NBDC Research ID: hum0237.v1



Aims: Application to future medicine by analyzing Alzheimer's disease associated genes

Methods: Genome wide association study

Participants/Materials: Alzheimer's disease


Dataset IDType of DataCriteriaRelease Date
hum0237.v1.gwas.v1 GWAS for Alzheimer's disease Unrestricted-access 2021/03/05

*Release Note

*When the research results including the data which were downloaded from NHA/DRA, are published or presented somewhere, the data user must refer the papers which are related to the data, or include in the acknowledgment. Learn more





Alzheimer's disease (ICD10: F00): 3,962 cases

4,074 controls

Targets genome wide SNPs
Target Loci for Capture Methods -
Platform Affymetrix [Japonica Array, GeneChip 6.0 microarrays]
Library Source DNAs extracted from peripheral blood cells
Cell Lines -
Reagents (Kit, Version) Axiom 2.0 Reagent kit
Genotype Call Methods (software) Axiom Analysis suite

IMPUTE2 with 3.5K Japanese reference panel

IMPUTE2 with 1000 Genomes Project reference panel (1000 Genomes Phase 3)


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).

Marker Number (after QC) 4,852,957 SNVs
Analysis Method (software) PLINK
NBDC Dataset ID


(Click the Dataset ID to download the file)

Dictionary file

Total Data Volume 520 MB (txt)
Comments (Policies) NBDC policy



Principal Investigator: Kouichi Ozaki

Affiliation: Division for Genomic medicine, Medical Genome Center, National Center for Geriatrics and Gerontology

Project / Group Name: -

Funds / Grants (Research Project Number):

NameTitleProject Number
Program for Integrated Database of Clinical and Genomic Information, Japan Agency for Medical Research and Development (AMED) Genome wide association study and data storage of dementia in a large Japanese population JP18kk0205009



TitleDOIDataset ID
1 Ethnic and trans-ethnic genome-wide association studies identify new loci influencing Alzheimer’s disease risk in Japanese doi: 10.1038/s41398-021-01272-3 hum0237.v1.gwas.v1