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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.
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Dataset ID

NHA000068

Type of data
GWAS for POAG
Access criteria
Unrestricted-access
Total data volume
116 MB
File formats
  • HTML
  • ZIP
Research
hum0014
Date published
2018-04-04
Date modified
2018-04-04
Secondary ID
hum0014.v7.POAG-1.v1, hum0014.v7.POAG.v1

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
hum0014.v7.POAG.v1.zip116 MB
hum0014_README_POAG_GWAS.htmlDictionary file24.8 KB

Analysis method

Genotyping by array

Materials and participants
3980 POAG patients (Male: 1,997, Female: 1,983)
18,815 controls (Male: 7,817, Female: 10,998)
  • Sex
    Mixed
Disease
POAG patients (H401)
Sample description
gDNA extracted from peripheral blood cells
  • Tissue
    Peripheral blood
Sample provider
N/A
Experimental method
Genotyping by array
Target
N/A
Platform
Illumina HumanExome
Illumina HumanOmniExpress
Illumina HumanOmniExpressExome
Reference genome
GRCh37
QC and filtering
Genotyping QC: sample call rate < 0.98, SNV call rate < 0.99, HWE P < 1 x 10^-6
QC for reference panel: After excluding 11 closely related individuals, variants with HWE P < 1.0 x 10^-6, MAF < 0.01 were excluded.
QC after imputation: Variants with imputation quality of Rsq < 0.7 were excluded. We also excluded variants with |beta| > 4 in the uploaded files.
Imputation
minimac (ver. 0.1.1) [imputation (1000 genomes Phase I v3)]
Variant count
Autosomes: 5,961,428 SNPs
Male X chromosome: 147,351 SNPs
Female X chromosome: 147,353 SNPs
Data use policy
NBDC data sharing policy (JGAP000001)