NBDC Research ID: hum0103.v2
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SUMMARY
Aims: To investigate genomic alterations of Japanese biliary tract cancers
Methods: DNAs were extracted from biliary tract cancer and paired non-cancer (normal) tissues. NGS libaraies were prepared by using TruSeq DNA Sample Prep kit (Illumina) for whole genome sequencing (WGS) and Nextera Rapid Capture kit (Illumina) / Agilent SureSelect Exome V5 kit for whole exome sequencing (WES). Sequencing was perfomred by Illumina HiSeq 2000/2500.
Participants/Materials: WGS and WES data of Japanese biliary tract cancer patients.
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000109 | Controlled-access (Type I) | 2018/02/27 | |
| JGAS000109 (Data addition) | NGS (WGS) | Controlled-access (Type I) | 2019/06/21 |
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MOLECULAR DATA
| Participants/Materials |
biliary tract cancer (ICD10: C22, 23, 24): 14 cases + 3 cases cancer tissues: 23 samples + 6 samples paired non-cancer tissues: 14 samples + 3 samples |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2000/2500, NovaSeq 6000] |
| Library Source | DNAs extracted from cancer and paired non-cancer (normal) tissues from biliary tract cancer patients |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq DNA Sample Prep 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 | JGAD000117 (included in EGAS00001000678 [EGAD00001000809]) |
| Total Data Volume | 2.4 TB (fastq) + 375 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
biliary tract cancer (ICD10: C22, 23, 24): 81 cases cancer tissues: 138 samples paired non-cancer 128 samples |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2000/2500] |
| Library Source | DNAs extracted from cancer and paired non-cancer (normal) tissues from biliary tract cancer patients |
| Cell Lines | - |
| Library Construction (kit name) | Nextera Rapid Capture kit or SureSelect Exome V5 kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 125 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000118 |
| Total Data Volume | 1.7 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 | Genomic characterization of biliary tract cancers identifies their driver genes and predisposing mutations. | doi: 10.1016/j.jhep.2018.01.009 |
JGAD000117 JGAD000118 |
| 2 |
USERS (Controlled-access Data)
| Principal Investigator | Affiliation | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|
| Tatsuhiro Shibata | Division of Cancer Genomics, National Cancer Center Research Institute | JGAD000117, JGAD000118 | 2018/09/12-2022/09/30 | |
| Kengo Kinoshita | Tohoku Medical Megabank Organization | Construction of Japanese whole genome database | JGAD000117 | 2019/06/24-2022/03/31 |
