UK Biobank release and systematic evaluation of optimised polygenic risk scores for 53 diseases and quantitative traits
Authors/Creators
- Thompson, Deborah1
-
Wells, Daniel1
-
Selzam, Saskia1
- Peneva, Iliana1
-
Moore, Rachel1
- Sharp, Kevin1
- Tarran, Will1
- Beard, Ed1
-
Riveros-Mckay, Fernando1
-
Palmer, Duncan1
-
Seth, Priyanka1
- Harrison, James1
- Futema, Marta2
- Genomics England Research Consortium
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McVean, Gil1
-
Plagnol, Vincent1
-
Donnelly, Peter1
-
Weale, Michael1
- 1. Genomics plc, Oxford, UK
- 2. Cardiology Research Centre, Molecular and Clinical Sciences Research Institute, St George's University of London, London,, UK
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
NOTES
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 (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 (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.
DATA FILE CONTENT DESCRIPTION (DISEASE TRAITS)
| 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 |
DATA FILE CONTENT DESCRIPTION (QUANTITATIVE TRAITS)
| 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 |
FILE NAMES
The following is a list of traits and their corresponding file names.
DISEASE TRAITS
| 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 |
QUANTITATIVE TRAITS
| 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 |
Files
README.txt
Files
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Additional details
Related works
- Is supplement to
- Preprint: 10.1101/2022.06.16.22276246 (DOI)