NBDC Research ID: hum0187.v1
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SUMMARY
Aims: Impact of viral integration into the host genome on development of hepatocellular carcinoma
Methods: Virus capture sequencing (NGS)
Participants/Materials: hepatocellular carcinoma
| Data Set ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000194 | NGS (Target Capture) | Controlled Access (Type I) | 2020/05/12 |
* Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data.
MOLECULAR DATA
| Participants/Materials |
hepatocellular carcinoma (ICD10: C220): 243 cases tumor tissue: 243 samples non-tumor tissue: 59 samples |
| Targets | Target Capture |
| Target Loci for Capture Methods | Virus integration site (including viral genome sequences, viral-human fusion sequences, and nonspecific human genome sequences) |
| Platform | Illumina [MiSeq] |
| Library Source | gDNAs extracted from tumor and non-tumor tissues of hepatocellular carcinoma |
| Cell Lines | - |
| Library Construction (kit name) | Agilent SureSelect XT custom kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 200 bp |
| Japanese Genotype-phenotype Archive Data set ID | JGAD000277 |
| Total Data Volume | 640 GB（fastq） |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Hiroyuki Aburatani
Affiliation: RCAST, the University of Tokyo
Project / Group Name: Genome Science laboratory
URL： https://www.genome.rcast.u-tokyo.ac.jp/en/research
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Research on Development of New Medical Devices, Japan Agency for Medical Research and Development (AMED) | Clinical trial of cancer diagnosis assisting machine based on the mass spectrometry and artificial intelligence: Towards improving the survival rate of hepatic tumor and reducing medical expense | 19hk0102049h0002 |
| Practical Research for Innovative Cancer Control, Japan Agency for Medical Research and Development (AMED) | Large-scale integrated genomic analysis of Japanese intractable and life-style related cancers as an international contribution to ICGC and WHO-lead collaborative researches towards precision cancer treatment and prevention | 19ck0106265h0003 |
| Program for Basic and Clinical Research on Hepatitis, Division of Infectious Disease Research, Division of Infectious Disease Research, Japan Agency for Medical Research and Development (AMED) | Study on the pathogenesis of metabolism-associated liver cancer including those associated with viral hepatitis | 19fk0210040h0002 |
| KAKENHI Grant-in-Aid for Scientific Research (C) | Focal copy number alteration and its functional role in carcinogenesis: unmet needs in cancer genome analysis | 17K07195 |
PUBLICATIONS
| Title | DOI | Data Set ID | |
|---|---|---|---|
| 1 | Impact of AAV2 and Hepatitis B Virus Integration Into Genome on Development of Hepatocellular Carcinoma in Patients with Prior Hepatitis B Virus Infection | doi: 10.1158/1078-0432.CCR-18-4041 | JGAD000277 |
| 2 |
USRES (Controlled-Access Data)
| Principal Investigator: | Affiliation: | Data in Use (Data Set ID) | Period of Data Use |
|---|---|---|---|
