From: Epigenetics of renal cell carcinoma: the path towards new diagnostics and therapeutics
Method | Key features | Advantages | Disadvantages |
---|---|---|---|
Functional epigenomics | Methylated genes are re-expressed in cell lines by treatment with 5-aza-2'-deoxycytidine. Expression arrays determine reactivated genes | Links hypermethylated sites to gene silencing | Correlating correct methylated site to expression regulation is laborious. Cell lines are frequently more methylated than the corresponding tumors. |
Methylation-dependent immunoprecipitation (MeDIP) | Methylated DNA is separated from unmethylated DNA by immunoprecipitation and hybridized to a CpG island microarray | Global analysis; produces quantifiable results | Dependent on good immunoprecipitation efficiency; difficult to determine the extent of methylation across a specific CpG island |
Bead chip 'Infinium' | Bisulfite-modified DNA is hybridized to beads containing DNA oligonucleotides specific to CpG dinucleotide methylation. Single base extension determines methylation state | Global analysis at single CpG sites using targeted probes; quantitative data | Provides data for only one or two CpG dinucleotides per island; further work may be required to determine the extent of methylation at specific sites |
Next-generation sequencing | Combines isolation of methylated DNA using techniques such as MeDIP or restriction digest and high-throughput sequencing. Bisulfite-modified DNA can also be sequenced directly | Statistically robust; high coverage; single nucleotide resolution | Initial set-up costs high; probe design can be challenging |