| Population name | Pairo-Castineira |
| Genome | GRCh37 |
| Consortium | GenOMICC |
| Super population | EUR |
| Population description | critically ill patients with COVID-19 in the UK population |
| Population origin | Not specified |
| Case population size | 1676 |
| Control population size | 8375 |
| Comorbidities | 28% significant co-morbidity |
| Mean / median age | 57.3 ± 12.1 |
| Sex | 70% male; 30% female |
| Severity | Critical |
| Sample source | Nasopharyngeal swab / Whole blood |
| Method | Genotyping with Illumina Global Screening Array v.3.0. In some cases genotypes and imputed variants were confirmed with Illumina NovaSeq 6000 WGS. Variants were validated using a GWAS of genetic studies with 100 000 genomes and Generation Scotland datasets. |
| Bioinformatics | DRAGEN pipeline used for variant calling. Variants were genotyped with the GATK GenotypeGVCFs tool v.4.1.8.150 and annotated with bcftools v.1.10.2. PLINK 1.9 was used for quality control and association tests. King 2.1 used to remove duplicate individuals with gcta 1.9 used for PCA. Genetic ancestry was inferred using PCA. |
| Imputation details | TOPMed reference panel with BCFtools 1.9. and QCtools 1.3 used for quality control |
| Limitations | The critical sample size was small. Thus, replication of results was sought in the HGI hospitalised COVID-19 vs population analysis, with duplicated samples excluded. |