title: Identification of allelic expression imbalance genes in human hepatocellular carcinoma through massively parallel DNA and RNA sequencing.
abstract: Hepatocellular carcinoma (HCC) is a common malignant tumor worldwide. The prognosis and treatment of this disease have changed little in recent decades because the mechanisms underlying most events of this disease remain obscure. Allelic variation of gene expression is associated with many important biological processes, which provide a new perspective to understand HCC pathogenesis at the molecular level. To identify allelic expression imbalance (AEI) genes in HCCs, we developed a computational method that considered accurate mapping and vigorous AEI detection using paired DNA-seq and RNA-seq data. We analyzed the DNA-seq and RNA-seq data derived from two HCC samples and two cell lines. By applying a strict criterion, a total of 203 tumor-specific AEI genes were identified with high confidence, and several genes have been reported to be associated with the migration or proliferation of cancer cells, such as the genes RELN and DHRS3. In addition, we also found some novel AEI genes in HCCs, such as HNRNPR and PTAFR. Our study provides new insight into AEI events that may contribute to understanding gene expression regulation, cell proliferation and migration, and tumorigenesis.
authors.affiliation: Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, No. 800, Dongchuan Road, Minhang District, Shanghai, 200240, China.|National Engineering Center for Biochip at Shanghai, Shanghai, 201203, China.
authors.forename: Qiudao
authors.initials: Q
authors.lastname: Wang
authors.affiliation: Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, No. 800, Dongchuan Road, Minhang District, Shanghai, 200240, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: An
authors.affiliation: National Engineering Center for Biochip at Shanghai, Shanghai, 201203, China.
authors.forename: Qing
authors.initials: Q
authors.lastname: Yuan
authors.affiliation: National Engineering Center for Biochip at Shanghai, Shanghai, 201203, China.
authors.forename: Yao
authors.initials: Y
authors.lastname: Qi
authors.affiliation: National Engineering Center for Biochip at Shanghai, Shanghai, 201203, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Ou
authors.affiliation: Peking University Shenzhen Hospital, Shenzhen, 518036, China.
authors.forename: Junhui
authors.initials: J
authors.lastname: Chen
authors.affiliation: Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, No. 800, Dongchuan Road, Minhang District, Shanghai, 200240, China. jianhaung@sjtu.edu.cn.|National Engineering Center for Biochip at Shanghai, Shanghai, 201203, China. jianhaung@sjtu.edu.cn.|Shenzhen Key Laboratory of Infection and Immunity, Shenzhen Third People's Hospital, Guangdong Medical College, Shenzhen, 518112, China. jianhaung@sjtu.edu.cn.|Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center, Shanghai, 201203, China. jianhaung@sjtu.edu.cn.
authors.forename: Jian
authors.initials: J
authors.lastname: Huang
mesh_terms: D022981:Allelic Imbalance; D006528:Carcinoma, Hepatocellular / Q000235:genetics*; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008113:Liver Neoplasms / Q000235:genetics*; D000091042:Reelin Protein; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000379:methods; D017423:Sequence Analysis, RNA / Q000379:methods
keywords: Allelic expression imbalance; Cancer; DNA-seq; Hepatocellular carcinoma; RNA-seq; Tumor-specific AEI gene