High-throughput Methylation Profiling by MCA Coupled to CpG Island Microarray

Overview

Journal Genome Res

Specialty Genetics

Date 2007 Sep 6

PMID 17785535

Citations 71

Authors

Marcos R H Estecio

Pearlly S Yan

Ashraf E K Ibrahim

Carmen S Tellez

Lanlan Shen

Tim H-M Huang

Jean-Pierre J Issa

Affiliations

Soon will be listed here.

Abstract

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.

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