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 ID | Type of Data | Criteria | Release 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 |
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MOLECULAR DATA
| 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):
| Name | Title | Project Number |
|---|---|---|
| Ministry of Education, Culture, Sports, Science and Technology in Japan | Tailor-made Medical Treatment Program (the 3rd phase) | - |
PUBLICATIONS
| Title | DOI | Data 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 Investigator | Affiliation | Country/Region | Research Title | Data 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 |
