NBDC Research ID: hum0237.v1
SUMMARY
Aims: Application to future medicine by analyzing Alzheimer's disease associated genes
Methods: Genome wide association study
Participants/Materials: Alzheimer's disease
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| hum0237.v1.gwas.v1 | GWAS for Alzheimer's disease | Unrestricted-access | 2021/03/05 |
*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
MOLECULAR DATA
| Participants/Materials |
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 1.1.1.66 |
| Imputation方法 |
IMPUTE2 with 3.5K Japanese reference panel IMPUTE2 with 1000 Genomes Project reference panel (1000 Genomes Phase 3) |
| フィルタリング |
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) |
| Total Data Volume | 520 MB (txt) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
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):
| Name | Title | Project 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 |
PUBLICATIONS
| Title | DOI | Dataset 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 |
| 2 |
