NBDC Research ID: hum0103.v1

 

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.

 

Data Set IDType of DataCriteriaRelease Date
JGAS00000000109

NGS (WGS)

NGS (Exome)

Controlled Access (Type I) 2018/02/27

*Release Note

* Data users need to apply the Form 2 (Application Form 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

          cancer tissues: 23 data

          paired non-cancer tissues: 16 data

Targets WGS
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) 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 Data set ID JGAD00000000117 (included in EGAS00001000678 [EGAD00001000809])
Total Data Volume 2.4 TB (fastq)
Comments (Policies) NBDC policy

 

NGS (Exome)

Participants/Materials

biliary tract cancer (ICD10: C22, 23, 24): 81 cases

          cancer tissues: 138 data

          paired non-cancer 128 data

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) Illumina Nextera Rapid Capture kit or Agilent 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 Data set ID JGAD00000000118
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

TitleDOIData Set ID
1 Genomic characterization of biliary tract cancers identifies their driver genes and predisposing mutations. doi: 10.1016/j.jhep.2018.01.009

JGAD00000000117

JGAD00000000118

2

 

USERS (Controlled-Access Data)

Principal Investigator: Affiliation: Data in Use (Data Set ID)Period of Data Use
Tatsuhiro Shibata Division of Cancer Genomics, National Cancer Center Research Institute JGAD00000000117, JGAD00000000118 2018/09/12-2022/09/30