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Table 1 Recent methodologies applied to whole human genome DNA methylation analysis

From: Tackling the methylome: recent methodological advances in genome-wide methylation profiling

Technique Platform Reference Description
Enzyme-based    
   CHARM Microarray [35] Digestion of methylated DNA is done using the McrBc enzyme, which cuts between two methylated CpG sites. Unprocessed DNA is used as control. Increased sensitivity and specificity of the method is achieved by smoothing the data of neighboring genomic locations.
   HELP Microarray [33] HpaII restriction enzyme is used to eliminate the methylated fraction of the genome, and the enrichment for unmethylated fragments is compared in an array platform with DNA digested with MspI.
   MCAM Microarray [31] The methylated fraction of the genome is selectively enriched by PCR after sequential digestion of the DNA with SmaI and XmaI restriction enzymes. CpG islands are preferentially represented in this method.
   HELP-Seq NextGen [47] The general procedure is done as for standard HELP, and the original adapters are removed by digestion with MspI before sequencing. DNA methylation is measured, and enrichment of HpaII compared to MspI sequences.
   Methyl-Seq NextGen [43] Massively parallel sequencing of HpaII-digested DNA is performed and methylation frequency is inferred from the frequency of tags per regions (fewer tags equals more methylation). The sequencing of MspI-digested DNA is used to identify regions refractory to sequencing, but unlike HELP-Seq, it is not used to calculate the enrichment of HpaII fragments.
   MSCC NextGen [41] The method is similar to Methyl-Seq; however, sequencing of MspI libraries was reported to have little effect on the measurement of methylation and was abolished to reduce costs.
Affinity-based    
   MeDIP Microarray [34] Methylated DNA is captured in using anti-5-methylcytosine antibodies and hybridized in an array platform. In this way, the method is unbiased towards recognition sites like enzyme-based methods, but it has been shown that dense CpG islands are preferentially captured.
   MIRA Microarray [48] Antibodies against methyl-binding domain proteins are used to capture methylated DNA.
   MeDIP-Seq NextGen [49] The procedure is the same as MeDIP, followed by massively parallel sequencing after DNA capture instead of microarray hybridization.
Bisulfite-based    
   MethylC-Seq NextGen [44] The genome is fragmented by sonication, and modified adaptors are ligated to the DNA prior to bisulfite conversion. It is the only truly genome-wide method applied to the human genome at the moment, but the high cost of the method limits its application to large groups of samples.
Padlock,
BSPPs
NextGen [41, 42] Selected targets in the bisulfite-converted genome, typically thousands, are collected using molecular inversion probes. The method is extremely useful when there is interest in highly quantitative analysis of selected loci.