Genotyping and Imputation in Icelandic and UK Biobank

The GWASs in Iceland were performed with 32.5 million markers identified through whole-genome sequencing of 15,520 Icelanders to an average genome-wide coverage of 34X and subsequently imputed into 151,677 chip-typed individuals, as well as their first and second degree relatives. The imputation has been extensively described in recent publications^{54 (link)}. Genotyping of UK biobank samples was performed using a custom-made Affymetrix chip, UK BiLEVE Axiom^{55 (link)}, and with the Affymetrix UK Biobank Axiom array^{56 (link)}. Imputation was performed by the Wellcome Trust Centre for Human Genetics, using the Haplotype Reference Consortium (HRC) and the UK10K haplotype resources. This yields a total of 96 million imputed variants, however only 27 million variants imputed using the HRC reference set passed the quality filters used in our study.

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Olafsdottir T.A., Theodors F., Bjarnadottir K., Bjornsdottir U.S., Agustsdottir A.B., Stefansson O.A., Ivarsdottir E.V., Sigurdsson J.K., Benonisdottir S., Eyjolfsson G.I., Gislason D., Gislason T., Guðmundsdóttir S., Gylfason A., Halldorsson B.V., Halldorsson G.H., Juliusdottir T., Kristinsdottir A.M., Ludviksdottir D., Ludviksson B.R., Masson G., Norland K., Onundarson P.T., Olafsson I., Sigurdardottir O., Stefansdottir L., Sveinbjornsson G., Tragante V., Gudbjartsson D.F., Thorleifsson G., Sulem P., Thorsteinsdottir U., Norddahl G.L., Jonsdottir I, & Stefansson K. (2020). Eighty-eight variants highlight the role of T cell regulation and airway remodeling in asthma pathogenesis. Nature Communications, 11, 393.

Publication 2020

UK BiLEVE Axiom

Chip Genome Gwass Haplotype

Corresponding Organization :

Other organizations : National University Hospital of Iceland, Innovation Center Iceland, University of Iceland

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Variable analysis

independent variables

Whole-genome sequencing of 15,520 Icelanders
Genotyping of UK biobank samples using a custom-made Affymetrix chip, UK BiLEVE Axiom, and the Affymetrix UK Biobank Axiom array
Imputation using the Haplotype Reference Consortium (HRC) and the UK10K haplotype resources

dependent variables

Genetic variants identified through whole-genome sequencing and imputation

control variables

Not explicitly mentioned

controls

Positive controls: Not mentioned
Negative controls: Not mentioned

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