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 |
|---|---|---|---|
| JGAS00000000018 |
HLA alleles and SNPs in HLA region (7 loci) |
Controlled-Access (Type I) | 2015/06/02 |
| JGAS00000000018 | HLA-DQA1 alleles and SNPs were added | Controlled-Access (Type I) | 2018/06/05 |
* Data users need to apply the Form 2 (Application Form for Using NBDC Human Data) to reach the Controlled Access Data. Learn more
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 | JGAD00000000018 |
| 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 | JGAD00000000018 |
USERS (Controlled-Access Data)
| Principal Investigator: | Affiliation: | Data in Use (Data Set ID) | Period of Data Use |
|---|---|---|---|
| Takashi Kohno | National Cancer Center, Division of Genome Biology | JGAD00000000018 | 2016/02/15-2019/12/31 |
| Tsuneyo Mimori | Department of Rheumatology and Clinical Immunology, Kyoto University Graduate School of Medicine | JGAD00000000018 | 2016/06/06-2021/03/13 |
| Emiko Noguchi | Department of Medical Genetics, Faculty of Medicine, University of Tsukuba | JGAD00000000018 | 2016/08/25-2022/04/01 |
| Yukinori Okada | Department of Statistical Genetics, Osaka University Graduate School of Medicine | JGAD00000000018 | 2018/09/20-2021/03/31 |
| Eisei Noiri | The University of Tokyo・University Hospital | JGAD00000000018 | 2018/12/18-2019/07/30 |
