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Due to system maintenance, the application system, application review by the Data Access Committee will be unavailable during the following period.
Schedule: October 5th (Mon), 2026, 9:00 - October 7th (Wed), 2026, 15:00 (JST)
We apologize for any inconvenience this may cause and appreciate your understanding.

We are currently receiving a large number of applications for data submission, and the review process is taking longer than usual.We sincerely apologize for the delay and kindly ask for your understanding. When submitting an application, we would greatly appreciate it if you could allow sufficient time for the processing.

Following a change to our organizational structure effective April 1, 2026, this division has been renamed from the "Database Center for Life Science, Joint Support-Center for Data Science Research" to the "Database Division for Life Science (DBCLS), BioData Science Initiative (BSI), National Institute of Genetics (NIG)". Where the former name still appears in the guidelines, please read it as the new name.

Dataset ID

JGAD000261

Type of data
NGS (WGS): RK067
Access criteria
Controlled-access (Type I)
Total data volume
2.4 TB
File formats
  • FASTQ
  • VCF
  • XLSX
Research
hum0182
Date published
2020-10-21
Date modified
2021-04-19
DDBJ Search
JGAD000261 (opens in a new tab)
JGA Study
JGAS000180 (opens in a new tab)

Analysis method

WGS

Materials and participants
1) RK067 (a liver cancer patient): 1 case
2) NA18943 (HapMap): 1 sample
4) RK014, RK019, RK020, RK067, RK085, RK0143, RK147, RK156, RK157, RK167, RK281 (liver cancer patients): 11 cases
  • Health status
    Mixed
  • Subject count
    23 (Sample)
  • Cohort
    HapMap
  • Population
    Japanese
Sample description
1) DNA extracted from blood sample (normal cell) of a liver cancer patient
2) HapMap DNA sample
4) RK014, RK019, RK020, RK085, RK0143, RK147, RK156, RK157, RK167, RK281: DNA extracted from blood samples (normal cell) of liver cancer patients
RK014, RK019, RK020, RK067, RK085, RK0143, RK147, RK156, RK157, RK167, RK281: DNA extracted from tumor tissues of liver cancer patients
  • Tissue
    Peripheral blood
  • Tumor / normal
    Mixed
Cell line
NA18943
Sample provider
https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=NA18943&Product=DNA
Experimental method
WGS
Target
N/A
Reagent kit
Ligation Sequencing Kit (SQK-LSK108)
Fragmentation
g-TUBE (Covaris)
Platform
Oxford Nanopore Technologies MinION
Read type
Single-end
Read length
7463 bp (①④)
3479 bp (②)
Data use policy
NBDC data sharing policy (JGAP000001)

WGS

Materials and participants
3) RK001-RK338 (liver cancer patients): 174 cases
  • Health status
    Affected
  • Subject count
    174 (Individual)
  • Population
    Japanese
Sample description
DNA extracted from blood sample (normal cell) of liver cancer patients
  • Tissue
    Peripheral blood
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
WGS
Target
N/A
Reagent kit
Paired-End DNA Sample Prep Kit
TruSeq DNA Sample Prep Kit
TruSeq Nano DNA Library Prep Kit
Fragmentation
Ultrasonic fragmentation (Covaris)
Platform
Illumina Genome Analyzer IIx
Illumina HiSeq 2000
Read type
Paired-end
Read length
100 bp
Reference genome
GRCh37
Mapping
bwa
Read deduplication
Picard
QC and filtering
N/A
Analysis method
VCMM (Shigemizu et al. Sci Rep (2013))
Coverage (depth)
30x
Variant count
4378
5,239,921
Data use policy
NBDC data sharing policy (JGAP000001)