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 IDType of DataCriteriaRelease Date
JGAS000109

NGS (WGS)

NGS (Exome)

Controlled-access (Type I) 2018/02/27
JGAS000109 (Data addition) NGS (WGS) Controlled-access (Type I) 2019/06/21

*Release Note

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

 

MOLECULAR DATA

NGS (WGS)

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

 

NGS (Exome)

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

TitleDOIDataset 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 InvestigatorAffiliationResearch TitleData 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