NBDC Research ID: hum0028.v2

 

SUMMARY

Aims: Construction of the HLA imputation reference panel of the Japanese healthy controls

Methods: SNPs in the HLA region were genotyped by Illumina BeadChips (HumanOmniExpress BeadChip, HumanExome BeadChip, Immunochip, HumanHap550v3 Genotyping BeadChip) and HLA alleles (HLA-A/C/B/DRB1/DQA1/DQB1/DPA1/DPB1) were determined by WAKFlow HLA typing kit or sequence based method.

Participants/Materials: 908 Japanese healthy controls

URL: http://biobankjp.org/english/index.html

 

Dataset IDType of DataCriteriaRelease Date
JGAS000018

HLA alleles and SNPs

in HLA region (7 loci)

Controlled-access (Type I) 2015/06/02
JGAS000018 HLA-DQA1 alleles and SNPs were added Controlled-access (Type I) 2018/06/05

*Release Note

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

 

MOLECULAR DATA

JGAS000018

Participants/Materials: 908 Japanese healthy controls
Targets Target Capture
Target Loci for Capture Methods

HLA region (chr6:29,000,000-34,000,000, GRCh37)

8817 polymorphisms

(7149 SNPs, HLA 2-digit/4-digit polymorphisms: 226, HLA amino acid polymorphisms: 1442)

Platform Illumina BeadChips [HumanOmniExpress BeadChip, HumanExome BeadChip, Immunochip, HumanHap550v3 Genotyping BeadChip] and WAKFlow HLA typing kit
Source gDNAs extracted from peripheral blood cells
Cell Lines -
Library Construction (kit name) Illumina BeadChip Kits [HumanOmniExpress BeadChip, HumanExome BeadChip, Immunochip, HumanHap550v3 Genotyping BeadChip] and WAKFlow HLA typing kit
Genotyping Call Methods (software) GenCall software (GenomeStudio)
Filtering Methods Sample Call Rate < 0.98, SNP Call Rate < 0.99, HWE-P < 1x10^-6
Marker Number (after QC) 8817 SNPs (GRCh37)
Japanese Genotype-phenotype Archive Dataset ID JGAD000018
Total Data Volume 50 MB
Comments (Policies) NBDC policy

 

DATA PROVIDER

Principal Investigator: Michiaki Kubo

Affiliation: RIKEN Center for Integrative Medical Science

Project / Group Name: Laboratory for Genotyping Development and Laboratory for Statistical Analysis

URL: http://www.ims.riken.jp/english/

 

Funds / Grants (Research Project Number):

NameTitleProject Number
Ministry of Education, Culture, Sports, Science and Technology in Japan Tailor-made Medical Treatment Program (the 3rd phase) -

 

PUBLICATIONS

TitleDOIData ID
1 Construction of a population-specific HLA imputation reference panel and its application to Graves’ disease risk in Japanese doi:10.1038/ng.3310 JGAD000018

 

USERS (Controlled-access Data)

Principal InvestigatorAffiliationCountry/RegionResearch TitleData in Use (Dataset ID)Period of Data Use
Takashi Kohno National Cancer Center, Division of Genome Biology JGAD000018 2016/02/15-2019/12/31
Tsuneyo Mimori Department of Rheumatology and Clinical Immunology, Kyoto University Graduate School of Medicine JGAD000018 2016/06/06-2021/03/13
Emiko Noguchi Department of Medical Genetics, Faculty of Medicine, University of Tsukuba JGAD000018 2016/08/25-2022/04/01
Yukinori Okada Department of Statistical Genetics, Osaka University Graduate School of Medicine JGAD000018 2018/09/20-2021/03/31
Eisei Noiri The University of Tokyo・University Hospital JGAD000018 2018/12/18-2019/07/30
Emiko Noguchi Faculty of Medicine, University of Tsukuba Genome analysis for Wheat Dependent Exercise-Induced Anaphylaxis and Search for Appropriate Wheat Species JGAD000018 2020/02/28-2023/03/31
Emiko Noguchi Faculty of Medicine, University of Tsukuba Search for genetic factors associated with allergic diseases JGAD000018 2020/02/28-2023/03/31
Emiko Noguchi Faculty of Medicine, University of Tsukuba Identification of factors associated with allergic diseases and their associated phenotypes JGAD000018 2020/02/28-2021/03/31
Yohei Kirino Department of Stem Cell and Immune Regulation, Yokohama City University Graduate School of Medicine Genetic analysis for an immune-related adverse event caused by immune checkpoint inhibitors JGAD000018 2020/06/10-2022/03/31
Taisei Mushiroda Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences SNP analysis of wheat allergy JGAD000018 2021/03/16-2022/03/31
Emiko Noguchi Faculty of Medicine, University of Tsukuba Comprehensive analysis of the pathogenesis of chronic eosinophilic inflammatory diseases JGAD000018 2021/04/19-2022/04/01
Hajime Yoshifuji Department of Rheumatology and Clinical Immunology, Kyoto University Graduate School of Medicine To impute HLA alleles of patients with autoimmune diseases and healthy people to fine-map the HLA region to clarify the associations between the HLA locus and diseases susceptibility or diseases' phenotypes JGAD000018 2021/07/16-2026/03/13
Emiko Noguchi Department of Medical Genetics, Faculty of Medicine, University of Tsukuba Identification of the pathogenic factors for food allergy JGAD000018 2021/12/03-2025/03/31
Hajime Yoshifuji Department of Rheumatology and Clinical Immunology, Kyoto University Graduate School of Medicine Japan To impute HLA alleles of patients with autoimmune diseases and helathy people to fine-map the HLA region to clarify the associations between the HLA locus and diseases susceptibility or diseases' phenotypes JGAD000018 2022/06/20-2026/03/13
Emiko Noguchi Department of Medical Genetics, Faculty of Medicine, University of Tsukuba Japan Research on genetic predisposition to inflammatory lung disease JGAD000018 2022/09/19-2027/03/31
Koya Fukunaga Division of Medical Safety Science, National Institute of Health Sciences Japan Research on the biomarkers associated with drug-induced interstitial pneumonia JGAD000018 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 JGAD000018 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 JGAD000018 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 JGAD000018 2023/02/08-2026/03/31
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 JGAD000018 2023/04/10-2024/03/31
Emiko Noguchi Department of Medical Genetics, Faculty of Medicine, University of Tsukuba Japan Genome wide association study for WDEIA and exploration of wheat products JGAD000018 2024/05/09-2026/03/31
Takeshi Kaneko Respiratory medicine, Yokohama City University Hospital Japan Clarification of genetic factors involved in COVID-19 JGAD000018 2024/06/19-2025/03/31
Kouya Shiraishi Department of Clinical Genomics, National Cancer Center Research Institute Japan Search for genes involved in susceptibility to lung cancer JGAD000018 2024/06/24-2025/12/31