NBDC Research ID: hum0158.v1

 

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.

 

Data Set IDType of DataCriteriaRelease Date
JGAS00000000151

NGS (WGS)

NGS (RNA-seq)

Controlled Access (Type I) 2018/10/22

*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

liver cancer (ICD10:C220, 221, 227): 270 cases (281 samples)

          cancer tissues: 281 samples

          paired non-cancer tissues or blood samples: 259 samples

Targets WGS
Target Loci for Capture Methods -
Platform Illumina [HiSeq 2000/2500, 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 or TruSeq Nano DNA Low Throughput Library 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 JGAD00000000228
Total Data Volume 48 TB (fastq)
Comments (Policies) NBDC policy

 

NGS (RNA-seq)

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 Data set ID JGAD00000000229
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

TitleDOIData Set ID
1 Whole-genome mutational landscape and characterization of noncoding and structural mutations in liver cancer. doi: 10.1038/ng.3547

JGAD00000000228

JGAD00000000229

2

 

USERS (Controlled-Access Data)

Principal Investigator: Affiliation: Data in Use (Data Set ID)Period of Data Use