NBDC Research ID: hum0028.v1

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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


Data Set IDType of DataCriteriaRelease Date

HLA alleles and SNPs

in the HLA region

Controlled-Access (Type I) 2015/06/02

*Release Note

* Data users need to apply the Form 2 (Application Form for Using NBDC Human Data) to reach the Controlled Access Data. Learn more





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)


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 Data set ID JGAD00000000018
Total Data Volume 50 MB
Comments (Policies) NBDC policy



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)




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 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