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Dataset ID

NHA000210

Type of data
GWAS for severe COVID-19
Access criteria
Unrestricted-access
Total data volume
272 MB
File formats
  • TXT
  • ZIP
Research
hum0343
Date published
2026-08-13
Date modified
2026-08-13
Secondary ID
hum0343.v5.covid19.v1

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
hum0343.v5.covid19.v1.zip272 MB
hum0343.v5.covid19.v1_dictionary_file.txtDictionary file421 B

Analysis method

Genome wide SNPs

Materials and participants
severe COVID-19 (ICD-10: U071): 3,087 cases
Healthy controls: 55,896 individuals
  • Health status
    Mixed
  • Subject count
    58,983 (Individual)
Disease
severe COVID-19 (U071)
Sample description
DNAs extracted from peripheral blood cells
  • Tissue
    Peripheral blood
Sample provider
N/A
Experimental method
Genotyping by array
Target
N/A
Reagent kit
Infinium Asian Screening Array Kit
Platform
Illumina Infinium Asian Screening Array
QC and filtering
Sample QC: We excluded samples with
(1) sample call rate < 0.98
(2) deviation from the East Asian cluster based on PCA
(3) duplicate/twin samples
Variant QC: We excluded variants with
(1) variant call rate < 0.99
(2) allele count < 5
(3) Hardy-Weinberg equilibrium P < 1.0 × 10^-6
(4) >5% allele frequency deviation from the Japanese reference population
Genotype imputation was performed using an in-house Japanese whole-genome sequencing reference panel (n = 11,754). Variants with imputation INFO > 0.7 and allele frequency > 0.005 were retained. Genome-wide association analysis was conducted using REGENIE with age, sex, age × age, age × sex, and PC1-10 as covariates.
Imputation
haplotype phasing: SHAPEIT4
imputation: Minimac4
Analysis method
genotyping: GenomeStudio
association analysis: REGENIE
Variant count
8,993,355
Processed data type
Imputed genotype data
Phenotype data
Included
Data use policy
NBDC data sharing policy (JGAP000001)