Table 1 Methods of detection for methylated DNA sequences

Methylation-specific PCR

MSP

Non-quantitative; quick way to determine if gene is methylated after sodium bisulfite modification

^{36, 37}

Quantitative multiplex methylation-specific PCR

QM-MSP or MethyLight

Quantitatively detects methylated alleles and can differentiate between monoallelic and biallelic sequences

^{38, 39}

McrBC-methylation-sensitive-arbitrarily-primed PCR

McrBC-msAP-PCR

Detects band intensity of methylated sites using enzyme McrBC

⁴⁰

Methylated CpG island recovery assay

MIRA

Array based; uses genomic DNA to detect methylated sites

^{41, 42}

Combined bisulfite restriction analysis

COBRA

Combines PCR and restriction enyzme analysis to detect methylated sites

⁴³

Differential methylation hybridization

DMH

Array based; can analyze>50 000 genomic fragments for methylation at once

⁴⁴

Microarray methylation assessment of a single mass

MMASS

Array based; compares genome-wide methylated to unmethylated sequences in a single sample

⁴⁵

Methylation target array

MTA

Array based; detects hypermethylation of multiple loci in a variety of tumors

⁴⁶