NBDC Research ID: hum0311.v6

 

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

                 Genome-wide association study (GWAS) for peptic ulcers

Participants/Materials: BBJ 1st cohort (n = 11,716 + 180,882 + 1,285 + 2,570 + 40,907), BBJ 2nd cohort (n = 42,689), ToMMo (n = 49,621), UK biobank (n = 456,327), and FinnGen (n = 230,635)

URL: https://biobankjp.org/en/index.html

 

Dataset IDType of DataCriteriaRelease 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
hum0311.v5.gwas.v1 GWAS for peptic ulcers Unrestricted-access 2023/07/27
JGAS000561 (Data addition) NMR metabolic biomarkers for 40,907 patients from BBJ 1st cohort Controlled-access (Type I) 2024/05/22

*Release Note

* Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more

*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

JGAS000412

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

 

JGAS000541

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

 

JGAS000561

Participants/Materials

1,285 + 2,570 + 40,907 patients from BBJ 1st cohort (1,286 + 2,573 + 41,411 samples)     Total: 43,830 patients (45,270 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 + 217.9 MB (xlsx)
Comments (Policies) NBDC policy

 

hum0311.v5.gwas.v1

Participants/Materials

peptic ulcer (ICD10: K27.9), duodenal ulcer (ICD10: K26.9), gastric ulcer (ICD10: K25.9)

    - BBJ1-180K: ulcers (n = 19,713), control (n = 153,178)

    - BBJ1-12K: ulcers (n = 1,001), control (n = 8,617)

    - BBJ2-42K: ulcers (n = 3,637), control (n = 34,647)

    - EAS meta-analysis: ulcers (n = 29,739), control (n = 240,675)

      (BBJ180K, BBJ1-12K, BBJ2-42k, and TMM-50K)

    - Cross-ancestry meta-analysis (EAS and EUR): ulcers (n = 52,032), control (n = 905,344)

      (BBJ180K, BBJ1-12K, BBJ2-42k, TMM-50K, FinnGen, and UKB)

* Detailed information on participants

Targets genome wide variants
Target Loci for Capture Methods -
Platform

BBJ1-180K: Illumina [HumanOmniExpress、HumanExome、OmniExpressExome BeadChip]

BBJ1-12K and BBJ2-42K: Illumina [Infinium Asian Screening Array BeadChip]

ToMMo: Thermo Fisher Scientific [Axiom Japonica Array JPAv2]

UK Biobank: Applied Biosystems [UK BiLEVE Axiom Array、UK Biobank Axiom Array]

FinnGen: Thermo Fisher Scientific [FinnGen1 ThermoFisher Array or other genotyping arrays]

Library Source DNAs extracted from peripheral blood cells
Cell Lines -
Reagents (Kit, Version)

BBJ: HumanOmniExpress, HumanExome, OmniExpressExome BeadChip kit, Infinium Asian Screening Array BeadChip kit

ToMMo: Axiom 2.0 Reagent kit

UK Biobank: UK BiLEVE Axiom Array、UK Biobank Axiom Array

FinnGen: FinnGen1 ThermoFisher Array or other genotyping arrays

Genotype Call Methods (software)

Genotype Call: GenomeStudio

Pre-phasing: eagle2

Imputation: minimac4 [reference: 1KGP p3v5 ALL]

Association Analysis (software) SAIGE (v0.44)
Filtering Methods

Variants with imputation quality (Rsq) < 0.3 or MAC < 20 were excluded

*Sample QC and Variant QC were described in the Dictionary file

Meta-analysis (software) METAL
Marker Number (after QC)

BBJ1-180K GWAS: ~12,013,066 variants

BBJ1-12K GWAS: ~10,836,527 variants

BBJ2-42K GWAS: ~11,504,022 variants

EAS-specific meta-analysis : ~13,846,852 variants

Cross-ancestry meta-analysis : ~19,078,654 variants

* Detailed information on marker number

NBDC Dataset ID

hum0311.v5.gwas.v1

(Click the Dataset ID to download the files)

Dictionary file

Total Data Volume

9.7 GB (txt)

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):

NameTitleProject 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

TitleDOIDataset ID
1 East Asian-specific and cross-ancestry genome-wide meta-analyses provide mechanistic insights into peptic ulcer disease doi: 10.1038/s41588-023-01569-7 hum0311.v5.gwas.v1
2 Genotype imputation accuracy and the quality metrics of the minor ancestry in multi-ancestry reference panels doi: 10.1093/bib/bbad509 JGAS000541

 

USERS (Controlled-access Data)

Principal InvestigatorAffiliationCountry/RegionResearch TitleData 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
Masaki Kato kansai medical university Japan Exploratory and validation study of genetic and biological factors for the development of precision medicine algorithms for psychiatric disorders JGAD000529 2023/08/25-2028/06/30
Koya Fukunaga Division of Medical Safety Science, National Institute of Health Sciences Japan Research on the biomarkers associated with drug-induced interstitial pneumonia JGAD000529
JGAD000660
2023/02/05-2026/03/31
Koya Fukunaga Division of Medical Safety Science, National Institute of Health Sciences Japan Research on the biomarkers associated with drug-induced liver injury JGAD000529
JGAD000660
2023/02/05-2024/03/31
Koya Fukunaga Division of Medical Safety Science, National Institute of Health Sciences Japan Research on the biomarkers associated with drug-induced myopathy JGAD000529
JGAD000660
2023/02/05-2026/03/31
Koya Fukunaga Division of Medical Safety Science, National Institute of Health Sciences Japan Research on the diagnosis, treatment, and biomarkers for severe cutaneous adverse reactions JGAD000529
JGAD000660
2023/02/08-2026/03/31
Shigeo Kamitsuji Statistical Analysis Division, StaGen Co., Ltd. Japan Genome-Wide Association Study to identify genetic factors for strabismus in Japanese population JGAD000529 2023/02/13-2027/02/28
Yuta Kochi Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University Japan Genetic study of complex diseases through comprehensive analysis of functional genetic variations JGAD000660 2023/04/10-2024/03/31
Hiroki Kimura Department of Psychiatry, Nagoya University Graduate school of medicine Japan Research on elucidation of susceptibility to brain and mental illness (vulnerability to disease onset) and efficacy and side effects of drugs (treatment responsiveness) through genetic analysis JGAD000529 2023/11/17-2025/10/28
Chikashi Terao Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences Japan Research on personalized medicine based on genomics information JGAD000529 2023/11/21-2026/03/31
Yoshihiro Asano National Cerebral and Cardiovascular Center Japan Nationwide Platform for the Promotion of Genomic Medicine in Cardiovascular Diseases JGAD000529 2023/12/14-2035/03/31
Tsukasa Okamoto The Center for Personilized Medicine for Healthy Aging, Tokyo Medical and Dental University Japan Prospective study on analysis of genes causing or related to interstitial pneumonia JGAD000529 2024/04/12-2025/03/31
Chikashi Terao Clinical Research Center, Shizuoka General Hospital Japan Investigation of Genetic Factors Associated with Human Phenotypic Traits JGAD000529,
JGAD000660,
JGAD000683
2024/04/17-2028/12/03
Emiko Noguchi Department of Medical Genetics, Faculty of Medicine, University of Tsukuba Japan Genome wide association study for WDEIA and exploration of wheat products JGAD000529 2024/05/09-2026/03/31
Masao Nagasaki Division of Biomedical Information Analysis, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University Japan Development and application of bioinformatics methods to facilitate the detection of genes associated with multifactorial disorders based on large-scale whole genome sequencing data of Japanese individuals JGAD000529 2024/06/24-2027/03/31
Kouya Shiraishi Department of Clinical Genomics, National Cancer Center Research Institute Japan Search for genes involved in susceptibility to lung cancer JGAD000529 2024/06/24-2025/12/31
Norihiro Kato Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine Japan Study of genetic predisposition of primary aldosteronism and its clinical significance JGAD000529 2024/06/24-2029/03/31
Taisei Mushiroda Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences Japan Search of genomic biomarkers associated with drug-induced eruptions JGAD000529,
JGAD000660
2024/08/01-2028/03/31