title: Genomic and transcriptome profiling identified both human and HBV genetic variations and their interactions in Chinese hepatocellular carcinoma.
abstract: Interaction between HBV and host genome integrations in hepatocellular carcinoma (HCC) development is a complex process and the mechanism is still unclear. Here we described in details the quality controls and data mining of aCGH and transcriptome sequencing data on 50 HCC samples from the Chinese patients, published by Dong et al. (2015) (GEO#: GSE65486). In additional to the HBV-MLL4 integration discovered, we also investigated the genetic aberrations of HBV and host genes as well as their genetic interactions. We reported human genome copy number changes and frequent transcriptome variations (e.g. TP53, CTNNB1 mutation, especially MLL family mutations) in this cohort of the patients. For HBV genotype C, we identified a novel linkage disequilibrium region covering HBV replication regulatory elements, including basal core promoter, DR1, epsilon and poly-A regions, which is associated with HBV core antigen over-expression and almost exclusive to HBV-MLL4 integration.
authors.affiliation: AstraZeneca Asian and Emerging Market iMed, Zhangjiang Hi-Tech Park, Shanghai, PR China.
authors.forename: Hua
authors.initials: H
authors.lastname: Dong
authors.affiliation: AstraZeneca Asian and Emerging Market iMed, Zhangjiang Hi-Tech Park, Shanghai, PR China.
authors.forename: Ziliang
authors.initials: Z
authors.lastname: Qian
authors.affiliation: Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Fudan University, Shanghai, PR China.
authors.forename: Lan
authors.initials: L
authors.lastname: Zhang
authors.affiliation: R&D Information, AstraZeneca, Shanghai, PR China.
authors.forename: Yunqin
authors.initials: Y
authors.lastname: Chen
authors.affiliation: Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Fudan University, Shanghai, PR China.
authors.forename: Zhenggang
authors.initials: Z
authors.lastname: Ren
authors.affiliation: AstraZeneca Asian and Emerging Market iMed, Zhangjiang Hi-Tech Park, Shanghai, PR China.
authors.forename: Qunsheng
authors.initials: Q
authors.lastname: Ji
keywords: HBV; HCC; RNASeq; aCGH