| Population name | Namkoong |
| Genome | GRCh37 |
| Consortium | Japan COVID-19 Task Force |
| Super population | EAS |
| Population description | Japanese COVID-19 hospitalised patients consisting of 990 critical individuals requiring artificial respiratory support or intensive care. 1391 with non severe disease and 12 with unknown effect. Severe cases were older in age and predominantly male gender. Controls included the general Japanese population |
| Population origin | Japan |
| Case population size | 2393 |
| Control population size | 3289 |
| Comorbidities | Other than age >65, no comorbidities were described for the case or control populations. |
| Mean / median age | 56.0 ± 18.9 |
| Sex | 64.2% male, 35.8% female |
| Severity | Severe |
| Sample source | Nasopharyngeal swab / Whole blood |
| Method | Illumina Infinium Asian Screening Array used for cases and controls and SNP results used for the GWAS analysis. |
| Bioinformatics | PCA analysis was applied to remove outliers and non Japanese individuals. GWAS conducted using logistic regression for each variant using PLINK2 software. Meta-analysis of the Japanese discovery GWAS and the pan-ancestry analysis was conducted using an inverse-variance method assuming a fixed-effects model. Logistic regression and R statistical software used for ABO blood group analysis. |
| Imputation details | Minimac4 software used for imputation. A Japanese population-specific imputation reference panel combined with 1000 Genomes Project Phase used. QC filters of MAF ? 0.1% and imputation score >0.5 applied. Where lead variants were obtained by imputation, accuracy was assessed using WGS data. HLA genotype imputation was performed using DEEP*HLA software (version 1.0). |
| Limitations | The reference panels are used to impute the data do not seem to be uploaded to a repository, which would be crucial for other studies looking to include East Asian genetic diversity into panels for populations with high levels of admixture including people of East Asian origin. The article has not yet been peer-reviewed as of entry into this database. |