NBDC Research ID: hum0311.v4
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SUMMARY
Aims: The BioBank Japan (BBJ) is a biobank established in the Institute of Medical Science, the University of Tokyo to collect clinical information and biological materials (DNA and serum samples). It collected about 200 thousand participants of 47 diseases started in 2003 (BBJ 1st cohort), and 67 thousand participants of 38 diseases started in 2013 (BBJ 2nd cohort), both in collaboration with 12 medical centers." This project is aiming at further utilization of the materials, and clinical and genomic information managed by BBJ to contribute to precision medicine by storing, managing, and providing the materials and data, as well as identifying biomarkers associated with disease risk, prognosis, and drug sensitivity.
Methods: Asian Screening Array (ASA-24v1-0_A2)
Imputation results based on TOPMed r2 (GRCh38)
Quantification of 250 metabolic biomarkers by NMR spectroscopy
Participants/Materials: 11,716 + 180,882 + 1,285 + 2,570 patients from BBJ 1st cohort and 42,689 patients from BBJ 2nd cohort
URL： https://biobankjp.org/en/index.html
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000412 | Genotype data for 11,716 patients from BBJ 1st cohort and 42,689 patients from BBJ 2nd cohort | Controlled-access (Type I) | 2021/11/30 |
| JGAS000541 | Imputation data and index data for 180,882 patients from BBJ 1st cohort | Controlled-access (Type I) | 2022/07/28 |
| JGAS000561 | NMR metabolic biomarkers for 1,285 patients from BBJ 1st cohort | Controlled-access (Type I) | 2022/09/08 |
| JGAS000561 (Data addition) | NMR metabolic biomarkers for 2,570 patients from BBJ 1st cohort | Controlled-access (Type I) | 2023/04/24 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| Participants/Materials |
11,716 patients from BBJ 1st cohort and 42,689 patients from BBJ 2nd cohort ICD10: C34, C15, C16, C18-C21, C22, C25, C23, C24, C61, C50, C53, C54, C56, C81-C86, C90-C93, I63, G45.9, I67.1, G40, J45, A15-A19, J44.9, J84.1-9, I21.0-9, I20.0, I20.1, I20.8, I20.9, R00, I44.0-3, I45.5-6, I47-I49, I50, I70.9, B18.1, B18.2, K74.6, N04, N20-N23, M80-M81, E10, E11, E88.8, E78.0-5, E78.8-9, E05.0, M05-M06, J30.1, L91.0, L20, L51.1-2, L27.0, D25, N80, R56.0, H40, H25-H26, K05, G12.2, I61, C64 |
| Targets | genome wide SNPs |
| Target Loci for Capture Methods | - |
| Platform | Illumina [Asian Screening Array (ASA-24v1-0_A2)] |
| Library Source | DNAs extracted from peripheral blood cells or saliva |
| Cell Lines | - |
| Reagents (Kit, Version) | Infinium Asian Screening Array-24 v1.0 BeadChip Kit |
| Genotype Call Methods (software) | GenomeStudio |
| Marker Number (after QC) | 657,060 SNVs (GRCh38) |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000529 |
| Total Data Volume | 1,020 GB (idat, csv, plink binary) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
180,882 patients from BBJ 1st cohort ICD10: A15-A16, B16-B17.0, B18.0-B18.1, B17.1, B18.2, C15, C16, C18, C22, C23-C24, C25, C33-C34, C50, C53, C54, C56, C61, C81, D25, E05, E10, E78.0-E78.5, G12, G40-G41, H25-H26, H40-H42, I20, I21-I22, I44-I49, I50, I60, I69.0, I63, I69.3, I70, J30, J41-J44, J45-J46, J80-J84, K05, K74.3-K74.6, L00-L99, L20, M05-M06, M80-M82, N04, N20-N23, N80, R00-R9 |
| Targets | genome wide SNVs |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HumanOmniExpressExome, HumanOmniExpress, HumanExome] |
| Library Source | DNAs extracted from peripheral blood cells or saliva |
| Cell Lines | - |
| Reagents (Kit, Version) | HumanOmniExpressExome-8, HumanOmniExpress-12, HumanExome-12 kit |
| Genotype Call Methods (software) |
GenomeStudio Software Eagle software (v2.4.1) without a reference panel Minimac4 software (v1.0.2) |
| Reference Genome Sequence | TOPMed reference panel (Version R2 on GRC38) |
| Filtering Methods |
Before imputation, we excluded SNPs using the following criteria: - Heterozygosity count for each chip < 5 - P-value for Hardy–Weinberg equilibrium (HWE) for each chip < 1.0 x 10^-6 * - Genotype concordance rate with whole-genome sequencing (WGS) for 939 samples < 99.5% and its non-reference discordance rate >= 0.5% - Lower call rate SNPs if the position was the same when merging datasets - Call rate < 99% * P-values for chrX SNPs were calculated by using female samples We also excluded samples using the following criteria ： - Call Rate < 98% - Samples whose inferred sex was not matched with the clinical information - Lower call rate samples for duplicated or monozygotic twin in the dataset - Outliers from East Asian clusters from principal component analysis with 1KGp3v5 samples. |
| Marker Number (after QC) |
autosomes: 515,587 SNVs (GRCh38) X-chromosome: 11,140 SNVs (GRCh38) |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000660 |
| Total Data Volume | 11.1 TB (vcf, tbi) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
1,285 + 2,570 patients from BBJ 1st cohort: 1,286 + 2,573 samples Total: 3,841 patients (3,859 samples) ICD10: R00, I44.0-3, I45.5-6, I47-I49, I70.9, L20, J45, I67.1, I63, G45.9, C50, I50, I21.0-9, H25-H26, C53, B18.1, B18.2, C18-C21, J44.9, L51.1-2, L27.0, E10, E11, E88.8, N80, G40, C15, D25, C23, C24, H40, E05.0, K05, R56.0, C81-C86, C90-C93, C22, J30.1, E78.0-5, E78.8-9, J84.1-9, L91.0, K74.6, C34, N04, M80-M81, C56, C25, A15-A19, C61, M05-M06, I20.1, I20.8, I20.9, C16, N20-N23, I20.0, C54 |
| Targets | metabolome (NMR) |
| Target Loci for Capture Methods | - |
| Platform | Bruker [AVANCE III HD] |
| Source | serum samples |
| Cell Lines | - |
| Parameters | Nightingale Health's proprietary software (quantification library 2020) |
| Noise reduction & Data correction | Nightingale Health's proprietary software (quantification library 2020) |
| Annotation | Nightingale Health's proprietary software (quantification library 2020) |
| Quantification Methods (software) | Nightingale Health's proprietary software (quantification library 2020) |
| Metabolic biomarkers | 250 metabolites (List) |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000683 |
| Total Data Volume | 7.1 + 15.3 MB (xlsx) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Koichi Matsuda
Affiliation: Graduate school of Frontier Science, The University of Tokyo
Project / Group Name: Management of disease-oriented biobank in Japan for utilization
URL： https://biobankjp.org/en/index.html
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) | Management of disease-oriented biobank in Japan for utilization |
JP20km0605001 JP21km0405215 |
| Platform Program for Promotion of Genome Medicine, Japan Agency for Medical Research and Development (AMED) | Phenotype-wide association study of 180,000 Biobank Japan samples using high density imputation of TOPMED reference panel | JP21km0405215 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | |||
| 2 |
USERS (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Seishi Ogawa | Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University | Japan | Analysis on the relationship between clonal hematopoiesis and COVID-19 infection. | JGAD000529 | 2022/08/15-2026/03/31 |
| Yukinori Okada | Department of Statistical Genetics, Osaka University Graduate School of Medicine | Japan | Development of statistical genetic analysis methods using the whole-genome data from B cell lines of Japanese individuals | JGAD000529, JGAD000660 | 2022/09/12-2025/03/31 |
