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Dataset ID

NHA000197

Type of data
GWAS for JPSC-AD study
Access criteria
Unrestricted-access
Total data volume
161 MB
File formats
  • Markdown
  • ZIP
Research
hum0466
Date published
2024-11-20
Date modified
2024-11-20
Secondary ID
hum0466.v1.gwas.v1

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
Readme_2024_JPSC-AD_WML-GWAS.mdDictionary file3.5 KB
hum0466.v1.gwas.v1.zip161 MB

Analysis method

Genotyping by array (GWAS)

Materials and participants
JPSC-AD study participants (ICD10: R90.8): 9,479 individuals
  • Subject count
    9479 (Individual)
Disease
JPSC-AD study participants (R908)
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
N/A
Platform
Illumina Japanese Screening Array
QC and filtering
Sample QC: Gender discrepancy, sample call rate <98%, close relatives, and outliers (distance > 10sd short, 11sd long) were excluded.
Genotyping QC: Hardy-Weinberg equilibrium >1.0x10⁻⁶, call rate >99%, monomorphic, minor allele count <5, and frequency difference >6% with reference panel were excluded.
Post-imputation QC: Variants with minor allele frequency (MAF) <0.5% and Rsq <0.7 were excluded.
Imputation
Imputation reference panel: whole genome sequences of 1,037 (BioBank Japan) and 2,504 (1000 Genomes Project (Phase 3v5)) (hum0014)
Analysis method
Genotype call: GenomeStudio
Genotype imputation: Minimac4 v1.0.0
Variant count
8,495,153 variants
Data use policy
NBDC data sharing policy (JGAP000001)