Methylation-specific oligonucleotide microarray: A new potential for high-throughput methylation analysis

Raad S. Gitan, Huidong Shi, Chuan Mu Chen, Pearlly S. Yan, Tim Hui Ming Huang

Research output: Contribution to journalArticle

252 Citations (Scopus)

Abstract

Oligonucleotide microarray-based hybridization is an emerging technology for genome-wide detection of DNA variations. We have extended this principle and developed a novel approach, called methylation-specific oligonucleotide (MSO) microarray, for detecting changes of DNA methylation in cancer. The method uses bisulfite-modified DNA as a template for PCR amplification, resulting in conversion of unmethylated cytosine, but not methylated cytosine, into thymine within CpG islands of interest. The amplified product, therefore, may contain a pool of DNA fragments with altered nucleotide sequences due to differential methylation status. A test sample is hybridized to a set of oligonucleotide (19-23 nucleotides in length) arrays that discriminate methylated and unmethylated cytosine at specific nucleotide positions, and quantitative differences in hybridization are determined by fluorescence analysis. A unique control system is also implemented to test the accuracy and reproducibility of oligonucleotides designed for microarray hybridization. This MSO microarray was applied to map methylated CpG sites within the human estrogen receptor α (ERα) gene CpG island in breast cancer cell lines, normal fibroblasts, breast tumors, and normal controls. Methylation patterns of the breast cancer cell lines, determined by MSO microarray, were further validated by bisulfite nucleotide sequencing (P<0.001). This proof-of-principle study shows that MSO microarray is a promising technique for mapping methylation changes in multiple CpG island loci and for generating epigenetic profiles in cancer.

Original languageEnglish (US)
Pages (from-to)158-164
Number of pages7
JournalGenome Research
Volume12
Issue number1
DOIs
StatePublished - Jan 26 2002

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Oligonucleotide Array Sequence Analysis
Methylation
CpG Islands
Cytosine
Nucleotides
Breast Neoplasms
DNA
Cell Line
Thymine
DNA Methylation
Epigenomics
Oligonucleotides
Estrogen Receptors
Neoplasms
Fibroblasts
Fluorescence
Genome
Technology
Polymerase Chain Reaction
Genes

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Methylation-specific oligonucleotide microarray : A new potential for high-throughput methylation analysis. / Gitan, Raad S.; Shi, Huidong; Chen, Chuan Mu; Yan, Pearlly S.; Huang, Tim Hui Ming.

In: Genome Research, Vol. 12, No. 1, 26.01.2002, p. 158-164.

Research output: Contribution to journalArticle

Gitan, Raad S. ; Shi, Huidong ; Chen, Chuan Mu ; Yan, Pearlly S. ; Huang, Tim Hui Ming. / Methylation-specific oligonucleotide microarray : A new potential for high-throughput methylation analysis. In: Genome Research. 2002 ; Vol. 12, No. 1. pp. 158-164.
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