NBDC Research ID: hum0012.v1
SUMMARY
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/
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000012 | Genotype data of 3712 participants in Nagahama Zero-ji preventive cohort study | Controlled-access (Type I) | 2015/08/19 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| Materials |
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 Dataset ID | JGAD000012 |
| 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.
DATA PROVIDER
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):
| Name | Title | Project 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 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | A genome-wide association study of serum levels of prostate specific antigen in the Japanese population. | doi: 10.1136/jmedgenet-2014-102423 | JGAD000012 |
| 2 | Three missense variants of metabolic syndrome-related genes are associated with alpha-1 antitrypsin levels | doi:10.1038/ncomms8754 | JGAD000012 |
USERS (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Emiko Noguchi | Department of Medical Genetics, Faculty of Medicine, University of Tsukuba | JGAD000012 | 2016/08/25-2022/04/01 | ||
| Yukinori Okada | Department of Statistical Genetics, Osaka University Graduate School of Medicine | Development of statistical genetic analysis methods using the whole-genome data from B cell lines of Japanese individuals | JGAD000012 | 2019/10/17-2021/03/31 | |
| Yoshihiro Asano | Department of Cardiovascular Medicine, Graduate School of Medicine, Osaka University | Sensitive gene analysis of hereditary cardiovascular disease | JGAD000012 | 2021/06/18-2022/05/31 | |
| Yoshinori Yoshida | Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application, Kyoto University | Japan | Prospective REgistry to eVAluate the predIctors and clinicaL management of HCM | JGAD000012 | 2022/12/26-2024/03/31 |
