Skip to content
NBDC Human Database

No datasets in the cart.

Go to the cart

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

NHA000078

Type of data
meta analysis of 4 GWASs for T2DM
Access criteria
Unrestricted-access
Total data volume
233 MB
File formats
  • XLSX
  • ZIP
Research
hum0014
Date published
2019-01-25
Date modified
2019-01-25
Secondary ID
hum0014.v13.T2DMmeta.v1

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
header_definition_hum0014.v13.xlsxDictionary file9.8 KB
hum0014.v13.T2DMmeta.v1.zip233 MB

Analysis method

Genotyping by array

Materials and participants
[GWAS-1]
- 9,804 T2DM patients (ICD-10: E11)
- 6,728 controls
[GWAS-2]
- 5,639 T2DM patients (ICD-10: E11)
- 19,407 controls
[GWAS-3]
- 18,688 T2DM patients (ICD-10: E11)
- 121,950 controls
[GWAS-4]
- 2,483 T2DM patients (ICD-10: E11)
- 7,065 controls
  • Health status
    Mixed
  • Subject count
    191,764 (Individual)
Disease
T2DM patients (E11)
Sample description
gDNA extracted from peripheral blood cells
  • Tissue
    Peripheral blood
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
Genotyping by array
Target
N/A
Reagent kit
Human610-Quad BeadChip Kit
HumanExome BeadChip Kit
HumanOmniExpress BeadChip Kit
HumanOmniExpressExome BeadChip Kit
Platform
Illumina Human610-Quad
Illumina HumanExome
Illumina HumanOmniExpress
Illumina HumanOmniExpressExome
Reference genome
GRCh37
QC and filtering
Genotyping QC:
exclusion criteria of GWAS1, GWAS3, GWAS4
(i) hetero count < 5
(ii) HWE P < 1.0 × 10^-6 on each chip
(iii) genotype concordance rate < 0.99 with in-house WGS data
(iv) SNV call rate < 0.99

exclusion criteria of GWAS2
(i) SNV call rate < 0.99
(ii) MAF < 0.01
(iii) differential missingness P < 1.0 × 10^-6
(iv) HWE P < 1.0 × 10^-6

Imputation QC:
HWE P < 1 × 10^-6 or MAF < 0.01 in the reference panel
Imputation quality (Rsq) < 0.3 in more than two GWAS
Imputation
minimac [imputation(1000 genomes Phase 3)]
Analysis method
GenCall software (GenomeStudio)
Variant count
12,557,761 SNPs
Processed data type
GWAS summary statistics
Phenotype data
Included
Data use policy
NBDC data sharing policy (JGAP000001)