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Dataset ID

NHA000171

Type of data
GWAS for intracranial germ cell tumors
Access criteria
Unrestricted-access
Total data volume
228 MB
File formats
  • DOCX
  • ZIP
Research
hum0197
Date published
2022-06-10
Date modified
2022-06-10
Secondary ID
hum0197.v9.gwas.GCT.v1

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
header_description_hum0197.v9.docxDictionary file23.4 KB
hum0197.v9.gwas.GCT.v1.zip228 MB

Analysis method

genome wide SNPs

Materials and participants
Intracranial germ cell tumors cases (ICD10: C719): 133
Control participants: 762
  • Health status
    Mixed
  • Subject count
    895 (Individual)
Disease
Intracranial germ cell tumors cases (C719)
Sample description
DNAs extracted from peripheral blood cells
  • Tissue
    Peripheral blood
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
Genotyping by array
Target
N/A
Reagent kit
Infinium Asian Screening Array Kit
Platform
Illumina Infinium Asian Screening Array
QC and filtering
Sample QC:
We excluded individuals (i) with genotyping call rate < 0.97, (ii) in close kinship (PI_HAT > 0.17), and (iii) estimated of non-East Asian ancestry were excluded.
Variant QC:
We excluded variants with (i) genotyping call rate < 0.99, (ii) minor allele count < 5, (iii) P value for Hardy-Weinberg equilibrium < 1.0 × 10−5 in controls, and (iv) > 10% allele frequency difference with the imputation reference panel or the allele frequency panel of Tohoku Medical Megabank Project.
Post-imputation QC:
We excluded imputed variants with Rsq < 0.7 and minor allele frequency < 0.5%.
Imputation
shapeit2 for haplotype phasing
minimac3 for imputation
Analysis method
GenomeStudio for genotyping
PLINK2
Variant count
7,803,874 (autosomal variants)
181,867 (X-chromosomal variants)
Processed data type
GWAS summary statistics
Data use policy
NBDC data sharing policy (JGAP000001)