| Population name | Upadhyai |
| Genome | GRCh38 |
| Consortium | University Institutes in India |
| Super population | EUR |
| Population description | European individuals from the AncestryDNA COVID-19 host genetic study |
| Population origin | European ancestry |
| Case population size | 1492 |
| Control population size | 197 |
| Comorbidities | Not specified but according to AncestryDNA data (Roberts et al., 2020) |
| Mean / median age | not specified |
| Sex | not specified |
| Severity | Severe |
| Sample source | NA |
| Method | GWAS was performed using the original AncestryDNA COVID-19 genotyping dataset (EGA Accession no. EGAD00010002012) with 675,370 SNVs to identify genetic variants that show significant frequency variation between asymptomatic versus severely infected COVID-19 patients. |
| Bioinformatics | "PCA analysis was performed using PLINK v1.9 with only individuals of European ancestry being used for further analysis. For QC, data with high levels of missingness (>20%) were filtered out using PLINK v1.9 with a MAF threshold of 0.01. Standard case-control-based association analyses were performed in PLINK v1.9 with a multiple-testing corrected p-value < 0.001 being considered significant. Significant SNVs (multiple-testing corrected p-value <0.001) were annotated using SNPnexus web-based server for GRCh38. |
| Imputation details | not specified |
| Limitations | a. Limited availability of data from COVID-19 patients, b. For the SARS-CoV-2 infected cohort, patients were categorized into various COVID-19 outcomes based on a self-reported questionnaire which may have affected the likelihood of miscategorization, c. the unavailability of genomic data for COVID19 patients in the ICU or those who may have succumbed might cause some discrepancies in the final outcomes of the study and, d. GWAS findings may not be exclusively ascribed to SARS-CoV-2 infections |