Virus Dataset Detail

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Dataset Information
Accession GSE94660
Status 2018/3/1
Title RNA sequencing (RNA-SEQ) of 21 HBV-HCC patients with non-neoplastic liver and tumor tissues
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: Chronic Hepatitis B virus (HBV) infection leads to liver fibrosis which is a major risk factor in Hepatocellular carcinoma (HCC) and an independent risk factor of recurrence after HCC tumor resection. HBV genome can be inserted into human genome, and chronic inflammation may trigger somatic mutations. Several studies characterized HBV integration sites in HCC patients with regard to frequently occurring hotspots. However, how HBV integration and other genomic changes contribute to the risk of tumor recurrence with regard to different degree of liver fibrosis is not clearly understood. In this study, we aim to find potential molecular mechanisms underlying tumor recurrence of HBV-associated HCC (HBV-HCC) with different degree of liver fibrosis. Methods: We performed RNA sequencing of 21 pairs of tumor and non-neoplastic liver tissues of HBV-HCC patients and performed comprehensive genomic analysis of our RNAseq data and public available sequencing data related to HBV-HCC. We developed a robust pipeline for sensitively identifying HBV integration sites based on sequencing data. Simulations with sequencing data showed that our method outperformed existing methods. We also compared SNPs of each sample with SNPs in cancer census database and inferred patient’s pathogenic SNP loads in tumor and non-neoplastic liver tissues. Conclusions: The HBV-integration and pathogenic SNP load patterns for HCC recurrence risk vary depending on liver fibrosis stage, suggesting potentially different tumorigenesis mechanisms for low and high liver fibrosis patients.
Samples
GSM ID Sample info Characteristics Description
GSM2480436 Tumor tissue of P105 tissue:Tumor tissue; disease state:HBV-HCC P105A
GSM2480437 Non-neoplastic liver tissue of P105 tissue:Non-neoplastic liver tissue; disease state:HBV-HCC P105D
GSM2480438 Tumor tissue of P106 tissue:Tumor tissue; disease state:HBV-HCC P106A
GSM2480439 Non-neoplastic liver tissue of P106 tissue:Non-neoplastic liver tissue; disease state:HBV-HCC P106D
GSM2480440 Tumor tissue of P112 tissue:Tumor tissue; disease state:HBV-HCC P112A
GSM2480441 Non-neoplastic liver tissue of P112 tissue:Non-neoplastic liver tissue; disease state:HBV-HCC P112D
GSM2480442 Tumor tissue of P131 tissue:Tumor tissue; disease state:HBV-HCC P131A
GSM2480443 Non-neoplastic liver tissue of P131 tissue:Non-neoplastic liver tissue; disease state:HBV-HCC P131D
GSM2480444 Tumor tissue of P138 tissue:Tumor tissue; disease state:HBV-HCC P138A
GSM2480445 Non-neoplastic liver tissue of P138 tissue:Non-neoplastic liver tissue; disease state:HBV-HCC P138D
GSM2480446 Tumor tissue of P140 tissue:Tumor tissue; disease state:HBV-HCC P140A
GSM2480447 Non-neoplastic liver tissue of P140 tissue:Non-neoplastic liver tissue; disease state:HBV-HCC P140D
GSM2480448 Tumor tissue of P152 tissue:Tumor tissue; disease state:HBV-HCC P152A
GSM2480449 Non-neoplastic liver tissue of P152 tissue:Non-neoplastic liver tissue; disease state:HBV-HCC P152D
GSM2480450 Tumor tissue of P157 tissue:Tumor tissue; disease state:HBV-HCC P157A
GSM2480451 Non-neoplastic liver tissue of P157 tissue:Non-neoplastic liver tissue; disease state:HBV-HCC P157D
GSM2480452 Tumor tissue of P158 tissue:Tumor tissue; disease state:HBV-HCC P158A
GSM2480453 Non-neoplastic liver tissue of P158 tissue:Non-neoplastic liver tissue; disease state:HBV-HCC P158D
GSM2480454 Tumor tissue of P161 tissue:Tumor tissue; disease state:HBV-HCC P161A
GSM2480455 Non-neoplastic liver tissue of P161 tissue:Non-neoplastic liver tissue; disease state:HBV-HCC P161D
GSM2480456 Tumor tissue of P16 tissue:Tumor tissue; disease state:HBV-HCC P16A
GSM2480457 Non-neoplastic liver tissue of P16 tissue:Non-neoplastic liver tissue; disease state:HBV-HCC P16D
GSM2480458 Tumor tissue of P170 tissue:Tumor tissue; disease state:HBV-HCC P170A
GSM2480459 Non-neoplastic liver tissue of P170 tissue:Non-neoplastic liver tissue; disease state:HBV-HCC P170D
GSM2480460 Tumor tissue of P171 tissue:Tumor tissue; disease state:HBV-HCC P171A
GSM2480461 Non-neoplastic liver tissue of P171 tissue:Non-neoplastic liver tissue; disease state:HBV-HCC P171D
GSM2480462 Tumor tissue of P176 tissue:Tumor tissue; disease state:HBV-HCC P176A
GSM2480463 Non-neoplastic liver tissue of P176 tissue:Non-neoplastic liver tissue; disease state:HBV-HCC P176D
GSM2480464 Tumor tissue of P179 tissue:Tumor tissue; disease state:HBV-HCC P179A
GSM2480465 Non-neoplastic liver tissue of P179 tissue:Non-neoplastic liver tissue; disease state:HBV-HCC P179D
GSM2480466 Tumor tissue of P49 tissue:Tumor tissue; disease state:HBV-HCC P49A
GSM2480467 Non-neoplastic liver tissue of P49 tissue:Non-neoplastic liver tissue; disease state:HBV-HCC P49D
GSM2480468 Tumor tissue of P62 tissue:Tumor tissue; disease state:HBV-HCC P62A
GSM2480469 Non-neoplastic liver tissue of P62 tissue:Non-neoplastic liver tissue; disease state:HBV-HCC P62D
GSM2480470 Tumor tissue of P6 tissue:Tumor tissue; disease state:HBV-HCC P6A
GSM2480471 Non-neoplastic liver tissue of P6 tissue:Non-neoplastic liver tissue; disease state:HBV-HCC P6D
GSM2480472 Tumor tissue of P75 tissue:Tumor tissue; disease state:HBV-HCC P75A
GSM2480473 Non-neoplastic liver tissue of P75 tissue:Non-neoplastic liver tissue; disease state:HBV-HCC P75D
GSM2480474 Tumor tissue of P94 tissue:Tumor tissue; disease state:HBV-HCC P94A
GSM2480475 Non-neoplastic liver tissue of P94 tissue:Non-neoplastic liver tissue; disease state:HBV-HCC P94D
GSM2480476 Tumor tissue of P99 tissue:Tumor tissue; disease state:HBV-HCC P99A
GSM2480477 Non-neoplastic liver tissue of P99 tissue:Non-neoplastic liver tissue; disease state:HBV-HCC P99D
Platform GPL16791  : Illumina HiSeq 2500 (Homo sapiens)
Literature 29212479  
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* p<0.05 ** p<0.01