Genomic and transcriptome profiling identified both human and HBV genetic variations and their interactions in Chinese hepatocellular carcinoma.

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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.", "claims": [{"id": "claim-method", "statement": "To further understand HCC patients infected with the mutated HBV, HBV linkage disequilibrium was investigated in the 34 HCC patients who had HBV genotype C.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26697315", "locator": "sections[7] \"HBV genotype C variations and their linkage disequilibrium in HCC patients\" paragraph 4", "quote": "To further understand HCC patients infected with the mutated HBV, HBV linkage disequilibrium was investigated in the 34 HCC patients who had HBV genotype C."}], "state": "complete"}, {"id": "claim-data-access", "statement": "aCGH profiling data have been deposited to the GEO database and can be found here: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65484.\nRNASeq profiling data have been deposited to the GEO database and can be found here: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65485.\nSuperseries accession GSE65486 links the CGH and RNA-Seq studies together: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65486.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26697315", "locator": "sections[2] \"Direct link to deposited data\" paragraphs 1-4", "quote": "aCGH profiling data have been deposited to the GEO database and can be found here: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65484.\nRNASeq profiling data have been deposited to the GEO database and can be found here: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65485.\nSuperseries accession GSE65486 links the CGH and RNA-Seq studies together: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65486."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified a novel linkage-disequilibrium region in HBV genotype C associated with core-antigen overexpression, using proportion and Fisher’s exact tests, with source data accessed through GEO accession GSE65486.", "kind": "quantitative", "target": {"value": 0.17, "unit": "odds ratio", "tolerance": null, "source": "Specifically, only 14% (1/7) of HBx A1762T/G1764A mutants were found in the MLL4 fusion positive HCC compared to 50% (13/26) of that identified in MLL4 wild-type HCC (Fisher exact test, p = 0.195, odds ratio = 0.17)."}, "evidence": [{"asset": "source:pmid:26697315", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "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."}, {"asset": 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