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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)
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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

JGAD000289

Type of data
SNP-chip for pediatric germ cell tumors
Methylation array for pediatric germ cell tumors
NGS (Target Capture) for pediatric germ cell tumors
NGS (RNA-seq) for pediatric germ cell tumors
Access criteria
Controlled-access (Type I)
Total data volume
444 GB
File formats
  • BAM
  • IDAT
  • CEL
Research
hum0035
Date published
2020-12-21
Date modified
2020-12-21
DDBJ Search
JGAD000289 (opens in a new tab)
JGA Study
JGAS000204 (opens in a new tab)

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
380genesregions.xlsxlist of 380 genes & regions13.4 KB

Analysis method

Genotyping by array

Materials and participants
51 patients with pediatric germ cell tumors (ICD10: C809)
  • Health status
    Affected
  • Subject count
    51 (Individual)
Disease
patients with pediatric germ cell tumors (C809)
Sample description
DNAs extracted from neuroblastoma cell lines, HBL cell lines, tumor tissues of NB, HBL and pediatric germ cell tumors, and peripheral blood cells of NB as non-tumor tissues
  • Tissue
    Peripheral blood
  • Tumor / normal
    Mixed
Cell line
Hepatoblastoma cell line
Sample provider
N/A
Experimental method
Genotyping by array
Target
N/A
Reagent kit
CytoScan HD Kit
Platform
Affymetrix CytoScan HD
Analysis method
Copy Number for GeneChip software (CNAG) and allele-specific copy-number analysis using anonymous references (AsCNAR)
Variant count
CytoScan HD Array: 2,696,550 CNVs
Data use policy
NBDC data sharing policy (JGAP000001)

メチル化アレイ

Materials and participants
51 patients with pediatric germ cell tumors (ICD10: C809)
  • Health status
    Affected
  • Subject count
    51 (Individual)
Disease
patients with pediatric germ cell tumors (C809)
Sample description
DNAs extracted from tumor tissues of pancreatoblastoma, hepatoblastoma and pediatric germ cell tumors, and HBL cell lines
  • Tumor / normal
    Mixed
Cell line
Hepatoblastoma cell line
Sample provider
N/A
Experimental method
Methylation array
Target
N/A
Reagent kit
Infinium MethylationEPIC BeadChip Kit
Platform
Illumina Infinium MethylationEPIC
QC and filtering
N/A
Normalization
N/A
Analysis method
N/A
Probe count
450 (K probes raw data)
Data use policy
NBDC data sharing policy (JGAP000001)

RNA-seq

Materials and participants
49 patients with pediatric germ cell tumors (ICD10: C809)
  • Health status
    Affected
  • Subject count
    49 (Individual)
  • Age group
    Child
Disease
patients with pediatric germ cell tumors (C809)
Sample description
RNAs extracted from tumor tissues of pancreatoblastoma, hepatoblastoma, pediatric germ cell tumors and neuroblastoma, and HBL cell lines
  • Tumor / normal
    Tumor
Cell line
Hepatoblastoma cell line
Sample provider
N/A
Experimental method
RNA-seq
Target
N/A
Reagent kit
NEBNext Ultra RNA Library Prep Kit for Illumina
TruSeq RNA Library Prep Kit
Fragmentation
included in the above library construction kit
Platform
Illumina HiSeq 2500
Read type
Paired-end
Read length
108 bp
Reference genome
GRCh37
Phenotype data
Included
Data use policy
NBDC data sharing policy (JGAP000001)

Targeted DNA sequencing

Materials and participants
51 patients with pediatric germ cell tumors (ICD10: C809)
  • Health status
    Affected
  • Subject count
    51 (Individual)
  • Age group
    Child
Disease
patients with pediatric germ cell tumors (C809)
Sample description
DNAs extracted from tumor tissues of hepatoblastoma, pediatric germ cell tumors and neuroblastoma, and HBL cell lines
  • Tumor / normal
    Tumor
Cell line
Hepatoblastoma cell line
Sample provider
N/A
Experimental method
Targeted DNA sequencing
Target
380 genes or regions associated with paediatric cancers
(list of 380 genes & regions)
Reagent kit
NEBNext Ultra DNA Library Prep Kit for Illumina
Fragmentation
Ultrasonic fragmentation (Covaris E220)
Platform
Illumina HiSeq 2000
Illumina MiSeq
Read type
Paired-end
Read length
100 bp
150 bp
Reference genome
GRCh37
Phenotype data
Included
Data use policy
NBDC data sharing policy (JGAP000001)