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Dataset ID

NHA000161

Type of data
GWAS for Alzheimer's disease
Access criteria
Unrestricted-access
Total data volume
142 MB
File formats
  • DOCX
  • ZIP
Research
hum0237
Date published
2021-03-05
Date modified
2021-03-05
Secondary ID
hum0237.v1.gwas.v1

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
Dictionary_file_hum0237_v1_gwas_v1.docxDictionary file19.7 KB
hum0237_v1_gwas_v1.zip142 MB

Analysis method

Genotyping by array

Materials and participants
Alzheimer's disease (ICD10: F00): 3,962 cases
4,074 controls
  • Health status
    Mixed
  • Subject count
    8036 (Individual)
Disease
Alzheimer's disease (F00)
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
Axiom 2.0 Reagent Kit
Platform
Affymetrix Genome-Wide Human SNP Array 6.0
Affymetrix Japonica Array
QC and filtering
Sample QCs: (1) sex inconsistencies (--check-sex), (2) inbreeding coefficient (--het 0.1), (3) genotype missingness (--missing 0.05), (4) kinship coefficient (--genome 0.2) and (5) exclusion of outliers from the clusters of East Asian populations in principal component analysis that was conducted together with 1000 Genomes Phase 3 data.
Marker (SNPs and Indels) QCs: (1) genotyping efficiency or call rate (--geno 0.95), (2) minor allele frequency (--freq 0.001), (3) Hardy-Weinberg equilibrium (--hwe 0.001).
Imputation
IMPUTE2 with 3.5K Japanese reference panel
IMPUTE2 with 1000 Genomes Project reference panel (1000 Genomes Phase 3)
Analysis method
Axiom Analysis suite 1.1.1.66
Variant count
4,852,957 SNVs
Processed data type
GWAS summary statistics
Data use policy
NBDC data sharing policy (JGAP000001)