ID
45201
Description
Principal Investigator: Zemin Zhang, PhD, Genentech Inc., San Francisco, CA, USA MeSH: Hepatocellular Carcinomas,Hepatitis B https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000384 Hepatitis B virus (HBV) infection is a major risk factor for hepatocellular carcinoma (HCC). In this study we sequenced the whole genome (~80X) and transcriptome of tumor and non-tumor samples from four HCC patients and identified over two hundred HBV integration sites. We found significant clonal expansion of HBV-integrated hepatocytes specifically in the tumor samples. We observed a diverse collection of genomic perturbations near viral integration sites, including gene disruption, viral promoter-driven human transcription, viral-human transcript fusion and DNA copy number alteration. We also sequenced one patient at ultra-high coverage (~240X) to build the most comprehensive HBV-integration landscape yet attempted. Our data suggest that the viral integration significantly expands carcinogenic opportunities in HBV-infected individuals.
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Versions (2)
- 8/18/22 8/18/22 - Simon Heim
- 10/12/22 10/12/22 - Adrian Schulz
Copyright Holder
Zemin Zhang, PhD, Genentech Inc., San Francisco, CA, USA
Uploaded on
October 12, 2022
DOI
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License
Creative Commons BY 4.0
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dbGaP phs000384 Genentech Whole Genome Sequencing of Four Hepatocellular Carcinoma Patients
This data table contains subject IDs, consent group information and status of hepatitis B virus infection among patients with hepatocellular carcinoma.
- StudyEvent: SEV1
- Eligibility Criteria
- This data table contains subject IDs, consent group information and status of hepatitis B virus infection among patients with hepatocellular carcinoma.
- The data table contains mapping of study subject IDs to sample IDs of four hepatocellular carcinoma patients. Samples are the final preps submitted for genotyping, sequencing, and/or expression data. For example, if one patient (subject ID) gave one sample, and that sample was processed differently to generate 2 sequencing runs, there would be two rows, both using the same subject ID, but having 2 unique sample IDs.
- The subject phenotype data table includes demographic information (n=2 variables; age and sex) , status of hepatitis B virus infection, and percentage of tumor content in tumor samples of patients with hepatocellular carcinoma.
- The sample attributes data table includes sample analyte type (DNA or RNA), body site where samples were collected, is tumor status, primary tumor location, status of hepatitis B virus infection, and histological type.
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This data table contains subject IDs, consent group information and status of hepatitis B virus infection among patients with hepatocellular carcinoma.
- StudyEvent: SEV1
- Eligibility Criteria
- This data table contains subject IDs, consent group information and status of hepatitis B virus infection among patients with hepatocellular carcinoma.
- The data table contains mapping of study subject IDs to sample IDs of four hepatocellular carcinoma patients. Samples are the final preps submitted for genotyping, sequencing, and/or expression data. For example, if one patient (subject ID) gave one sample, and that sample was processed differently to generate 2 sequencing runs, there would be two rows, both using the same subject ID, but having 2 unique sample IDs.
- The subject phenotype data table includes demographic information (n=2 variables; age and sex) , status of hepatitis B virus infection, and percentage of tumor content in tumor samples of patients with hepatocellular carcinoma.
- The sample attributes data table includes sample analyte type (DNA or RNA), body site where samples were collected, is tumor status, primary tumor location, status of hepatitis B virus infection, and histological type.
C1257890 (UMLS CUI [1,2])
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