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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

JGAD000733

Type of data
NGS (WGS)
Microarray (Gene expression profiling)
Methylation array
Access criteria
Controlled-access (Type I)
Total data volume
1.3 GB
File formats
  • VCF
  • IDAT
  • TXT
Research
hum0127
Date published
2024-01-24
Date modified
2024-01-24
DDBJ Search
JGAD000733 (opens in a new tab)
JGA Study
JGAS000604 (opens in a new tab)

Analysis method

発現アレイ

Materials and participants
Tumor tissue of 5063 Japanese cancer patients
Non cancerous tissue of 5063 Japanese cancer patients
(ICD10: C00-D48)
Gastrointestinal stromal tumor (GIST) (ICD10: C169): 30 cases
tumor tissue: 30 samples
paired peripheral blood cells: 29 samples
GIST
  • Health status
    Affected
  • Subject count
    5093 (Individual)
  • Population
    Japanese
Disease
Gastrointestinal stromal tumor (GIST) (C169)
Sample description
RNA extracted from tumor and non-cancerous tissues
  • Tumor / normal
    Mixed
Sample provider
N/A
Experimental method
Expression array
Target
All genes
Reagent kit
Low Input Quick Amp Labeling Kit
Platform
Agilent DNA Microarray Scanner
Agilent SurePrint G3 Human GE v2 8x60K Microarray
QC and filtering
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Normalization
75 percentile
Data use policy
NBDC data sharing policy (JGAP000001)

WGS

Materials and participants
Gastrointestinal stromal tumor (GIST) (ICD10: C169): 30 cases
tumor tissue: 30 samples
paired peripheral blood cells: 30 samples
  • Health status
    Affected
  • Subject count
    30 (Individual)
Disease
Gastrointestinal stromal tumor (GIST) (C169)
Sample description
DNAs extracted from peripheral blood cells (non-tumor tissues) and surgically dissected tumor tissues
  • Tissue
    Peripheral blood
  • Tumor / normal
    Mixed
Sample provider
N/A
Experimental method
WGS
Target
N/A
Reagent kit
TruSeq DNA PCR-Free Library Prep Kit
Fragmentation
Ultrasonic fragmentation (Covaris)
Platform
Illumina NovaSeq 6000
Read type
Paired-end
Read length
150 bp
Reference genome
GRCh37
Mapping
DRAGEN DNA Pipeline
Mapping quality
DRAGEN DNA Pipeline
Analysis method
Illumina DRAGEN Secondary Analysis
Coverage (depth)
Tumor samples: 130.3x
Tumor samples: 115.7–150.7x (Range)
Blood samples: 36.2x
Blood samples: 28.8–45.9x (Range)
Data use policy
NBDC data sharing policy (JGAP000001)

メチル化アレイ

Materials and participants
Gastrointestinal stromal tumor (GIST) (ICD10: C169): 19 cases
tumor tissue: 19 samples
paired peripheral blood cells: 19 samples
  • Health status
    Affected
  • Subject count
    19 (Individual)
Disease
Gastrointestinal stromal tumor (GIST) (C169)
Sample description
DNAs extracted from peripheral blood cells (non-tumor tissues) and surgically dissected tumor tissues
  • Tissue
    Peripheral blood
  • Tumor / normal
    Mixed
Sample provider
N/A
Experimental method
Methylation array
Target
N/A
Reagent kit
EZ DNA Methylation Kit
Infinium MethylationEPIC BeadChip Kit
Platform
Illumina Infinium MethylationEPIC
Illumina iScan
QC and filtering
N/A
Normalization
N/A
Analysis method
GenomeStudio Methylation Module v1.8
Probe count
866,836 probes
Data use policy
NBDC data sharing policy (JGAP000001)