| Population name | Asano |
| Genome | GRCh37 |
| Consortium | COVID Human Genetic Effort (HGE) |
| Super population | EUR, AFR, AMR, SAS, |
| Population description | Individuals from seven countries |
| Population origin | Not specified |
| Case population size | 1202 |
| Control population size | 331 |
| Comorbidities | Not sepcified |
| Mean / median age | 52.9 |
| Sex | all male |
| Severity | Critical |
| Sample source | Nasopharyngeal and Clinical characteristics |
| Method | Genomic DNA extracted for WGS and WES. For WES, libraries were generated with the Twist Human Core Exome Kit, the xGen Exome Research Panel IDT xGen, the Agilent SureSelect V7 kit or the SeqCap EZ MedExome kit from Roche, and the Nextera Flex for Enrichment-Exome kit (Illumina). Massively parallel sequencing was performed on the Illumina HiSeq4000 or NovaSeq6000 system. For WES analysis performed at CNAG Barcelona, Spain, capture was performed with the SeqCap EZ Human Exome Kit v3.0 (Roche Nimbl |
| Bioinformatics | GATK best-practice pipeline was used to analyze WES data. Reads were aligned to hg19 with the maximum exact matches algorithm in the BWA. PCR duplicates were removed with Picard tools. The GATK base quality score recalibrator was applied to correct sequencing artifacts. Sample genotypes with a coverage < 8X, a genotype quality (GQ) < 20, or a minor read ratio (MRR) < 20% was filtered out. We filtered out variant sites (i) with a call rate <50% in gnomAD genomes and exomes, (ii) a non-PASS filter in the gnomAD database, (iii) falling in low-complexity or decoy regions, (iv) that were multi-allelic with more than four alleles, (v) with more than 20% missing genotypes in our cohort, and (vi) spanning more than 20 nucleotides. Variant effects were predicted with VEP and the Ensembl GRCh37.75 reference database. An enrichment analysis focusing on X chromosome genes without known inborn errors of TLR3- and IRF7-dependent type I IFN immunity and without neutralizing auto-Abs against type I IF |
| Imputation details | Not specified |
| Limitations | Not specified |