title: Microarray-based methylation analysis using dual-color fluorescence hybridization.
abstract: BACKGROUND
  Aberrant DNA methylation of CpG sites is among the earliest and most frequent alterations in cancer. It is of great importance to develop simple, high-throughput and quantitative methods for methylation detection.
  
  
  METHODS
  A high-throughput methylation analysis method has been developed based on microarray and dual-color fluorescence hybridization. The genomic DNA was treated with bisulfite, resulting in conversion of non-methylated cytosine, but not methylated cytosine, into uracil within CpG islands of interest. PCR products of the treated genomic templates were spotted and immobilized onto a poly-l-lysine coated glass slide to fabricate a microarray and then interrogated by hybridization with dual-color probes to determine the methylation status. The hybridized signals were obtained with a scanner and the results were analyzed with the software Genepix Pro 3.0.
  
  
  RESULTS
  The methylation status of the CpG islands of IGFBP7 gene has been successfully evaluated by the microarray method for twenty-seven samples. All the investigated samples, including twenty human breast tumor tissues, six corresponding normal human breast tissues and one liver cell line, all CpG sites were found completely methylated.
  
  
  CONCLUSIONS
  The microarray technology has been proven to have potential for high-throughput detection of the methylation status for a given gene in multi-genomic samples, which could be a novel approach for rapidly screening DNA methylation marker for early stage cancer diagnosis.
authors.affiliation: State Key Laboratory of Bioelectronics, Southeast University, Nanjing, 210096, China.
authors.forename: Dongrui
authors.initials: D
authors.lastname: Zhou
authors.forename: Wanqiong
authors.initials: W
authors.lastname: Qiao
authors.forename: Yuan
authors.initials: Y
authors.lastname: Wan
authors.forename: Zuhong
authors.initials: Z
authors.lastname: Lu
mesh_terms: D001483:Base Sequence; D001943:Breast Neoplasms / Q000737:chemistry / Q000235:genetics; D019175:DNA Methylation; D004273:DNA, Neoplasm / Q000032:analysis; D005260:Female; D005453:Fluorescence; D006801:Humans; D015335:Molecular Probes; D008969:Molecular Sequence Data; D009693:Nucleic Acid Hybridization / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D014407:Tumor Cells, Cultured
chemical_list: D004273:DNA, Neoplasm; D015335:Molecular Probes