NBDC Research ID: hum0028.v1
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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/DQB1/DPA1/DPB1) were determined by WAKFlow HLA typing kit.
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 the HLA region |
Controlled-access (Type I) | 2015/06/02 |
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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, NCBI36) 8563 polymorphisms (7176 SNPs, HLA 2-digit/4-digit polymorphisms: 202, HLA amino acid polymorphisms: 1185) |
| 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) | 8563 SNPs (NCBI36) |
| 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: | 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 |
