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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

JGAD000334

Type of data
NGS (Exome)
NGS (RNA-seq)
SNP array
Methylation array
NGS (WGBS)
Access criteria
Controlled-access (Type I)
Total data volume
2.6 TB
File formats
  • BAM
  • bigWig
  • CEL
  • TXT
Research
hum0233
Date published
2021-06-04
Date modified
2021-06-04
DDBJ Search
JGAD000334 (opens in a new tab)
JGA Study
JGAS000236 (opens in a new tab)

Analysis method

WES

Materials and participants
Pediatric hepatoblastoma (ICD10: C22.0, C22.2): 112 cases
tumor tissue: 112 samples
non-tumor tissue: 112 samples
  • Health status
    Affected
  • Subject count
    112 (Individual)
  • Age group
    Child
Disease
Pediatric hepatoblastoma (C220, C222)
Sample description
DNAs extracted from tumor tissues and non-tumor tissues
  • Tissue
    Liver
  • Tumor / normal
    Mixed
Sample provider
N/A
Experimental method
WES
Target
N/A
Reagent kit
SureSelect Human All Exon V5
Fragmentation
Ultrasonic fragmentation (Covaris S2)
Platform
Illumina HiSeq 2500
Read type
Paired-end
Read length
100 bp
Reference genome
GRCh37
Mapping
BWA, Karkinos (in-house mapper)
QC and filtering
N/A
Coverage (depth)
N/A
Coverage (breadth)
N/A
Data use policy
NBDC data sharing policy (JGAP000001)

RNA-seq

Materials and participants
Pediatric hepatoblastoma (ICD10: C22.0, C22.2): 113 cases
tumor tissue: 111 samples
non-tumor tissue: 28 samples
(tumor and matched-non tumor pair: 26 cases + tumor tissues only: 85 cases + non-tumor tissues only: 2 cases)
  • Health status
    Affected
  • Subject count
    113 (Individual)
  • Age group
    Child
Disease
Pediatric hepatoblastoma (C220, C222)
Sample description
RNAs extracted from tumor tissues and non-tumor tissues
  • Tissue
    Liver
  • Tumor / normal
    Mixed
Sample provider
N/A
Experimental method
RNA-seq
Target
N/A
Reagent kit
TruSeq RNA Library Prep Kit
Fragmentation
included in the above library construction kit
Platform
Illumina HiSeq 2500
Read type
Paired-end
Read length
100 bp
Reference genome
GRCh37
Mapping
BWA, Finemap (in-house mapper)
QC and filtering
N/A
Read count
N/A
Coverage (depth)
N/A
Coverage (breadth)
N/A
Gene count
86,817
Processed data type
FPKM
Data use policy
NBDC data sharing policy (JGAP000001)

Genotyping by array

Materials and participants
Pediatric hepatoblastoma (ICD10: C22.0, C22.2): 112 cases
tumor tissue: 112 samples
non-tumor tissue: 112 samples
  • Health status
    Affected
  • Subject count
    112 (Individual)
  • Age group
    Child
Disease
Pediatric hepatoblastoma (C220, C222)
Sample description
DNAs extracted from tumor tissues and non-tumor tissues
  • Tissue
    Liver
  • Tumor / normal
    Mixed
Sample provider
N/A
Experimental method
Genotyping by array
Target
N/A
Reagent kit
Genome-Wide Human SNP Array 6.0 Kit
Platform
Affymetrix Genome-Wide Human SNP Array 6.0
Data use policy
NBDC data sharing policy (JGAP000001)

WGBS

Materials and participants
Pediatric hepatoblastoma (ICD10: C22.0, C22.2): 21 cases
tumor tissue: 20 samples
non-tumor tissue: 3 samples
(tumor and matched-non tumor pair: 2 cases + tumor tissues only: 18 cases + non-tumor tissues only: 1 case)
  • Health status
    Affected
  • Subject count
    21 (Individual)
  • Age group
    Child
Disease
Pediatric hepatoblastoma (C220, C222)
Sample description
DNAs extracted from tumor tissues and non-tumor tissues
  • Tissue
    Liver
  • Tumor / normal
    Mixed
Sample provider
N/A
Experimental method
WGBS
Target
N/A
Reagent kit
EZ DNA Methylation-Gold Kit
Fragmentation
fragmentation due to bisulfite conversion
Platform
Illumina HiSeq 2500
Read type
Paired-end
Read length
100 bp
Reference genome
GRCh37
Mapping
Bowtie2 v2.2.5 (Bismark v0.14.3)
QC and filtering
high mapping efficiency (58.3%)
Analysis method
Bismark (v0.14.3)
Read count
Total reads: 627,297,250 (mean) / Uniquely mapped reads: 364,372,627 (mean)
Coverage (depth)
19.7x
Data use policy
NBDC data sharing policy (JGAP000001)

メチル化アレイ

Materials and participants
Pediatric hepatoblastoma (ICD10: C22.0, C22.2): 146 cases
tumor tissue: 146 samples
non-tumor tissue: 32 samples
(tumor and matched-non tumor pair: 32 cases + tumor tissues only: 114 cases + non-tumor tissues only: 0 case)
  • Health status
    Affected
  • Subject count
    146 (Individual)
  • Age group
    Child
Disease
Pediatric hepatoblastoma (C220, C222)
Sample description
DNAs extracted from tumor tissues and non-tumor tissues
  • Tissue
    Liver
  • Tumor / normal
    Mixed
Sample provider
N/A
Experimental method
Methylation array
Target
N/A
Reagent kit
Infinium HumanMethylation450 BeadChip Kit
Platform
Illumina Infinium HumanMethylation450
Reference genome
GRCh37
QC and filtering
N/A
Normalization
following the standard protocol of Genome Studio
Analysis method
Genome Studio
Probe count
485,577
Processed data type
DNA methylation data
Data use policy
NBDC data sharing policy (JGAP000001)