| Population name | Zhang |
| Genome | GRCh37 |
| Consortium | COVID Human Genetic Effort (HGE) |
| Super population | not specified |
| Population description | Various nationalities from Asia, Europe, Latin America, and the Middle East. Subjects enrolled in clinical trials across France, French Guiana and Italy. Patients with life-threatening COVID-19 pneumonia requiring ICU admission (Death in 13.9% associated with COVID-19). Control population were asymptomatic or developed mild disease. |
| Population origin | Not specified |
| Case population size | 659 |
| Control population size | 534 |
| Comorbidities | Not specified |
| Mean / median age | 51.8± 15.9 |
| Sex | 25.5% female; 74.5% |
| Severity | Critical |
| Sample source | Nasopharyngeal swab / Whole blood |
| Method | Whole exome and whole genome sequencing of subjects and controls using Illumina NovaSeq6000 system. Variants analysed from 13 gene loci known to affect type I IFN pathways. Predicted loss of function (LOF) mutations further assessed in vitro for expression and functionality. |
| Bioinformatics | GATK was used to analyse WES. Read alignment analysed with Burrows–Wheeler Aligner software and Picard for QC. Variants curated using Integrative Genomics Viewer (IGV) and confirmed to affect the main functional protein isoform. HMZDelFinder and CANOES algorithms used to detect deletions. Logistic regression with the likelihood ratio test used to compare cases and controls with loss of function variants with PCA used to account for ethnic heterogeneity in PLINK 1.9 software. |
| Imputation details | NA |
| Limitations | Variants were classified according to genotype. Of the 24 LOF variants indicated, supplementary data provided RSID numbers for 6 variants only with the HGVS allocations missing for others. |