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Background  To detect genes correlated with hepatocellular carcinoma (HCC), we developed a triple combination array consisting of methylation array, gene expression array and single nucleotide polymorphism (SNP) array analysis.    Methods  A surgical specimen obtained from a 68-year-old female HCC patient was analyzed by triple combination array, which identified doublecortin domain-containing 2 ( DCDC2 ) as a candidate tumor suppressor gene of HCC. Subsequently, samples from 48 HCC patients were evaluated for their  DCDC2  methylation and expression status using methylation specific PCR (MSP) and semi-quantitative reverse transcriptase (RT) PCR, respectively. Then, we investigated the relationship between clinicopathological factors and methylation status of  DCDC2 .    Results   DCDC2  was revealed to be hypermethylated (methylation value 0.846, range 0–1.0) in cancer tissue, compared with adjacent normal tissue (0.212) by methylation array in the 68-year-old female patient. Expression array showed decreased expression of  DCDC2  in cancerous tissue. SNP array showed that the copy number of chromosome 6p22.1, in which  DCDC2  resides, was normal. MSP revealed hypermethylation of the promoter region of  DCDC2  in 41 of the tumor samples.  DCDC2  expression was significantly decreased in the cases with methylation ( P  = 0.048). Furthermore, the methylated cases revealed worse prognosis for overall survival than unmethylated cases ( P  = 0.048).    Conclusions  The present study indicates that triple combination array is an effective method to detect novel genes related to HCC. We propose that  DCDC2  is a tumor suppressor gene of HCC.

journal of experimental and clinical cancer research

Detection of doublecortin domain-containing 2 (DCDC2), a new candidate tumor suppressor gene of hepatocellular carcinoma, by triple combination array analysis