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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Keywords
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
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.
- 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.
Similar models
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.
- 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.
C2348585 (UMLS CUI [1,2])
C1299222 (UMLS CUI [1,2])
C0027627 (UMLS CUI [1,2])
C0007601 (UMLS CUI [1,3])