NBDC Research ID: hum0541.v1
SUMMARY
Aims: Elucidating the association between an individual's genetic architecture, including polymorphisms, and their susceptibility to disease and complex phenotypes is fundamental to the advancement of precision medicine. This study integrates biospecimens, clinical information, and previously generated research data from BioBnk Japan (BBJ), the National Center for Geriatrics and Gerontology (NCGG), and the Tohoku Medical Megabank Organization (ToMMo) to systematically characterize genetic associations across diverse human traits and phenotypes.
Methods: Clinical data were subjected to quality control, and outliers were removed. Phenotypic values were corrected for the effects of medication use, including lipid-lowering and antihypertensive therapies, and users of specific medications were excluded from specific analyses. Phenotypes were adjusted for age, sex, and principal components using linear regression models. The residuals were transformed using inverse rank normalization to generate the final phenotype dataset (63 phenotypes). Association analyses between these phenotypes and imputed genetic variants, generated using a Japanese reference panel, were performed using BOLT-LMM.
Participants/Materials: The phenotype matrix for the QTL analysis contains 63 phenotypes from the BioBank Japan (BBJ) cohort 1 (N = 176,894)
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000874 | Quantitative Trait Loci Phenotype Matrix | Controlled-access (Type I) | 2026/06/02 |
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MOLECULAR DATA
| Participants/Materials | BioBank Japan (BBJ) 1st cohort: 176,894 individuals |
| Targets | genome wide SNVs |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HumanOmniExpressExome BeadChip, HumanOmniExpress BeadChip, HumanExome BeadChip] |
| Source | DNA extracted from peripheral blood cells |
| Cell Lines | - |
| Reagents (Kit, Version) | HumanOmniExpressExome BeadChip, HumanOmniExpress BeadChip, HumanExome BeadChip |
| Genotype Call Methods (software) |
genotyping: GenomeStudio (v2.0.5) haplotype phasing: SHAPEIT2 (v.2.837) imputation: Minimac4 (v.1.0.0) |
| Association Analysis (software) | BOLT-LMM (v.2.3.4) |
| Filtering Methods |
Sample QC: We excluded samples with (1) Sample call rate < 0.98 (2) Samples with sex mismatches (3) non-East Asian ancestry (4) Samples overlapping with those in the reference panels Variant QC: We excluded variants with (1) variant call rate < 0.99 (2) number of heterozygotes < 5 (3) Hardy‒Weinberg equilibrium (P < 1 × 10-6 ) (4) palindromic variants |
| Marker Number (after QC) | 15,907,072 SNVs |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD001017 |
| Total Data Volume | 42.3 MB (txt) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Chikashi Terao
Affiliation: Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences
Project / Group Name: The Research for personalized medicine based on genomic information/The laboratory for Statistical and Translational Genetics, Center for Integrative Medical Sciences, RIKEN; Clinical Research Center, Shizuoka General Hospital
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Biobank - Construction and Utilization biobank for genomic medicine REalization (B-Cure), Japan Agency for Medical Research and Development (AMED) | Study of elucidating pathophysiology of immune or psychiatric disorders based on innate or acquired structural variations | JP21tm0424220 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Population-specific non-coding and coding putative causal variants shape quantitative traits | doi: 10.1038/s41588-024-01913-5 | JGAD001017 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
