| Population name | Fallerini |
| Genome | GRCh38 |
| Consortium | GEN-COVID Multicenter Study |
| Super population | EUR |
| Population description | A subset of male COVID-19 patients was selected from the Italian GEN-COVID cohort of 1,178 SARS-CoV-2-infected participants (Daga et al., 2021). Cases were selected according to the following inclusion criteria: i. male gender; ii. young age (<60 years); iii endotracheal intubation or CPAP/biPAP ventilation. As controls, participants were selected using the sole criterion of being oligo-asymptomatic not requiring hospitalization. Cases and controls represented the extreme phenotypic presentation |
| Population origin | Italy |
| Case population size | 79 |
| Control population size | 77 |
| Comorbidities | not specified |
| Mean / median age | <60 years |
| Sex | Male only |
| Severity | Severe |
| Sample source | TBD |
| Method | A nested case control study was performed on a subset of male participants with extreme COVID-19 phenotypes. A LASSO logistic regression analysis assessing only rare variants were considered in a boolean representation which discovered the TLR7 gene as important. By selecting for young males, rare (MAF < 1%) TLR7 missense variants predicted to impact on protein function (CADD scores) were discovered and in none of the SARS-CoV2 infected oligo-asymptomatic male participants. In order to functio |
| Bioinformatics | The principal components analysis (PCA) was applied prior to the LASSO logistic regression in order to remove samples that were clear outliers. A 10-fold cross-validation method was applied in order to test the performances of the LASSO logistic regression. To determine the significance of the association between TLR7 variants and COVID severity, the Fisher’s Exact Test was used. p Values < 0.05 were considered statistically significant. |
| Imputation details | NA |
| Limitations | Not specified |