Please cite as: CSH Protocols; 2008; doi:10.1101/pdb.prot4974

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Methylated CpG Island Amplification and Microarray (MCAM) for High-Throughput Analysis of DNA Methylation

Marcos R. H. Estécio1,3, Pearlly S. Yan2, Tim H-M. Huang2, and Jean-Pierre J. Issa1

1 Department of Leukemia, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
2 Human Cancer Genetics Program, Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA

3Corresponding author (mestecio{at}mdanderson.org)


INTRODUCTION

This protocol describes the use of methylated CpG island amplification (MCA) in combination with a microarray platform to analyze genome-wide DNA methylation in a high-throughput fashion. In this approach, termed MCAM, methylated CpG islands are selectively targeted using oligonucleotide adaptors after two rounds of digestion with a combination of methylation-sensitive and methylation-insensitive nucleases. They are then amplified using PCR. The resulting amplicons, representing the methylated fraction of the genome, are labeled with fluorochromes. Subsequently, a comparative hybridization of reference and test samples (typically normal and tumor DNA specimens) is done on a microarray platform.


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