NBDC Research ID: hum0158.v1
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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 |
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MOLECULAR DATA
| Participants/Materials |
liver cancer (ICD10: C220, 221, 227): 258 cases cancer tissues: 301 samples paired non-cancer tissues: 260 samples (257 blood samples, 3 liver tissues) |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2000, Genome Analyzer IIx] |
| 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) |
| 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: | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|
