To discover novel markers that are specific for certain stages of cancer with a high specificity selleck kinase inhibitor and sensitivity, large scale screening methods were developed such as Restriction Landmark Genomic Scanning, Differen tial Methylation Hybridization, Illumina Golden Gate Methylation, microarray based Integrated Analysis of Methylation by Isoschizomers and MeDIP in combination with methylation specific oli gonucleotide microarray. These approaches demon strated that large scale screening techniques have a large potential to find novel methylation targets in a whole range of cancers. To identify cancer related hypermethyl ated genes, also pharmacological unmasking expression microarray approaches were suited.

In this approach, the re activation of gene expression using microarray analysis was studied during functional reversal of DNA methylation and histone acetylation in cancer cell lines using demethylating agents and histone deacetylase inhibitors. This methodology generally results in a list of several hundreds of candidate genes. Although the analy sis of the promoter is used to narrow down the number of candidate genes, the number list is still too large. This methodology has proven relevant as its application resulted in the identifi cation of new potential methylated genes. However, the initial large scale screening approach will also detect many genes that are not directly methylation targets themselves Entinostat but become re activated due to the re expression of for instance transcription factors. Fur thermore, in most studies only re expression data after demethylation in cell lines were used.

Smiraglia and co workers calculated that more than 57% of the loci methylated in cell lines were never methylated in 114 pri mary cancers of different malignancy http://www.selleckchem.com/products/BIBF1120.html types. The small number of cell lines used to identify methylated genes does not allow to draw conclusions on the relevance of such cancer specific genes without testing a large series of primary tumours, which is not done in most studies. Finally, the completion of the sequence of the human genome provided information on genes, promoter gene structure, CG content and chromosomal localization. These data are useful to define criteria for the candidate genes to act as appropriate targets for DNA methylation.