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Due to system maintenance, the application system, application review by the Data Access Committee will be unavailable during the following period.
Schedule: October 5th (Mon), 2026, 9:00 - October 7th (Wed), 2026, 15:00 (JST)
We apologize for any inconvenience this may cause and appreciate your understanding.

We are currently receiving a large number of applications for data submission, and the review process is taking longer than usual.We sincerely apologize for the delay and kindly ask for your understanding. When submitting an application, we would greatly appreciate it if you could allow sufficient time for the processing.

Following a change to our organizational structure effective April 1, 2026, this division has been renamed from the "Database Center for Life Science, Joint Support-Center for Data Science Research" to the "Database Division for Life Science (DBCLS), BioData Science Initiative (BSI), National Institute of Genetics (NIG)". Where the former name still appears in the guidelines, please read it as the new name.

Dataset ID

JGAD000012

Type of data
Genotype data of 3712 participants in Nagahama Zero-ji preventive cohort study
Access criteria
Controlled-access (Type I)
Total data volume
126 GB
File formats
  • TAR
  • GZIP
Research
hum0012
Date published
2020-09-28
Date modified
2020-11-19
DDBJ Search
JGAD000012 (opens in a new tab)
JGA Study
JGAS000012 (opens in a new tab)

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
samples-platform_list.xlsxPlatforms used for the genotype-determination were different among samples135 KB

Analysis method

Genotyping by array

Materials and participants
3712 Japanese healthy controls
★Platforms used for the genotype-determination were different among samples★
  • Health status
    Healthy
  • Subject count
    3712 (Individual)
  • Cohort
    Nagahama Cohort
  • Population
    Japanese
Sample description
gDNA extracted from peripheral blood
  • Tissue
    Peripheral blood
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
Genotyping by array
Target
N/A
Reagent kit
Human610-Quad BeadChip Kit
HumanCoreExome BeadChip Kit
HumanExome BeadChip Kit
HumanOmni2.5 BeadChip Kit
Platform
Illumina Human610-Quad
Illumina HumanCoreExome
Illumina HumanExome
Illumina HumanOmni2.5
Illumina HumanOmni2.5S
QC and filtering
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.)
Analysis method
GenCall software (GenomeStudio)
Variant count
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
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
Phenotype data
Included
Data use policy
NBDC data sharing policy (JGAP000001)