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
Data Set 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 |
* Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data.
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 Data set 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 (Data Set 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 |