UK Biobank Genotyping and Imputation

Genotyping, quality control (QC), and imputation were performed centrally by UKBB, and details are fully described elsewhere (79 (link)). Briefly, genotype data are available for 488,377 individuals, 49,950 of whom were genotyped using the Applied Biosystems U.K. BiLEVE Axiom Array by Affymetrix [containing 807,411 markers (81 (link))]. The remaining 438,427 individuals were genotyped using the Applied Biosystems U.K. Biobank Axiom Array by Affymetrix (containing 825,927 markers). Both arrays were specifically designed for use in the UKBB project and share ~95% of marker content. Phasing was performed using SHAPEIT3, and imputation was conducted using IMPUTE4. For imputation, the Haplotype Reference Consortium (HRC) panel (82 (link)) was used wherever possible, and for SNPs not in that reference panel, a merged UK10K + 1000 Genomes reference panel was used. SNPs were imputed from both panels, but the HRC imputation was preferentially used for SNPs present in both panels. Both SNPs selected as instruments in this study demonstrated high imputation quality in UKBB (info scores of 0.98 and 0.95 for rs7209826 and rs188810925, respectively).

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Bovijn J., Krebs K., Chen C.Y., Boxall R., Censin J.C., Ferreira T., Pulit S.L., Glastonbury C.A., Laber S., Millwood I.Y., Lin K., Li L., Chen Z., Milani L., Smith G.D., Walters R.G., Mägi R., Neale B.M., Lindgren C.M, & Holmes M.V. (2020). Evaluating the cardiovascular safety of sclerostin inhibition using evidence from meta-analysis of clinical trials and human genetics. Science translational medicine, 12(549), eaay6570.

Publication 2020

BiLEVE Axiom Array Biobank Axiom Array

Genomes Haplotype Snps

Corresponding Organization :

Other organizations : Wellcome Centre for Human Genetics, University of Oxford, University of Tartu, Massachusetts General Hospital, Broad Institute, Medical Research Council, University Medical Center Utrecht, Peking University, University of Bristol, John Radcliffe Hospital, National Institute for Health Research

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Variable analysis

independent variables

Genotyping method (Applied Biosystems U.K. BiLEVE Axiom Array vs. Applied Biosystems U.K. Biobank Axiom Array)
Imputation method (Haplotype Reference Consortium (HRC) panel vs. merged UK10K + 1000 Genomes reference panel)

dependent variables

Imputation quality (info scores for rs7209826 and rs188810925)

control variables

Phasing method (SHAPEIT3)
Imputation tool (IMPUTE4)

controls

Positive control: Not explicitly mentioned
Negative control: Not explicitly mentioned

Annotations

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