NBDC Research ID: hum0187.v2
SUMMARY
Aims: Impact of viral integration into the host genome on development of hepatocellular carcinoma
Methods: Virus capture sequencing (NGS), Exome (NGS), RNA-seq (NGS), DNA_methylation (Infinium450K)
Participants/Materials: hepatocellular carcinoma
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000194 | NGS (Target Capture) | Controlled-access (Type I) | 2020/05/12 |
| JGAS000233 | NGS (Exome, RNA-seq), Methylation array | Controlled-access (Type I) | 2021/05/31 |
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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 Dataset ID | JGAD000277 |
| Total Data Volume | 640 GB（fastq） |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
hepatocellular carcinoma (ICD10: C220): 160 cases tumor tissue: 160 samples non-tumor tissue: 160 samples |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | DNAs extracted from tumor and non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | SeqCap EZ HGSC VCRome2.1 design1 (42 Mb, NimbleGen), SureSelect Human All Exon Kit V4/V5 (Agilent Technologies) |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris S2) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000328 |
| Total Data Volume | 7 TB (fastq, bam) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
hepatocellular carcinoma (ICD10: C220): 160 cases tumor tissue: 160 samples non-tumor tissue: 31 samples |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | RNAs extracted from tumor and non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq Stranded mRNA |
| Fragmentation Methods | included in the above library construction kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000329 |
| Total Data Volume | 7 TB (fastq, bam) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
hepatocellular carcinoma (ICD10: C220): 160 cases tumor tissue: 160 samples non-tumor tissue: 28 samples |
| Targets | Methylation array |
| Target Loci for Capture Methods | - |
| Platform | Illumina [Infinium Human Methylation 450K BeadChip] |
| Library Source | DNAs extracted from tumor and non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | Infinium HumanMethylation450 BeadChip |
| Algorithms for Calculating Methylation-rate (software) | Genome Studio |
| Filtering Methods | - |
| Probe Number (after QC) | 485,577 methylation sites |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000330 |
| Total Data Volume | 7 TB (txt) |
| 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 | JP19hk0102049 |
| 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 | JP19ck0106265 |
| Research Program on Hepatitis, Japan Agency for Medical Research and Development (AMED) | Study on the pathogenesis of metabolism-associated liver cancer including those associated with viral hepatitis | JP19fk0210040 |
| 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 | Dataset 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 | Accumulation of Molecular Aberrations Distinctive to Hepatocellular Carcinoma Progression | doi: 10.1158/0008-5472.CAN-20-0225 |
JGAD000328 JGAD000329 JGAD000330 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Takashi Kohno | Division of Genome Biology, National Cancer Center Research Institute | Identification of genetic risk factors in AYA (Adolescence and Young Adult) cancer | JGAD000277, JGAD000328, JGAD000329, JGAD000330 | 2021/11/29-2025/03/31 | |
| Jinyan Huang | School of Medicine, Zhejiang University | Comprehensive analysis of alternative splicing in malignant tumors | JGAD000277 | 2022/03/07-2024/01/01 | |
| Michiaki Hamada | Faculty of Science and Engineering, Waseda University | Japan | Construction of RNA-targeted Drug Discovery Database | JGAD000329 | 2022/12/26-2025/03/31 |
| Jian Cao | Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey | United States of America | Analyzing oncovirus in NBDC tumor sequencing data | JGAD000277, JGAD000328, JGAD000329, JGAD000330 |
2023/01/11-2025/12/31 |
