations and loss of heterozygosity at the same time	May lose DNA methylation information for the genomic region that are not covered by SNP microarray platform	[49,50]
DNA microarray based on affinity purification	MeDIP and MIRA	Efficient technologies for detection of highly methylated CpG sites in the genome, such as CGIs and repetitive sequences	Less sensitive to genomic regions containing low evel of DNA methylation	[24,60,61]
Next-generation sequencing	RRBS;Padlock probes; MeDIP-Seq; MIRA-Seq; Direct end sequencing	RRBS and padlock approaches are high-throughput and genome-wide bisulfite sequencing platforms; all methods based on next-generation sequencing provide much higher resolution for detecting DNA methylation	The cost remains a major concern for the whole-genome sequencing at this stage	[71,73,74]
Other technologies	MethyLight™ and Sequenom MassArray	Both methods are suitable for quantitative methylation profiling at multiple loci with large sample size	Only cover limited loci	[81–86]

CGI: CpG island; CHARM: Comprehensive high-throughput arrays for relative methylation; CpG: Cytosine–phosphate–guanine; DMH: Differential methylation hybridization; HELP: HpaII tiny fragment enrichment by ligation-mediated PCR; MeDIP: Methylated DNA immunoprecipitation; MIRA: Methylated-CpG island recovery assay; MSNP: Methylation sensitive SNP chip analysis; RRBS: Reduced representation bisulfite sequencing.