NBDC Research ID: hum0158.v2
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SUMMARY
Aims: To investigate genomic alterations of Japanese liver cancers
Methods: DNAs and RNAs were extracted from liver cancer tissues and paired non-cancer (normal) tissues or blood samples. NGS libaraies were prepared for whole genome sequencing (WGS) and RNA-seq. Sequencing was perfomred by Illumina HiSeq or Genome Analyzer.
Participants/Materials: DNAs and RNAs extracted from cancer tissues and normal tissues of Japanese liver cancer patients.
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000151 | Controlled-access (Type I) | 2018/10/22 | |
| JGAS000151 (Data addition) | NGS (WGS) | Controlled-access (Type I) | 2019/06/21 |
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MOLECULAR DATA
| Participants/Materials |
liver cancer (ICD10: C220, 221, 227): 258 cases + 5 cases cancer tissues: 301 samples + 5 samples paired non-cancer tissues: 265 samples (257 blood samples, 3 liver tissues + 5 blood samples) |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2000, Genome Analyzer IIx, NovaSeq 6000] |
| Library Source | DNAs extracted from cancer tissues and paired non-cancer tissues or blood samples from liver cancer patients |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq DNA LT Sample Prep Kit, TruSeq Nano DNA Low Throughput Library Prep Kit, Paired-End DNA Sample Prep Kit, TruSeq Nano DNA Library Preparation Kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000228 |
| Total Data Volume | 48 TB (fastq) + 581 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials: |
liver cancer (ICD10: C220, 221, 227): 238 cases cancer tissues: 238 samples paired non-cancer tissues: 201 samples |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2000, Genome Analyzer IIx] |
| Library Source | RNAs extracted from cancer tissues and paired non-cancer tissues from liver cancer patients |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq RNA Sample Prep Kit v2 or TruSeq Stranded mRNA Library Prep Kit |
| Fragmentation Methods | Heat treatment |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000229 |
| Total Data Volume | 3 TB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Hidewaki Nakagawa
Affiliation: RIKEN Center for Integrative Medical Sciences
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| - |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Whole-genome mutational landscape and characterization of noncoding and structural mutations in liver cancer. | doi: 10.1038/ng.3547 |
JGAD000228 JGAD000229 |
| 2 | Genomic and Transcriptomic Profiling of Combined Hepatocellular and Intrahepatic Cholangiocarcinoma Reveals Distinct Molecular Subtypes. | doi: 10.1016/j.ccell.2019.04.007 |
JGAD000228 JGAD000229 |
USERS (Controlled-access Data)
| Principal Investigator | Affiliation | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|
| Kengo Kinoshita | Tohoku Medical Megabank Organization | Construction of Japanese whole genome database | JGAD000228 | 2019/06/24-2022/03/31 |
| Teruhisa Hochin | Faculty of Information and Human Sciences, Kyoto Institute of Technology | Analysis of mutation of human genome using Machine Learning | JGAD000228, JGAD000229 | 2019/07/09-2021/03/31 |
| Kouya Shiraishi | Division of Genome Biology, National Cancer Research Institute | Elucidation of immune-system networks between host and tumor based on genomic analysis | JGAD000228, JGAD000229 | 2019/08/05-2023/03/31 |
| Osamu Ogasawara | Bioinformation and DDBJ Center, National Institute of Genetics | Evaluation of human genome analysis workflow using JGA/AGD genome data. | JGAD000228, JGAD000229 | 2019/10/11-2024/03/31 |
| Kichoon Lee | Department of Animal Sciences, The Ohio State University | Investigation on allele-specific gene expressions in humans | JGAD000228, JGAD000229 | 2021/05/24-2021/12/31 |
