DOI: 10.5281/zenodo.6631952
title: UK Biobank release and systematic evaluation of optimised polygenic risk scores for 53 diseases and quantitative traits

description: Summary-level GWAS data for 53 traits generated by Genomics plc as presented in: Thompson D. et al. UK Biobank release and systematic evaluation of optimised polygenic risk scores for 53 diseases and quantitative traits (https://doi.org/10.1101/2022.06.16.22276246) If you have any questions or comments regarding these files, please contact Genomics plc at research@genomicsplc.com <strong>NOTES</strong> These analyses were carried out using the full UK Biobank (UKB) imputation data release (v3b). After removal of exclusions and withdrawals, a subset of 337,151 UKB individuals, the White British Unrelated (WBU) subgroup, was defined as the intersection of two sample groups created by Bycroft et al 2018 (Nature 562, 203-209): the ‘White British ancestry’ group (UKB Data Field 22006) and the ‘used in genetic principal components’ group (UKB Data Field 22020), the latter being high quality samples that were filtered to avoid closely related individuals. All GWAS analyses were performed on the WBU subgroup. Phenotypes were defined as described in Supplementary Table 1 ‘Phenotype definitions’ using a combination of Hospital Episode Statistics, Cancer Registry reports (where applicable) and self-report responses. All analyses included Age at assessment, sex (for non-sex specific traits), genotyping chip, and 10 principal components as covariates. GWAS summary statistics for each trait were generated by applying PLINK 2.0 to the WBU subgroup, using a logistic regression for disease traits, and a linear regression model for quantitative traits. For chromosome X variants males were treated as having 0 or 2 alternative alleles. The results are not adjusted for genomic control. <strong>DATA FILE CONTENT DESCRIPTION (DISEASE TRAITS)</strong> cpra Variant ID in ‘CPRA’ format. Position reflects position in b37 chrom Chromosome pos Position in base pairs (b37, 1-based) alt Alternative allele (effect allele) beta Effect size (log odds ratio) standard_error Standard error of beta minus_log10_p Minus log(base 10) of P-value ref Reference allele (non-effect allele) ncase Number of cases ncontrol Number of controls <strong>DATA FILE CONTENT DESCRIPTION (QUANTITATIVE TRAITS)</strong> cpra Variant ID in ‘CPRA’ format. Position reflects position in b37 chrom Chromosome pos Position in base pairs (b37, 1-based) alt Alternative allele (effect allele) beta Effect size (log odds ratio standard_error Standard error of beta minus_log10_p Minus log(base 10) of P-value ref Reference allele (non-effect allele) ntotal Total sample size <strong>PHENOTYPE CODES</strong> The following is a list of traits and their phenotype codes (as used in file naming). <em><strong>DISEASE TRAITS</strong></em> Age-related macular degeneration AMD Alzheimer's disease AD Asthma AST Atrial fibrillation AF Bipolar disorder BD Bowel cancer CRC Breast cancer BC Cardiovascular disease CVD Coeliac disease CED Coronary artery disease CAD Crohn's disease CD Epithelial ovarian cancer EOC Hypertension HT Ischaemic stroke ISS Melanoma MEL Multiple sclerosis MS Osteoporosis OP Prostate cancer PC Parkinson's disease PD Primary open angle glaucoma POAG Psoriasis PSO Rheumatoid arthritis RA Schizophrenia SCZ Systemic lupus erythematosus SLE Type 1 diabetes T1D Type 2 diabetes T2D Ulcerative colitis UC Venous thromboembolic disease VTE <em><strong>QUANTITATIVE TRAITS</strong></em> Age at menopause AAM Apolipoprotein A1 APOEA Apolipoprotein B APOEB Body mass index BMI Calcium ACALMD Docosahexaenoic acid DOA Estimated bone mineral density T-score EBMDT Estimated glomerular filtration rate (creatinine based) EGCR Estimated glomerular filtration rate (cystatin based) EGCY Glycated haemoglobin HBA1C_DF High density lipoprotein cholesterol HDL Height HEIGHT Intraocular pressure IOP Low density lipoprotein cholesterol LDL_SF Omega-6 fatty acids OSFA Omega-3 fatty acids OTFA Phosphatidylcholines PDCL Phosphoglycerides PHG Polyunsaturated fatty acids PFA Resting heart rate RHR Remnant cholesterol (Non-HDL, Non-LDL cholesterol) RMNC Sphingomyelins SGM Total cholesterol TCH Total fatty acids TFA Total triglycerides TTG