Uk bileve axiom array

We studied the host genetics of SARS-CoV-2 infection in participants of the UK Biobank study, which took place between 2006 and 2010 and includes approximately 500,000 adults aged 40–69 at recruitment. In collaboration with UK health authorities, the UK Biobank has made available regular updates on COVID-19 status for all participants, including results from four main data types: qPCR test for SARS-CoV-2, anonymized electronic health records, primary care and death registry data. We report results based on phenotype data downloaded on the 4th January 2021 and excluded from the analysis 28,547 individuals with a death registry event prior to 2020. DNA samples were genotyped as described previously^{32 (link)} using the Applied Biosystems UK BiLEVE Axiom Array (N=49,950) or the closely related Applied Biosystems UK Biobank Axiom Array (N=438,427). Genotype data for variants not included in the arrays were inferred using the TOPMed reference panel, as described above.

Next generation exome sequencing data were available on 49 960 participants, of whom 49 908 also had SNP chip data that had passed quality control. SNP chip data were generated centrally by the UK Biobank, and the exome sequencing data were generated externally by Regeneron and returned to the UK Biobank resource as part of an external access application request.20 (link) A subset of 4037 participants were previously genotyped using the Applied Biosystems UK BiLEVE Axiom Array by Affymetrix (807 411 genetic markers), and the other 45 871 participants were previously genotyped using the Applied Biosystems UK Biobank Axiom Array (825 927 genetic markers) that shares 95% of its marker content with the BiLEVE.10 (link) Participants were genotyped in 106 batches of around 5000 samples. We included samples that passed central UK Biobank quality control on either of the UK Biobank SNP chips and used standard quality metrics to exclude problematic SNPs (missingness rate <5% and Hardy Weinberg P<1×10⁻⁶).11 (link) We used the UCSC genome browser liftover tool to convert SNP chip variant positions that were reported in human genome build 37 to 38 coordinates for direct comparison with sequencing data.

The genetic data and quality control procedure have been described elsewhere (Bycroft et al., 2018 (link)). In brief, the genomic DNA was extracted from peripheral blood and genotyped by Applied Biosystems UK Biobank Axiom Array (N = 14,328) and UK BiLEVE Axiom Array (N = 1,517). Individuals whose genotype missing rate >5%), heterogeneity rate >3 SD, or self-reported sex mismatched the one inferred from the genotypes were excluded. The included participants were of European ancestry. The genotypes were imputed off the combined haplotype reference of the UK10K and 1000 genome cosmopolitan panels. Our SNP association analysis was restricted to the genetic variations with minor allele frequency (MAF) > 1% and imputation quality score> 0.7. The genetic principal components were calculated from the genotypes of the UK Biobank array data (Abraham and Inouye 2014 (link))