Figure 1.

Scheme of chromatin conformation assay and microarray analysis. A three-dimensional structure of chromosomes contains loops with an enhancer and promoter regions, whereas the enhancer increases target gene promoter activity. CC capture assay: DNA is cross-linked using formaldehyde, digested, and ligated with the preference of cross-linked fragments. New sequences are formed where the loops have been. These new sequences are predicted via relevance machine vector algorithm. Specific primers to these sequences are synthesised and placed on the DNA microarray, which detects whether the loop was present or not. Resulting markers are analysed using multivariate analysis yielding specific epigenetic signatures for selected patient cohorts.