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 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

*Release Note

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

MOLECULAR DATA

JGAS000018


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