RT Journal
A1 Estécio, Marcos R.H.
A1 Yan, Pearlly S.
A1 Ibrahim, Ashraf E.K.
A1 Tellez, Carmen S.
A1 Shen, Lanlan
A1 Huang, Tim H.-M.
A1 Issa, Jean-Pierre J.
T1 High-throughput methylation profiling by MCA coupled to CpG island microarray
JF Genome Research 
JO Genome Research 
YR 2007 
FD October 01 
VO 17 
IS 10 
SP 000 
OP 000 
DO 10.1101/gr.6417007 
UL http://genome.cshlp.org/content/early/2007/09/04/gr.6417007.abstract 
AB An abnormal pattern of DNA methylation occurs at specific genes in almost all neoplasms. The lack of high-throughput methods with high specificity and sensitivity to detect changes in DNA methylation has limited its application for clinical profiling. Here we overcome this limitation and present an improved method to identify methylated genes genome-wide by hybridizing a CpG island microarray with amplicons obtained by the methylated CpG island amplification technique (MCAM). We validated this method in three cancer cell lines and 15 primary colorectal tumors, resulting in the discovery of hundreds of new methylated genes in cancer. The sensitivity and specificity of the method to detect hypermethylated loci were 88% and 96%, respectively, according to validation by bisulfite-PCR. Unsupervised hierarchical clustering segregated the tumors into the expected subgroups based on CpG island methylator phenotype classification. In summary, MCAM is a suitable technique to discover methylated genes and to profile methylation changes in clinical samples in a high-throughput fashion.