NBDC Research ID: hum0195.v1
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SUMMARY
Aims: To elucidate the genetic changes in progression of gastrointestinal and hepatobiliary tumors
Methods: whole genome sequencing, whole exome sequencing and RNA sequencing analysis
Participants/Materials:
nodule-in-nodule hepatocellular carcinoma
liver cirrhosis and hepatocellular carcinoma after hepatitis C virus eradication, hepatitis C virus positive cirrhosis and hepatocellular carcinoma and hepatitis C virus negative hepatocellular carcinoma
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000190 | NGS (WGS) | Controlled-access (Type I) | 2021/03/26 |
| JGAS000234 | NGS (Exome, RNA-seq) | Controlled-access (Type I) | 2021/03/26 |
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MOLECULAR DATA
| Participants/Materials |
nodule-in-nodule hepatocellular carcinoma (ICD10: C220): 5 cases (total: 23 samples) tumor tissues: 14 samples non-tumor tissues: 5 samples lymphocytes isolated from peripheral blood: 4 samples |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNAs extracted from tumor tissues, non-tumor tissues, and lymphocytes isolated from peripheral blood of hepatocellular carcinoma |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq DNA PCR-Free Sample Prep Kit |
| Fragmentation Methods | Ultrasonic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000273 |
| Total Data Volume | 1 TB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
liver cirrhosis and hepatocellular carcinoma after hepatitis C virus eradication (ICD10: K746, C220): 12 cases tumor tissues: 12 samples lymphocytes isolated from peripheral blood: 12 samples |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Thermo Fisher Scientific [Ion Proton] |
| Library Source | DNAs extracted from tumor tissues and lymphocytes isolated from peripheral blood of hepatocellular carcinoma |
| Cell Lines | - |
| Library Construction (kit name) | Ion AmpliSeq Exome RDY kit |
| Fragmentation Methods | Enzymatic Fragmentation |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000331 |
| Total Data Volume | 450 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
liver cirrhosis and hepatocellular carcinoma after hepatitis C virus eradication (ICD10: K746, C220): 20 cases non-tumor tissues: 20 samples hepatitis C virus positive cirrhosis and hepatocellular carcinoma (ICD10: K746, C220): 3 cases tumor tissues: 8 samples non-tumor tissues: 3 samples hepatitis C virus negative hepatocellular carcinoma (ICD10: C220): 2 cases tumor tissues: 7 samples non-tumor tissues: 2 samples |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 4000, NovaSeq 6000] |
| Library Source | RNAs extracted from tumor tissues and non-tumor tissues of hepatocellular carcinoma |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq RNA Sample Preparation v2 Guide, Part # 15026495 |
| Fragmentation Methods | Enzymatic Fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 101 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000332 |
| Total Data Volume | 450 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Atsushi Takai
Affiliation: Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (C) | Exploration for the molecular mechanism on multistep hepatocarcinogenesis using organoid culture system and whole genome sequencing analysis | 19K08443 |
| KAKENHI Grant-in-Aid for Scientific Research (B) | Role of regeneration nodule in cirrhotic liver on tumorigenesis | 17H04158 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Multiregional whole-genome sequencing of hepatocellular carcinoma with nodule-in-nodule appearance reveals stepwise cancer evolution | doi: 10.1002/path.5533 | JGAD000273 |
| 2 | Oncogenic transcriptomic profile is sustained in the liver after the eradication of the hepatitis C virus | doi: 10.1093/carcin/bgab014 | JGAD000332 |
| 3 | DNA methyltransferase 3B plays a protective role against hepatocarcinogenesis caused by chronic inflammation via maintaining mitochondrial homeostasis | doi: 10.1038/s41598-020-78151-2 | JGAD000332 |
USRES (Controlled-access Data)
| Principal Investigator: | Affiliation: | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|
