The UK Biobank database received ethical approval from the National Research Ethics Service Committee North West-Haydock (reference 11/NW/0382), and all procedures adhered to the World Medical Association Guidelines. All participants provided informed consent. The cohort comprises individuals aged between 40 and 69 years, primarily of White British ancestry, with a minority representing other ancestries. Approximately 50,000 participants were analyzed using the Applied Biosystems UK BiLEVE Axiom Array by Affymetrix, while the remaining around 450,000 participants were run on the Applied Biosystems UK Biobank Axiom Array, which shares 95% marker content with the former (Bycroft et al. 2018 (link)).
The genotype data we downloaded comprised 93,095,623 imputed SNPs for 487,411 individuals. We conducted the following preprocessing steps on the genotype data: initially, we excluded SNPs with a minor allele frequency (MAF) of less than 0.01 and an imputation INFO score of less than 0.8. Subsequently, we retained SNPs with a genotype call probability greater than 0.9 using the qctool. We also ensured that only biallelic SNPs were included. Finally, we excluded SNPs with a P value of less than 10−6 based on Hardy–Weinberg equilibrium testing and those with a genotype missing rate greater than 0.05 for both White and non-White British populations.
The genotype data we downloaded comprised 93,095,623 imputed SNPs for 487,411 individuals. We conducted the following preprocessing steps on the genotype data: initially, we excluded SNPs with a minor allele frequency (MAF) of less than 0.01 and an imputation INFO score of less than 0.8. Subsequently, we retained SNPs with a genotype call probability greater than 0.9 using the qctool. We also ensured that only biallelic SNPs were included. Finally, we excluded SNPs with a P value of less than 10−6 based on Hardy–Weinberg equilibrium testing and those with a genotype missing rate greater than 0.05 for both White and non-White British populations.
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