NBDC Research ID: hum0496.v2
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), OBi Hondo population (n=1,420)
| 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 |
| hum0496.v2.freq.v1 | allele counts and frequencies of 526,270 SNPs about general population living in Okinawa Prefecture | Un-restricted Access | 2026/02/27 |
*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 or saliva |
| 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 |
| Participants/Materials |
General Population living in Okinawa Prefecture n=10,135 Ryukyu Cluster (n = 8,715) Hondo Cluster (n = 1,420) |
| Targets | genome wide SNPs |
| Target Loci for Captur Methods |
- |
| Platform | Illumina [Infinium Asian Screening Array v1.0 BeadChip] |
| Source | DNAs extracted from peripheral blood or saliva |
| Cell Lines | - |
| Reagents (Kit, Version) | Infinium Asian Screening Array-24 Kit |
| Genotype Call Methods (softwares) | GenCall software (GenomeStudio) |
| Filtering Methods |
QC1. Genotyping QC (Exclusion Criteria) SNP call rate < 0.98 pHWE < 1×10−6 Sample call rate < 0.98 SNPs not included in the latest manifest file (ASA-24v1-0_E2.csv) QC2. Blast QC All Top Genomic Seq sequences listed in the Illumina Manifest file were blasted against the GRCh38 database, and non-single map SNPs were excluded. QC3. Other Exclusion Criteria (i) SNPs with ≥3 genotype mismatches, based on comparison with WGS (in-house) genotypes for 158 samples. (ii) SNPs with an allele frequency difference ≥ 0.1, based on comparison between the Ryukyu cluster and in-house WGS data (n = 273). (iii) SNPs with an allele frequency difference ≥ 0.05, based on comparison between the Hondo cluster and ToMMo 54k. (iv) SNPs with an allele frequency difference ≥ 0.1, based on comparison between the Hondo cluster and 1KG30xJPT Note 1) (iii) was applied to SNPs that were not assessed in (i) and (ii). (iv) was applied to SNPs that were not assessed in (i), (ii), and (iii). Note 2) SNPs not applied in (i) through (iv) due to absence of genotype data of in-house WGS data or allele frequency data in external database, are flagged as “NoCheck” in the table. |
| Marker Number (after QC) |
526,270 SNPs (with 22,635 SNPs flagged as “NoCheck”) 503,635 SNPs (without 22,635 SNPs flagged as “NoCheck”) |
| NBDC Dataset ID |
(Click the Dataset ID to download the file) |
| Total Data Volume | 76.8 MB (tsv) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Shiro Maeda / Minako Imamura
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 | - |
| Advanced medical research grant in the Faculty of Medicine, University of the Ryukyus | Disease Genome Research in the Ryukyu Population and Its Clinical Applications | - |
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 |
| 2 |
