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Dataset ID

NHA000169

Type of data
GWAS for COVID-19
Access criteria
Unrestricted-access
Total data volume
1.4 GB
File formats
  • XLSX
  • ZIP
Research
hum0343
Date published
2022-05-26
Date modified
2022-05-26
Secondary ID
hum0343.v1.covid19.v1

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
gwas-1.zipGWAS-1370 MB
gwas-2.zipGWAS-2362 MB
gwas-3.zipGWAS-3363 MB
gwas-4.zipGWAS-4350 MB
hum0343.v1.covid19.v1_header_definition.xlsxDictionary file9.8 KB

Analysis method

Genome wide SNPs

Materials and participants
[GWAS-1]
COVID-19 (ICD-10: U071): 2,393 cases, Healthy controls: 3,289 individuals
[GWAS-2]
Severe COVID-19: 990 cases and 3,289 healthy controls from [GWAS-1]
[GWAS-3]
COVID-19 under age 65: 1,484 cases and 2,377 healthy controls under age 65 from [GWAS-1]
[GWAS-4]
Severe COVID-19 under age 65: 440 cases and 2,377 healthy controls under age 65 from [GWAS-3]
  • Health status
    Mixed
  • Subject count
    5682 (Individual)
Disease
COVID-19 (U071)
Sample description
DNAs extracted from peripheral blood cells
  • Tissue
    Peripheral blood
  • Tumor / normal
    Normal
Experimental method
Genotyping by array
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 < 0.97
(2) excess heterozygosity of genotypes > mean + 3SD
(3) related samples with PI_HAT > 0.175
(4) outlier samples from East Asian clusters in principal component analysis with 1000 Genomes Project samples.
Genotyping QC: We excluded variants with
(1) variant call rate < 0.99
(2) significant call rate differences between cases and controls with P < 5.0×10-8
(3) deviation from Hardy-Weinberg equilibrium with P < 1.0×10-6
(4) minor allele count < 5
Imputation QC: MAF ≥ 0.1% and imputation score (Rsq) > 0.5
Imputation
haplotype phasing: SHAPEIT4 (autosome), SHAPEIT2 (X-chromosome)
imputation: Minimac4
Analysis method
genotyping: GenomeStudio
Association Analysis: PLINK2
Variant count
13,484,569 variants ([GWAS-1])
13,199,053 variants ([GWAS-2])
13,241,602 variants ([GWAS-3])
12,764,136 variants ([GWAS-4])
Processed data type
Imputed genotype data
Phenotype data
Included
Data use policy
NBDC data sharing policy (JGAP000001)