Fig. 1

Pipeline to select candidate methylation markers using The Cancer Genome Atlas (TCGA) database. Marker discovery is based on a selection procedure using methylation data (right section) and gene expression data (left section). The DNA methylation analysis resulted in a list of Infinium 450 k probes that were: (1) located in promoter CpG islands, (2) unmethylated in normal colon tissue, and (3) hypermethylated in tumor samples over all four stages cancer development. This list was compared with a list of genes downregulated in tumor compared to normal samples, and we checked the methylation status of the remaining probes in normal samples from 14 different cancer types, resulting in a list of 221 genes. Finally, we designed and tested primers for the probes with the highest sensitivity and specificity based on the TCGA data, resulting in the top five potential early detection markers for CRC