| Population name | Cantalupo |
| Genome | GRCh38 |
| Consortium | Universities, Hospitals and Institutes in Italy |
| Super population | EUR |
| Population description | GWAS data obtained from hospitalised cohort of the COVID-19 HGI. The first replication study was performed on genetic data from the 23andMe study hospitalised cohort. The second replication study was performed on genetic data from a selected Italian hospitalised cohort. WES data was obtained from a hospitalised cohort in Southern Italy. |
| Population origin | Italy |
| Case population size | 6406 |
| Control population size | 902088 |
| Comorbidities | not specified |
| Mean / median age | not specified |
| Sex | not specified |
| Severity | Severe |
| Sample source | NA |
| Method | Summary statistics from GWAS meta-analysis of severe COVID-19 cases (COVID-19 HGI) were used to analyse the 3p21.31 region previously associated with severe COVID-19. 52 selected SNPs with suggestive statistical significance and that were eQTLs for CCR5 in lung were assessed.The three SNPs with the highest eQTLs p values in lung were investigated further. To validate the association between rs35951367 and a severe form of COVID-19 disease, we use two independent cohorts of cases and controls. Th |
| Bioinformatics | Allele and genotype frequencies were obtained from gnomAD ; eQTLs analysis was performed by using public data from Genotype-Tissue Expression (GTEx) Portal. CCR5 gene expression was obtained from NCBI Gene Expression Omnibus (GEO) Database and plotted using R2: Genomics Analysis and Visualization Platform. DUET was used to evaluate effect of missense variants on CCR5 protein. Sequece reads were alligned and mapped using BWA-mem (V0.7.17)and SAMTools (V1.8). Duplicate reads were removed with Picard (V2.18.9). SNV's and small indels were dteected using the GATK HaplotypeCaller with fubctional annotation of variants using ANNOVAR. Off-target variants and SNPs were excluded with allele frequencies greater than 1% in non-Finnish European populations of the 1000 Genomes Project, ExAC (v3) and GnomAD (v2.1.1) databases. To remove possible false positives, variants falling in genomic duplicated regions were also excluded. The set of exonic variants was filtered to remove synonymous SNVs. For t |
| Imputation details | NA |
| Limitations | Not specified |