NBDC Research ID: hum0466.v1
SUMMARY
Aims: - Identification of risk and protective factors for dementia and depression
- Elucidation of the overall picture of risk and protective factors for dementia and depression
- Establishment of preventive strategy for dementia and depression
Methods: Genotyping, imputation, and genome-wide association study were performed.
Participants/Materials: Of the 9,479 community residents collected at the 8 facilities participating in the Japan Prospective Studies Collaboration for Aging and Dementia (JPSC-AD) study.
URL: https://www.eph.med.kyushu-u.ac.jp/jpsc/en/
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| hum0466.v1.gwas.v1 | GWAS for JPSC-AD study | Unrestricted-access | 2024/11/20 |
*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 | JPSC-AD study participants (ICD10: R90.8): 9,479 individuals |
| Targets | Genome wide SNPs |
| Target Loci for Capture Methods | - |
| Platform | Japanese Screening Array-24 v1.0 Consortium BeadChip [Illumina] |
| Source | DNAs extracted from peripheral blood cells |
| Cell Lines | - |
| Reagents (Kit, Version) | - |
| Genotype Call Methods (software) |
Genotype call: GenomeStudio Genotype imputation: Minimac4 v1.0.0 Imputation reference panel: whole genome sequences of 1,037 (BioBank Japan) and 2,504 (1000 Genomes Project (Phase 3v5)) (hum0014) |
| Association Analysis & Meta Analysis (software) | BOLT-LMM |
| Filtering Methods |
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. |
| Marker Number (after QC) | 8,495,153 variants |
| NBDC Dataset ID |
(Click the gwas number to download files) |
| Total Data Volume | 153.6 MB (txt) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Toshiharu Ninomiya
Affiliation: Department of Epidemiology and Public Health, Graduate School of Medical Sciences, Kyushu University
Project / Group Name: JPSC-AD study
URL: https://www.eph.med.kyushu-u.ac.jp/jpsc/en/
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Research and Development Grants for Dementia, Japan Agency for Medical Research and Development (AMED) | Genome and Neuroimaging Research on Dementia Based on Large-Scale Prospective Cohort Data | JP24dk0207053 |
| Suntory Holdings Limited | - | - |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Common protein-altering variant in GFAP is associated with white matter lesions in the older Japanese population. npj Genomic Med | doi: 10.1038/s41525-024-00431-x | hum0466.v1.gwas.v1 |
