Figure 1.

Schematic diagram of the methylated CpG island amplification microarray (MCAM) method. Enrichment for methylated DNA and reduction of genome complexity is achieved by serial digestion with SmaI (methylation sensitive) and XmaI (methylation insensitive) restriction enzymes, followed by ligation of adaptors and PCR amplification. The resulting amplicons, representative of the methylated fraction of tumor and normal cells, are labeled and co-hybridized in a microarray platform. Image acquisition and data analysis allow identification of methylated and non-methylated genes by comparing intensity values of Cy5 and Cy3 dyes for each pair of tumor and control samples. In this example, the M-A plot of normalized data from the cancer cell line MDA-MB-435 compared to normal peripheral blood is presented, from which amplicons were co-hybridized to a custom Agilent microarray containing 44,000 olinucleotide probes targeting human promoter CpG islands.