title: Microarray-based method to analyze methylation status of E-cadherin gene in leukemia.
abstract: BACKGROUND
  Aberrant DNA methylation of the CpG sites of the tumor suppressor gene is closely associated with carcinogenesis. Recently, several studies have indicated the aberrant methylation of E-cadherin gene could be a potential marker for leukemic patients.
  
  
  METHODS
  We used bisulfite-modified DNA as a template for PCR amplification, resulting in conversion of unmethylated, but not methylated, cytosine into thymine within CpG islands of interest. The amplified product containing a pool of DNA fragments with altered nucleotide sequences was then hybridized with an oligonucleotide-based microarray. Five sets of oligonucleotide probes were designed to detect the methylation patterns of E-cadherin gene CpG islands in leukemia samples. The results were further validated by methylation-specific PCR (MSP).
  
  
  RESULTS
  We found that all leukemia samples were methylated at different levels within the target sequences. The specific regions (the CpG sites #16-19 and #20-22) were revealed as hotspots for methylation in leukemic patients. These results showed that the microarray assay could successfully detect methylation changes of E-cadherin gene in leukemia quantitatively.
  
  
  CONCLUSIONS
  The oligonucleotide-based microarray can be a quick and reliable tool to map methylation status in CpG islands. This established microarray could be potentially useful for clinical researches and diagnosis.
authors.affiliation: State Key Laboratory of Bioelectronics, Department of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
authors.forename: Wenli
authors.initials: W
authors.lastname: Zheng
authors.forename: Yan
authors.initials: Y
authors.lastname: Wang
authors.forename: Junfeng
authors.initials: J
authors.lastname: Luo
authors.forename: Fan
authors.initials: F
authors.lastname: Zhang
authors.forename: Baoan
authors.initials: B
authors.lastname: Chen
authors.forename: Zuhong
authors.initials: Z
authors.lastname: Lu
mesh_terms: D015820:Cadherins / Q000235:genetics*; D019175:DNA Methylation; D017931:DNA Primers; D006801:Humans; D007938:Leukemia / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D016133:Polymerase Chain Reaction
chemical_list: D015820:Cadherins; D017931:DNA Primers