NBDC Research ID: hum0195.v3
SUMMARY
Aims: To elucidate the genetic changes in the progression of gastrointestinal and hepatobiliary tumors
Methods: whole genome sequencing, whole exome sequencing, RNA sequencing, and targeted deep 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
- gastric cancer and gastric submucosal tumor
| 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 |
| JGAS000269 | NGS (Exome, Target Capture, RNA-seq) | Controlled-access (Type I) | 2022/03/02 |
| JGAS000269 (Dataset addition) | NGS (Exome) | Controlled-access (Type I) | 2022/03/18 |
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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 |
JGAS000234, JGAS000269, JGAS000269 (Dataset addition) (Exome)
| 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 chronic gastritis with gastric cancer (ICD10: C169): 11 cases tumor tissues: 11 samples, non-tumor tissues: 38 samples, peripheral blood: 11 samples gastric cancer (ICD10: C169): 1 + 1 case tumor tissues: 2 samples non-tumor tissues: 2 + 3 samples & peripheral blood: 1 + 1 sample gastric submucosal tumor (ICD10: D371): 3 cases non-tumor tissues: 6 samples, peripheral blood: 3 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 DNAs extracted from tumor tissues, non-tumor tissues, and peripheral blood samples of gastric cancer and gastric submucosal tumor |
| 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: hepatocellular carcinoma JGAD000375: gastric cancer JGAD000629: gastric cancer (Dataset addition) |
| Total Data Volume |
JGAD000331: 450 GB (fastq) JGAD000375: 523.6 GB (fastq) JGAD000629: 268.8 GB（fastq） |
| Comments (Policies) | NBDC policy |
JGAS000234, JGAS000269 (RNA-seq)
| 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 gastric cancer (ICD10: C169): 6 cases intestinal metaplasia (IM) 5 samples, non-IM 3samples |
| 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 Total RNAs extracted from non-tumor tissues (only gland duct) of IM samples and non-IM samples |
| 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 | |
| Total Data Volume |
JGAS000234: 450 GB (fastq) JGAS000375: 20.9 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
gastric cancer (ICD10: C169): 26 case (including 2 same cases in exome analysis) non-tumor tissues: 96 samples |
| Targets | Target Capture |
| Target Loci for Capture Methods | 98 genes |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNAs extracted from non-tumor tissues of gastric cancer |
| Cell Lines | - |
| Library Construction (kit name) | xGen custom-designed Gene Capture Pools (IDT) |
| Fragmentation Methods | enzymatic fragmentation （enzymatic fragmentation kit Lotus (IDT) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000375 |
| Total Data Volume | 523.6 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 | Expansion of gastric intestinal metaplasia with copy number aberrations contributes to field cancerization | doi: 10.1158/0008-5472.CAN-21-1523 | JGAD000375 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Jinyan Huang | School of Medicine, Zhejiang University | Comprehensive analysis of alternative splicing in malignant tumors | JGAD000273 | 2022/03/07-2024/01/01 | |
| Michiaki Hamada | Faculty of Science and Engineering, Waseda University | Japan | Construction of RNA-targeted Drug Discovery Database | JGAD000332 | 2022/12/26-2025/03/31 |
