| Population name | Li |
| Genome | GRCh37 |
| Consortium | Universities, Hospitals and the CDC in China |
| Super population | EAS |
| Population description | Severe or critical COVID-19 cases and mild or moderate control cases were obtained from two cohorts (Huoshenshan and Union hospitals in Wuhan, China). For validation of allele frequencies of the significantly associated SNPs 954 COVID-19 unknown controls of Chinese Ancestry and 2504 Chinese Ancestry individuals from the 1000 genomes project (Phase 3, November 2014) were also included. |
| Population origin | China |
| Case population size | 885 |
| Control population size | 546 |
| Comorbidities | Hypertension, diabetes, coronary artery diseases, chronic hepatitis B, chronic obstructive pulmonary disease, chronic renal diseases, and cancer (statistics not specified) |
| Mean / median age | not specified |
| Sex | not specified |
| Severity | Severe |
| Sample source | Nasopharyngeal swab |
| Method | Genomic DNA was extracted from peripheral whole blood using the QIAamp DNA blood kits (Qiagen). Quality of the isolated genomic DNA was verified using two methods: (1) DNA degradation and contamination on 1% agarose gels; and (2) DNA concentration measured using a Qubit DNA Assay Kit and a Qubit 2.0 Fluorometer (Life Technologies, MA, USA). The Affymetrix Axiom® World Arrays was used for genotyping. |
| Bioinformatics | Genotype callings were performed using Axiom Analysis Suite. SNPs were excluded from further analyses if they were not in chr 1–23 or X, had call rates <90% among all subjects in this study, deviated significantly from HWE among all subjects in this study or had minor allele frequencies (MAF) < 1%. A total of 558,642 SNPs were finally retained. To identify the ancestry outliers, PCA was performed using EIGENSOFT (v3). Autosomal SNPs were used for PCA based on the following criteria: call rate >90%, HW P>0.0001, MAF >10% and LD-pruned r2<0.10. Twenty principal components were estimated for all the cases and controls. PCA analyses was performed on the same SNPs for samples from the 1000 Genomes Project and the COVID-19 unknown controls. GWA tests were performed on SNPTEST software using logistic regression models adjusting for covariates and the top five PCAs. eQTL analysis to determine the causative genes were performed using the QTLbase, GTEx v8, Immunopop QTL browser and two independe |
| Imputation details | Imputation was performed using SHAPEIT (v2) and IMPUTE (v4). A prephasing strategy for the Huoshenshan and Union cohorts was performed by SHAPEIT, using the 1K Project data (Phase 3, November, 2014) as the reference based on hg19. IMPUTE4 was used to impute the phased haplotypes constructed by SHAPEIT. For the imputation of chr X, males were coded as diploid in non-pseudoautosomal regions. SNPs with IMPUTE4 info scores below 0.6 or MAF < 0.01 were excluded. A separate independent imputation anal |
| Limitations | Further functional studies required for the roles of the two loci in COVID-19 pathogenesis |