NBDC Research ID: hum0496.v1
SUMMARY
Aims: Okinawa Bio-information Bank (OBi) is a bio resource bank that integrates human genomic DNA, plasma (or serum), and clinical information to elucidate the unique genetic background and disease susceptibility mechanisms of Okinawans.
Methods: We obtained imputed genotyping data for up to 9,235,975 SNPs. Association studies for the serum levels of ALT, AST, and GGT were performed in OBi and BioBank Japan (BBJ) separately , then these association data were combined by meta-analyses.
Participants/Materials: OBi Ryukyu population (n=8,715), BBJ Ryukyu population (n=7,004)
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| hum0496.v1.gwas.v1 | GWAS for serum levels of ALT, AST and GGT | Unrestricted-access | 2025/02/27 |
*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 |
ALT: n=15,224 (OBi-Ryukyu n=8,440, BBJ-Ryukyu n=6,784) AST: n=15,203 (OBi-Ryukyu n=8,406, BBJ-Ryukyu n=6,797) GGT: n=14,496 (OBi-Ryukyu n=8,434, BBJ-Ryukyu n=6,062) |
| Targets | Genome wide SNPs |
| Target Loci for Capture Methods | - |
| Platform |
OBi: Illumina [Infinium Asian Screening Array v1.0 BeadChip] BBJ: Illumina [Infinium OmniExpress, HumanExome, Infinium OmniExpressExome v1.0, Infinium OmniExpressExome v1.2] |
| Source | DNAs extracted from peripheral blood cells |
| Cell Lines | - |
| Reagents (Kit, Version) | - |
| Genotype Call Methods (software) |
minimac4 Imputation: reference 3,256 Japanese WGS from the BBJ and 2,504 individuals from the 1KGP (phase3v5) |
| Association Analysis & Meta Analysis (software) |
Association Analysis: BOLT-LMM (v.2.3.6) Meta Analysis: METAL software (v.2020-05-05) |
| Filtering Methods |
Sample QC: sample call rate ≧0.98 Genotyping QC: SNP call rate ≧ 0.98, MAF ≧ 0.01, p-values for Hardy–Weinberg equilibrium (HWE) test > 1×10−6 Imputation QC: MAF ≧ 0.005, Rsq ≧ 0.7 |
| Marker Number (after QC) |
ALT: 9,224,376 variants AST: 9,222,117 variants GGT: 9,235,975 variants |
| NBDC Dataset ID |
(Click the gwas number to download files) |
| Total Data Volume | 2.2 GB (txt) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Shiro Maeda
Affiliation: Faculty of Medicine, University of the Ryukyus
Project / Group Name: -
| Name | Title | Project Number |
|---|---|---|
| Promotion project of innovation-eco system collaborating organization from the Okinawa prefecture | Disease Genome Research and Genomic Medicine for the Health and Longevity of Okinawans | - |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | A variant in HMMR/HMMR-AS1 is associated with serum alanine aminotransferase levels in the Ryukyu population | doi: 10.1038/s41598-025-90195-w | hum0496.v1.gwas.v1 |
