NBDC Research ID: hum0012.v1



Aims : Contribution to the promotion of the citizen’s health and the development of the preventive medicine

Methods : Genotypes were determined by using of several SNP-arrays (Multipurpose prospective cohort study about the citizen)

Materials : 3712 Japanese participants

URL: http://zeroji-cohort.com/english/


Data Set IDType of DataCriteriaRelease Date
JGAS00000000012 Genotype data of 3712 participants in Nagahama Zero-ji preventive cohort study Controlled Access (Type I) 2015/08/19

*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





3712 Japanese healthy controls

Platforms used for the genotype-determination were different among samples

Targets genome wide SNPs
Target Loci for Capture Methods -
Platform Illumina Genotyping Arrays
Source gDNA extracted from peripheral blood
Cell Lines -
Reagents (Kit, Version)

Illumina Human610-Quad Beadchip Kit

HumanOmni2.5-4v1 BeadChip Kit

HumanOmni2.5-8v1 BeadChip Kit

HumanOmni2.5S-8v1 BeadChip Kit

HumanExome-12v1 BeadChip Kit

HumanCoreExome-12v1 BeadChip Kits

Genotype Call Methods (softwares) GenCall software (GenomeStudio)

Marker Numbers (without any filtering)

※Illumina Final Report format files

Human610-Quad: 620,901 SNPs

HumanOmni2.5-4v1: 2,443,177 SNPs

HumanOmni2.5-8v1: 2,379,855 SNPs

HumanOmni2.5S-8v1: 2,015,318 SNPs

HumanExome-12v1: 247,870 SNPs

HumanCoreExome-12v1: 538,448 SNPs

Filtering Methods

Surrounding sequences of each probe were aligned by using of BLAST algorithm.

(Probes for copy number variants, unmapped probes, and multi-mapped probes were removed.)

Marker Numbers (after QC)

※ped/map format files

Human610-Quad: 597,140 SNPs

HumanOmni2.5-4v1: 2,431,379 SNPs

HumanOmni2.5-8v1: 2,372,060 SNPs

HumanOmni2.5S-8v1: 2,008,033 SNPs

HumanExome-12v1: 246,805 SNPs

HumanCoreExome-12v1: 518,247 SNPs

Japanese Genotype-phenotype Archive Data set ID JGAD00000000012
Total Data Volume 5 GB (Illumina Final Report format or ped/map format*1)
Comments (Policies) NBDC policy

*1 The Illumina Final Report format files: Genotype data for each sample of each platform. The ped/map format files: Genotype lists for all samples of each platform. The sample-platform correspondence table is here.



Principal Investigator: Fumihiko Matsuda

Affiliation: Center for Genomic Medicine Kyoto University Graduate School of Medicine

Project / Groupe Name: Nagahama Zero-ji preventive cohort project

URL: http://zeroji-cohort.com/english/

Funds / Grants (Research Project Number):

NameTitleProject Number
Special Research Grant (Management Expenses Grants) Regional cohort project using genomic medicine -
Takeda Science Foundation (The Specific Research Grant) Elucidation of genetic factors responsible for lifestyle diseases using the 10,000 genome cohort -

Health and Labor Sciences Research Grants

- Research Project on Applying Health Technology

Investigating the cause for intractable diseases using comprehensive integrated omics analyses and the establishment of new diagnostics / treatment 11103334



TitleDOIData Set ID
1 A genome-wide association study of serum levels of prostate specific antigen in the Japanese population. doi: 10.1136/jmedgenet-2014-102423 JGAD00000000012
2 Three missense variants of metabolic syndrome-related genes are associated with alpha-1 antitrypsin levels doi:10.1038/ncomms8754 JGAD00000000012


USERS (Controlled Access Data)

PIAffiliationData in Use (Data Set ID)Period of Data Use
Emiko Noguchi Department of Medical Genetics, Faculty of Medicine, University of Tsukuba JGAD00000000012 2016/08/25-2022/04/01