| Population name | Wang |
| Genome | GRCh38 |
| Consortium | Universities, Hospitals and Institutes in China |
| Super population | EAS |
| Population description | COVID-19 hospitalised patients from Shenzhen Third People’s Hospital, China. Of the recruited patients, 25 (7.5%), 12 (3.6%), 225 (67.8%), 53 (16.0%), and 17 (5.1%) patients were defined as asymptomatic, mild, moderate, severe, and critically ill, respectively. |
| Population origin | Chinese |
| Case population size | 332 |
| Control population size | 966 |
| Comorbidities | >50% of patients with one comorbidity, not specified. Severe COVID category had 58.8% of patients with a comorbidity vs. mild at 45.1% |
| Mean / median age | not specified |
| Sex | 135 male; 149 female |
| Severity | Severe |
| Sample source | Nasopharyngeal swab |
| Method | "Deep whole genome sequencing (46x) was used to maximise statistical power due to small sample size with the DNBSEQ platform. Loss of function, rare and common variants were analysed. Loss of function and rare variants were assessed in related individuals and common variants were also analysed in the study cohort. Both single variant and gene-based GWAS werewere performed. Joint-calling of the genetic variants of the unrelated COVID-19 patients (n = 284) and the publicly available Chinese genome |
| Bioinformatics | "Variation detection and genotyping performed using GATK joint genotyping framework. Sentieon Genomics software was used to perform genome alignment and variant detection. The analysis pipeline was bulit according to the Broad institute best practices workflows with variant calibration and filtration using GATK and variant prediction with Variant effect predictor software. PLINK and KING were used for kinship analysis with the Genesis R package for PCA used for genotype–phenotype association tests using the default parameters. Genome-wide significance for single variant association test as 5e–8, suggestive significance as 1e–5 and for gene-based association test as 1e–6." |
| Imputation details | not specified |
| Limitations | a. Sample size of 332 is only just sufficient to identify genome-wide significant genetic variants with MAF greater than 0.2 and odds ratio greater than 1.8 given type I error rate 0.05. b. Patients recuited from hospital had limited information from asymptomatic individuals in comparison to the severe cases. |