Parallel assessment of CpG methylation by two-color hybridization with oligonucleotide arrays

Robert P. Balog, Y. Emi Ponce De Souza, Hue M. Tang, Gina M. DeMasellis, Boning Gao, Adrian Avila, Desmond J. Gaban, David Mittelman, John D. Minna, Kevin J. Luebke, Harold R. Garner

Research output: Contribution to journalArticlepeer-review

33 Scopus citations


We have developed a method for the parallel analysis of multiple CpG sites in genomic DNA for their state of methylation. Hypermethylation of CpG islands within the promoters and 5′ exons of genes has been found to be a mechanism of transcriptional inactivation associated with a variety of tumors. The method that we developed relies on the differential reactivity of methylated and unmethylated cytosines with sodium bisulfite, which exclusively converts unmethylated cytosines to deoxyuracils. The resulting sequence changes are determined with single-nucleotide resolution by hybridization to an oligonucleotide array. Cohybridization with a reference sample containing a different label provides an internal standard for assessment of methylation state. This method provides advantages in parallelism over existing methods of methylation analysis. We have demonstrated this technique with a region from the promoter of the tumor suppressor gene p16, which is hypermethylated in many cancers.

Original languageEnglish (US)
Pages (from-to)301-310
Number of pages10
JournalAnalytical biochemistry
Issue number2
StatePublished - Oct 15 2002


  • CpG island
  • Hypermethylation
  • Oligonucleotide array
  • Sodium bisulfite
  • Tumor suppressor

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Molecular Biology
  • Cell Biology


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