Abstract Background: Hepatocellular carcinoma (HCC) has a high rate of recurrence and a poor prognosis. To detect genes correlated with HCC, we have developed a new technique, triple combination array analysis, 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 using triple combination array analysis, which identified a candidate cancer-related gene of HCC. Subsequently, samples from nine cell lines and 48 HCC patients were evaluated for their methylation and expression status of the identified gene using methylation-specific polymerase chain reaction (MSP) and quantitative real-time reverse transcriptase PCR, respectively. Results: Using the triple combination array analysis, cyclin J (CCNJ) was detected as a candidate cancer-related gene. CCNJ was located on chromosome 10q24.1 and the copy number, using SNP chip array, revealed no loss of heterozygosity. According to expression array results, The expression of CCNJ in tumor tissue decreased at two points of the expression array chip, and the decreased values of the chip were −1.3 and −2.3. CCNJ was found to be hypermethylated (methylation value 0.906, range 0-1.0) in cancer tissue compared with adjacent normal tissue (0.112) using the methylation array. Using MSP, hypermethylation of the promoter region of CCNJ was shown to occur in 37 (77.1%) tumor samples. CCNJ expression was significantly decreased in cases with methylation (p<0.0001). Furthermore, HCC patients with methylated CCNJ had a significantly worse prognosis for recurrence-free survival (p=0.0353) and tended to have a worse prognosis for overall survival than those with unmethylated CCNJ (p=0.0838). Conclusion: The present study indicates that triple combination array analysis is an effective method to detect novel genes related to HCC. We suggest that CCNJ acts as a cancer-related gene in HCC. Citation Format: Nao Takano, Shuji Nomoto, Mitsuhiro Hishida, Yoshikuni Inokawa, Masamichi Hayashi, Mitsuro Kanda, Yukiyasu Okamura, Yoko Nishikawa, Chie Tanaka, Daisuke Kobayashi, Suguru Yamada, Goro Nakayama, Tsutomu Fujii, Hiroyuki Sugimoto, Masahiko Koike, Michitaka Fujii, Shin Takeda, Yasuhiro Kodera. Detection of the Cyclin J (CCNJ) as a new cancer-related gene in human hepatocellular carcinoma by using a method of triple combination array analysis. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4717. doi:10.1158/1538-7445.AM2014-4717