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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

JGAD000380

Type of data
NGS (Exome; somatic mutation)
NGS (Exome; germline mutation)
NGS (Exome; CNV)
NGS (DNA Amplicon-seq, Exome)
Microarray
NGS (RNA Amplicon-seq)
Access criteria
Controlled-access (Type I)
Research
hum0127
Date published
2021-03-09
Date modified
2021-03-09
DDBJ Search
JGAD000380 (opens in a new tab)

Analysis method

WES

Materials and participants
Pair samples of tumor tissue and peripheral blood (white blood cell) from 5419 Japanese cancer patients
(ICD10: C00-D48)
  • Health status
    Affected
  • Subject count
    5419 (Individual)
  • Population
    Japanese
Sample description
DNAs extracted from white blood cells (as a germ line) and surgically dissected tumor tissues
  • Tissue
    Leukocyte, Peripheral blood
  • Tumor / normal
    Mixed
Sample provider
N/A
Experimental method
WES
Target
All genes
Reagent kit
Ion AmpliSeq Exome RDY Kit
Fragmentation
N/A
Platform
Thermo Fisher Scientific Ion Proton
Read type
Single-end
Read length
180 bp
Reference genome
GRCh37
Mapping
Torrent Suite
QC and filtering
Torrent Suite
Analysis method
Torrent Suite plugin Variant Caller
Processed data type
Somatic variant calls
Data use policy
NBDC data sharing policy (JGAP000001)

WES

Materials and participants
White blood cells (as a germ line) of 5419 Japanese cancer patients
(ICD10: C00-D48)
  • Health status
    Affected
  • Subject count
    5419 (Individual)
  • Population
    Japanese
Sample description
DNAs extracted from white blood cells
  • Tissue
    Leukocyte
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
WES
Target
Hereditary tumor-associated genes (49 genes)
Reagent kit
Ion AmpliSeq Exome RDY Kit
Fragmentation
N/A
Platform
Thermo Fisher Scientific Ion Proton
Read type
Single-end
Read length
180 bp
Reference genome
GRCh37
Mapping
Torrent Suite
QC and filtering
Torrent Suite
Analysis method
Torrent Suite plugin Variant Caller
Processed data type
Germline variant calls
Data use policy
NBDC data sharing policy (JGAP000001)

WES

Materials and participants
Pair samples of tumor tissue and peripheral blood (white blood cell) from 5433 Japanese cancer patients
Pair samples of tumor tissue and peripheral blood (white blood cell) from 5433 Japanese cancer patients
(ICD10: C00-D48)
  • Health status
    Affected
  • Subject count
    5433 (Individual)
  • Population
    Japanese
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
WES
Target
880 genes (cancer driver gene and tumor supprresor gene)
Reagent kit
Ion AmpliSeq Exome RDY Kit
Fragmentation
N/A
Platform
Thermo Fisher Scientific Ion Proton
Read type
Single-end
Read length
180 bp
Mapping
Torrent Suite
QC and filtering
Torrent Suite
Analysis method
N/A
Processed data type
CNV
Data use policy
NBDC data sharing policy (JGAP000001)

Amplicon-seq (腫瘍) + WES (血液)

Materials and participants
Pair samples of tumor tissue and peripheral blood (white blood cell) from 5407 Japanese cancer patients
(ICD10: C00-D48)
  • Health status
    Affected
  • Subject count
    5407 (Individual)
  • Population
    Japanese
Sample description
DNAs extracted from white blood cells (as a germ line) and surgically dissected tumor tissues
  • Tissue
    Leukocyte, Peripheral blood
  • Tumor / normal
    Mixed
Sample provider
N/A
Experimental method
Amplicon-seq
WES
Target
a panel of 409 cancer related genes
(Ion AmpliSeq Comprehensive Cancer Panel)
Exome
Reagent kit
Ion AmpliSeq Library Kit
Fragmentation
N/A
Platform
Thermo Fisher Scientific Ion Proton
Read type
Single-end
Read length
100 bp (Panel)
180 bp (Exome)
Reference genome
GRCh37
Mapping
Torrent Suite
QC and filtering
Torrent Suite
Analysis method
Torrent Suite plugin Variant Caller
Processed data type
Somatic variant calls
Data use policy
NBDC data sharing policy (JGAP000001)

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
5063 Japanese cancer patients
  • 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
Processed data type
Gene expression profile
Data use policy
NBDC data sharing policy (JGAP000001)

RNA Amplicon-seq

Materials and participants
Tumor tissues of 95 Japanese cancer patients
(ICD10: C00-D48)
  • Health status
    Affected
  • Subject count
    95 (Individual)
  • Population
    Japanese
Sample description
RNAs extracted from surgically dissected tumor tissues
  • Tumor / normal
    Tumor
Sample provider
N/A
Experimental method
Amplicon-seq
Target
Custom panel of 491 fusion genes
Reagent kit
Ion AmpliSeq Library Kit
Fragmentation
N/A
Platform
Thermo Fisher Scientific Ion Proton
Read type
Single-end
Read length
100 bp
Mapping
Torrent Suite
QC and filtering
Torrent Suite
Analysis method
Ion Reporter
Processed data type
Fusion gene
Data use policy
NBDC data sharing policy (JGAP000001)