DOI: 10.5281/zenodo.6631951
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, with the exception of coronary artery disease (CAD). GWAS data was generated for both a “narrow” and a “broad” definition of CAD. The former was used as part of the training data for the Enhanced CAD PRS, the latter was used as part of the training data for the Enhanced CVD PRS. The phenotype definitions for “narrow” and a “broad” CAD are as follows: Narrow CAD<br> (includes angina) ICD10 codes (where .X indicates all subcodes) from both hospital and death records: I21, I22, I23, I24.1, I25.2, I20.X. ICD9 codes: 410-412, 42979, 413.X. OPCS-4 codes (K40.1–40.4, K41.1–41.4, K45.1–45.5,K49.1–49.2, K49.8–49.9, K50.2, K75.1–75.4, K75.8–75.9), self-reported heart attack (UKB codes 1075 in field 20002; code 1 in field 6150), self-reported coronary angioplasty (ptca) or coronary artery bypass graft (UKB codes 1070 and 1095 in field 20004), self-reported angina. Broad CAD<br> (includes angina and all ischaemic heart disease) As for Narrow CAD, plus ICD10 codes I24.X, I25X, and ICD9 codes 414.X (where .X indicates all subcodes). Note that there is no GWAS for cardiovascular disease (CVD) per se. This is because the UKB training data for the Enhanced CVD PRS consisted of separate GWASs for “narrow” CAD and ischaemic stroke. 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 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>FILE NAMES</strong> The following is a list of traits and their corresponding file names. <em><strong>DISEASE TRAITS</strong></em> Age-related macular degeneration amd_strict_UKB_WBU.csv.gz Alzheimer's disease alzheimers_disease_UKB_WBU.csv.gz Asthma asthma_UKB_WBU.csv.gz Atrial fibrillation atrial_fibrillation_UKB_WBU.csv.gz Bipolar disorder bipolar_disorder_UKB_WBU.csv.gz Bowel cancer CRC_UKB_WBU.csv.gz Breast cancer BC_UKB_WBU_women.csv.gz Coeliac disease celiac_disease_UKB_WBU.csv.gz Narrow coronary artery disease NARROW_CAD_UKB_WBU.csv.gz Broad coronary artery disease BROAD_CAD_UKB_WBU.csv.gz Crohn's disease crohns_disease_UKB_WBU.csv.gz Epithelial ovarian cancer OC_UKB_WBU.csv.gz Hypertension HT_UKB_WBU.csv.gz Ischaemic stroke IS_stroke_UKB_WBU.csv.gz Melanoma melanoma_UKB_WBU.csv.gz Multiple sclerosis multiple_sclerosis_UKB_WBU.csv.gz Osteoporosis OP_WBU_training.csv.gz Prostate cancer PC_UKB_WBU.csv.gz Parkinson's disease parkinsons_disease_UKB_WBU.csv.gz Primary open angle glaucoma POAG_WBU_training.csv.gz Psoriasis psoriasis_UKB_WBU.csv.gz Rheumatoid arthritis rheumatoid_arthritis_UKB_WBU.csv.gz Schizophrenia schizophrenia_UKB_WBU.csv.gz Systemic lupus erythematosus lupus_UKB_WBU.csv.gz Type 1 diabetes t1d_UKB_WBU.csv.gz Type 2 diabetes T2D_UKB_WBU.csv.gz Ulcerative colitis ulcerative_colitis_UKB_WBU.csv.gz Venous thromboembolic disease VTE_UKB_WBU.csv.gz <em><strong>QUANTITATIVE TRAITS</strong></em> Age at menopause age_at_menopause_UKB_WBU.csv.gz Apolipoprotein A1 apolipoprotein_a1_UKB_WBU.csv.gz Apolipoprotein B apolipoprotein_b_UKB_WBU.csv.gz Body mass index bmi_UKB_WBU.csv.gz Calcium calcium_UKB_WBU.csv.gz Docosahexaenoic acid docosahexaenoic_acid_UKB_WBU.csv.gz Estimated bone mineral density T-score BMD_WBU_training.csv.gz Estimated glomerular filtration rate (creatinine based) egfr_UKB_WBU.csv.gz Estimated glomerular filtration rate (cystatin based) egfr_cys_UKB_WBU.csv.gz Glycated haemoglobin hba1c_UKB_WBU_nodiabetes.csv.gz High density lipoprotein cholesterol hdl_cholesterol_UKB_WBU.csv.gz Height height_UKB_WBU.csv.gz Intraocular pressure iop_WBU_training.csv.gz Low density lipoprotein cholesterol ldl_UKB_WBU_nostatins.csv.gz Omega-6 fatty acids omega_6_fatty_acids_UKB_WBU.csv.gz Omega-3 fatty acids omega_3_fatty_acids_UKB_WBU.csv.gz Phosphatidylcholines phosphatidylcholines_UKB_WBU.csv.gz Phosphoglycerides phosphoglycerides_UKB_WBU.csv.gz Polyunsaturated fatty acids polyunsaturated_fatty_acids_UKB_WBU.csv.gz Resting heart rate resting_heart_rate_UKB_WBU.csv.gz Remnant cholesterol (Non-HDL, Non-LDL cholesterol) remnant_cholesterol__UKB_WBU.csv.gz Sphingomyelins sphingomyelins_UKB_WBU.csv.gz Total cholesterol total_cholesterol_UKB_WBU.csv.gz Total fatty acids total_fatty_acids_UKB_WBU.csv.gz Total triglycerides total_triglycerides_UKB_WBU.csv.gz