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 IDType of DataCriteriaRelease 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

*Release Note

* Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more

 

MOLECULAR DATA

JGAS000190 (WGS)

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

JGAD000332

JGAD000375

Total Data Volume

JGAS000234: 450 GB (fastq)

JGAS000375: 20.9 GB (fastq)

Comments (Policies) NBDC policy

 

JGAS000269 (Target Capture)

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):

NameTitleProject 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

TitleDOIDataset 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 InvestigatorAffiliationCountry/RegionResearch TitleData 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