Oligonucleotide-based microarray for DNA methylation analysis: Principles and applications

Huidong Shi, Sabine Maier, Inko Nimmrich, Pearlly S. Yan, Charles W. Caldwell, Alexander Olek, Tim Hui Ming Huang

Research output: Contribution to journalReview articlepeer-review

103 Scopus citations


Gene silencing via promoter CpG island hypermethylation offers tumor cells growth advantages. This epigenetic event is pharmacologically reversible, and uncovering a unique set of methylation-silenced genes in tumor cells can bring a new avenue to cancer treatment. However, high-throughput tools capable of surveying the methylation status of multiple gene promoters are needed for this discovery process. Herein we describe an oligonucleotide-based microarray technique that is both versatile and sensitive in revealing hypermethylation in defined regions of the genome. DNA samples are bisulfite-treated and PCR-amplified to distinguish CpG dinucleotides that are methylated from those that are not. Fluorescently labeled PCR products are hybridized to arrayed oligonucleotides that can discriminate between methylated and unmethylated alleles in regions of interest. Using this technique, two clinical subtypes of non-Hodgkin's lymphomas, mantle cell lymphoma, and grades 1/11 follicular lymphoma, were further separated based on the differential methylation profiles of several gene promoters. Work is underway in our laboratory to extend the interrogation power of this microarray system in multiple candidate genes. This novel tool, therefore, holds promise to monitor the outcome of various epigenetic therapies on cancer patients.

Original languageEnglish (US)
Pages (from-to)138-143
Number of pages6
JournalJournal of cellular biochemistry
Issue number1
StatePublished - Jan 1 2003
Externally publishedYes


  • Cancer
  • CpG islands
  • DNA methylation
  • Oligonucleotide microarray

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Cell Biology


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