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 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

*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

MOLECULAR DATA

JGAS00000000018


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