Uk biobank gwas summary statistics FinnGen is a study that, in contrast, includes both population-based and disease-oriented cohorts. IEU analysis of UK Biobank phenotypes. Instructions on how to download summary statistics are sent to you by e-mail. Five thousand six hundred fifty-seven cases and Using the MTAG POAG GWAS summary statistics and large-scale protein quantitative trait locus (pQTL) (especially from cohort studies such as UK Biobank (UKB)) were diagnosed at a higher rate In a 2022 article, the authors highlighted the key points to note when validating pre-existing scores, specifically when using UK Biobank data. While VarExp benefits computationally from using GWAS summary statistics, it needs to invert the correlation matrix between SNPs, which prevents from using a large number of SNPs . Called and imputed genotypes for the full cohort please. Inverse-variance weighting (IVW) was Through extensive simulations and analysis of many complex traits in the UK Biobank, we demonstrate that this approach closely approximates gold-standard analytical strategies based on external validation, and substantially outperforms state-of-the-art PRS methods. The i-LDSC software and its application to these biobanks represent a step towards resolving further genetic contributions of sources of non-additive genetic effects to complex trait variation. In East Asian (EAS) populations, Biobank Japan (BBJ) 5, 12, 13, 14 has made important discoveries and publicly released genome-wide association summary statistics, thereby facilitating numerous other genetic studies. doi: jmg-2023-109295. Using SPACox, we have carried out GWAS survival analysis for 13 selected phenotypes. Previously, we published genome-wide associations of 3,144 brain imaging-derived phenotypes, with a discovery sample of 8,428 individuals. 13, which most UK Biobank data are available via application at https://www. Methods Brain imaging data was from the 40,000 participant release from early 2020, as processed by WIN/FMRIB on behalf of UK Biobank (Alfaro-Almagro, NeuroImage, 2018). uk/). We aimed to determine summary statistics to the European Bioinformatics Institute (EBI) GWAS repository. The GWAS results generated from any UK Biobank samples were excluded. 6% East Asian, and 4. However, the increasing number of GWAS summary statistics and the diversity Genetic Analysis of Venous Thromboembolism in UK Biobank Identifies the ZFPM2 Locus and Implicates Obesity as a Causal Risk Factor. 2022. Building on the initial genome-wide association analyses, we’ve now estimated the heritability For MetS, we extracted GWAS summary statistics generated from UK BioBank (n = 291,107 individuals) (Lind, 2019). Bi-allelic SNPs shared between the two datasets were identified and harmonised (by ‘flipping’) with respect to the All analysis summary statistics are available from the following link. p2; 2022. Methods: Using data from 291,107 individuals in the UK biobank, a GWAS was performed versus the binary trait MetS (harmonized NCEP criteria). If you have any questions about the suitability of these summary statistics for your analysis, please contact grp-ukbbcanceroutcomes@groups. Each GWAS can be browsed with the manhattan plot, risk loci, MAGMA (i. However, existing methods are computationally demanding and infeasible to handle biobank-scale data. This produced new adjusted P-values for each trait. We used GWAS summary statistics from 2 publicly available biobank-scale cohorts: UK Biobank (UKB) and FinnGen (FG) . We obtained the GWAS summary statistics computed by the UK Biobank project for each pulmonary function parameter. This public release of data represents an extraordinary advance for genetics, pushing the envelope for data sharing and rapid uptake by the research community. we simulate a phenotype using HapMap3 variants of chromosome 6 for 10,000 individuals from the UK Biobank and then run GWAS with or without PC19 as covariate. Metadata associated with summary statistics can be downloaded from GWAS summary statistics of cross-population meta-analysis (BBJ & UK Biobank & FinnGen) Citation: Sakaue, S. Publications. Summary statistics from genome-wide association studies (GWAS) have facilitated the development of various summary data-based methods, which typically require a reference sample for linkage The whole analysis only requires xQTL and GWAS summary statistics and reference LD. the GWAS catalog contains more than 1,400 summary using individual-level data from two large cohorts (iPSYCH and UK Biobank) as well as large GWAS summary statistics that excluded these cohorts. But in practice, GWAS summary statistics are used for PRS model training With the re-release of UK Biobank genotype imputation (which we term imputed-v3), we have generated an updated set of GWAS summary statistics for the genetics community. The "UK Biobank CAD GWAS" dataset includes results for the 34,541 cases Objective: To use genome-wide association study (GWAS) by subtraction, a method for deriving novel GWASs from existing summary statistics, to derive genome-wide summary statistics for paternal smoking. Overview of SuSiEx. We next assessed our method in estimating π using simulations based on the imputed genotype data from the UK Biobank. 466078 Besides, genetic correlation analysis between snoring and cardiometabolic traits was conducted within the European population from the UKB study, based on the GWAS summary statistics obtained from We performed a GWAS of self-report chronotype (phenotype summarised in Table 1) using 11,977,111 imputed variants in 449,734 individuals of European-ancestry from the UK Biobank and meta-analysed Genome-wide association summary statistics are available at the database of Genotypes and Phenotypes (dbGaP) under accession phs000179. Information about updates, including the timelines for data&#160;releases, are posted The UKB-PPP is a collaboration between the UK Biobank (UKB) and thirteen biopharmaceutical companies characterising the plasma proteomic profiles of 54,219 UKB participants. Using the UK Biobank as a global reference of worldwide populations: application to measuring ancestry diversity from GWAS summary statistics Florian Privé 1 National Centre for Register-based Research, Aarhus University, Aarhus 8210, Denmark GWAS summary statistics for HapMap3 sites passing QC (MAF > 0. 23 Abstract 24 Summary statistics derived from large-scale biobanks facilitate the sharing of genetic discoveries while 25 minimizing the risk of compromising individual-level data privacy. Functional analyses of chondrocytes provide further insight into Summary statistics of a genome-wide association study of intracranial aneurysms in 10,754 cases and 306,882 controls. We provide GWAS results in the Japanese population (mainly from BBJ) using the PheWeb platform, with public access to the full summary statistics. For each pair of GWAS summary statistics with four and ten genotype principal components, We prepared a dataset of 33 serum and urine biomarkers from 337199 individuals in UK Biobank. To choose the threshold, below which weighted p-values are considered as small when analyzing large genes, we performed an empirical assessment of the approximation on the material of summary statistics for neuroticism from UK Biobank dataset . , et al. We evaluate the genetic basis of 35 blood and urine laboratory measurements in the UK Biobank (n = 363,228 individuals). They recommend obtaining summary statistics using PLINK 2 as a first step. International Classification of Diseases (ICD10) codes are used to store information on participants’ health Here, we investigated the genetics of weighted functional brain network graph theory measures from 18,445 participants of the UK Biobank (44–80 years). Included in this collection are the GWAS summary statistics, as well as the sex comparison statistics, pertaining to the aforementioned sex-stratified models, for each of the 530 phenotypes. Although genome-wide association studies UK Biobank data are available via application at https://www. uk). The replication rates are high for all four methods: among the significant genes identified in the GLGC GWAS, 161 MTAG was used to perform multi-trait meta-analysis across the GWAS summary statistics from the RNFL and GCIPL thickness analyses. The eighteen measures studied showed low Outcome data were from summary statistics of 167 metabolites from the UK Biobank (n = 115,078). However, existing methods are computationally demanding and ChrX GWAS summary statistics for HDL-C, LDL-C, nonHDL-C, TC and TG (180 files) The meta-analysis summary statistics include all studies (i. 2021; 22: 183. In an effort to generate and share GWAS summary statistics from the 500K UK Biobank release to the scientific community, we faced a set of practical challenges in efficiently running GWAS analyses on such a large With the UK Biobank’s release of biochemical marker measurements in urine, red blood cell, and serum samples collected from study participants, the Neale lab has updated our collection of publicly-available This atlas is a database of publicly available GWAS summary statistics. To replicated our findings, we applied these four approaches to summary statistics from the LDL-C UK Biobank GWAS (N = 343,621) and identified 474, 223, 254, and 175 genes using MSG, S-MultiXcan, sCCA+ACAT, and UTMOST, respectively. Here, we introduce GxEsum, a method for estimating the phenotypic variance explained by genome First, we estimate the genetic predisposition for T2D by computing the T2D PRS using GWAS summary statistics from the UK Biobank. National Cancer Institute. We performed a GWAS of self-report chronotype (phenotype summarised in Table 1) using 11,977,111 imputed variants in 449,734 individuals of European-ancestry from the UK Biobank and meta-analysed We collected genotype and phenotype data and GWAS summary statistics of all Europeans from the UK Biobank , and only GWAS summary statistics from FinnGen and BioBank Japan . 's study in genetic correlation estimation ( Ning et al. (Nature Genetics 2021) when using the PGCALZ2 data which excluded the UK Biobank and 23andMe data ChrX GWAS summary statistics for HDL-C, LDL-C, nonHDL-C, TC and TG (180 files) The meta-analysis summary statistics include all studies (i. A full The UK Biobank (UKBB) project is a prospective cohort study with deep genetic and phenotypic data collected on almost 500,000 individuals from across the United Asian, 10. The inverse variance weighted (IVW) method was the primary method for Summary of fine-tuned PRSs for UK Biobank imaging traits. The genotype data for these samples have been cleaned, imputed and released to the scientific community. Although genome-wide association studies The range of case numbers in biobank GWAS, summary statistics for which are often available in a uniformly processed and convenient format, do make such collections suitable for the construction of a test set of real GWAS on which to evaluate the performance of tests of shared genetic architecture across varied sample sizes. Emdin, DPhil, 1, 2 Pradeep Natarajan, Of the publicly available disease GWAS summary statistics, only the CARDIoGRAMplusC4D 37 coronary artery disease Interestingly, many of these external GWAS summary statistics-based PRS methods approximate the results of the internal individual-level data approaches, making some assumptions in the process (e. Complete download (zip, 1 GWAS summary statistics from the published paper: Iron and risk of dementia: Mendelian randomization analysis in UK Biobank Casanova et al. In previous analyses, this overlap was handled by removing overlapping individuals from the UKBB analysis. GWAS summary statistics from either European ancestries or more diverse ancestries all have a substantial proportion estimated from Today, GWAS summary statistics are widely available for a broad range of diseases and traits in public databases, e. 6% Filipino. Result: A GWAS by subtraction was implemented using a weighted linear model that defined the child-genotype paternal-phenotype association as the camp of approaches is based on statistical models for ge-netic effects but is limited to the analysis of a small num-ber of traits due to computational demands. report on a GWAS Catalog community workshop on the sharing of summary statistics to ensure that these are findable, accessible, interoperable, and reusable (FAIR). European descent was determined in the UK Biobank through the Summary statistics of genome-wide association study (GWAS) for structural and diffusion IDPs were obtained from 33,224 individuals in the UK Biobank cohort. d 32,87) was performed on the GWAS summary statistics using in-sample LD scores estimated in 10,000 random white British UK Biobank individuals at SNPs with minor allele frequency > 5% as reference UK Biobank SNP–metabolic trait summary statistics were downloaded (https: Full GWAS summary statistics are publicly available through the NHGRI-EBI GWAS catalogue Fill this online form to gain access to FinnGen GWAS or the meta-analysis summary statistics. Imputation of height GWAS summary statistics conducted in UK Biobank. gene-based) results, SNP heritability Results are compiled in a publicly accessible database that allows querying genome-wide association results for 9,113,133 genetic variants, as well as downloading GWAS summary We have made all of the GWAS summary statistics openly available via the new BIG40 brain imaging genetics server. More details about our resource are provided in Appendix B of the Supplementary Material. PRSs are generally derived based on summary statistics from large meta-analyses of multiple genome-wide association studies (GWASs). We considered five GWAS summary-statistics-based methods (C + T 4, Lassosum 6, LDpred 5, PRS-CS 7 GWAS Explorer, an open-source tool to explore, visualize, and access GWAS summary statistics. Data 1: List of 3,994 traits tested for association with rare variants in individuals of European ancestry from the UK Biobank cohort. 65%) of variants were flagged as either palindromic SNPs with flipped strands or variants having very different allele frequencies compared to gnomAD. SNPs with P-value =0 or >1, or non-numeric value such as “NA” were excluded. Here, we introduce PUMAS, a novel method to fine-tune PRS models using summary statistics from genome-wide association studies (GWASs). 2. , VarExp, which is recently published. Methods to combine GWAS summary statistics with additional information to perform in silico functional follow-up are plentiful 21,22,23,24,25 and range from fine-mapping For UK Biobank traits, Example Based on UK Biobank GWAS Summary Statistics As a real data example, we applied the different estimation methods on the same 30 UK Biobank phenotypes used in Ning et al. bioRxiv, 660506 (2019). 13059_2021_2479_MOESM10_ESM. Summary statistics of GWAS for seven For the UK Biobank, we conducted a GWAS of pneumonia using individual-level genetic and phenotypic data from the UK Biobank. We obtained GWAS summary statistical data for 18 cardiometabolic diseases (CMDs) including AAA, 15 metabolic traits, and 6 immune cell traits (Fig. 5 million SNPs. We observed that across 18 biobanks that shared GWAS summary statistics to the meta-analysis for asthma, very small proportions (0. Within this dataset, we carefully define 21 distinct ancestry groups from all four corners of the world. 13. This research was conducted under the project of UK Biobank Application Number 45270. Only European ancestry samples were included. , LDpred-inf 8 and sBLUP 15 approximate the genomic BLUP, 16 assuming that linkage disequilibrium [LD] patterns in the external data from which the GWAS 2. There are 959 participants that overlap between PGC MDD and UKBB cohorts. Tanigawa*, et al, Genetics of 38 blood and urine biomarkers in the UK Biobank. Toggle navigation GWAS Catalog. SuSiEx extends the single-population fine-mapping model, SuSiE 13, by integrating population-specific GWAS summary statistics and LD reference panels from multiple populations Based on promising initial results in UK Biobank, we collated sex-stratified GWAS summary statistics, as available, from other participating studies (Supplementary Table 6). Here we present a new open resource of genome-wide association study The UK Biobank project is a prospective cohort study with deep genetic and phenotypic data collected on almost 500,000 individuals from across the United Kingdom. Finally, we a Summary of the UK Biobank genotype and phenotype data used in the study. Dataset described in: Genome-wide association study of intracranial aneurysms identifies 17 risk loci and genetic overlap with clinical risk factorsBakker, M. Google Scholar. For the MR analysis, the In unclassified HF, the meta-analysis of MVP and UK Biobank GWAS results Using LDSC and the MVP GWAS summary statistics, we estimated the heritability (h 2) of unclassified HF, HFpEF and HFrEF We are thrilled to announce the release of GWAS summary statistics from the Pan-UK Biobank resource, which consists of genome-wide association analyses of 7,221 phenotypes across 6 continental ancestry groups in the UK Biobank. , the UK Biobank [UKBB]) and only covers <10% of EAS Studies with available summary statistics. 003% to 0. GWAS summary statistics have become essential tools for various genetic analyses, including meta-analysis, fine-mapping, and risk prediction. 1A). We imputed GWAS Z-statistics (ran on directly genotyped data) using summary statistics imputation within 1 Mb-wide regions, by blinding one at the time and therefore allowing the remaining SNVs to be used for tagging. GWAS summary statistics for individual ocular diseases and meta-analysis have been returned to For GWAS multiancestral analysis we used REGENIE with the approach described for the NFE ancestry group to generate GWAS summary statistics for SAS, AFR, EAS and AMR cohorts. However, the impact of age on genetic effects is Here, we extracted deep feature representations of brain MRI scans from UK Biobank, and performed a genome-wide association study on them. Data from UK Biobank is accessible to researchers by applying to: https: GxEsum: a novel approach to estimate the phenotypic variance explained by genome-wide GxE interaction based on GWAS summary statistics for biobank-scale data. Registered researchers receive emails or alerts via the Access Management System (AMS) when new data are available for release. The Neale Lab has been working to make some basic analyses of that data freely available; you can read more about the overall effort here. For UK Biobank we present summary statistic results from the UK Biobank hospital in-patient health-related outcomes summary information data (Data-Field 41202); computational grouping of phenotypes with cancer (Category 100092) registry, death registry data (Category 100093), algorithmically-defined outcomes (Category 42), and verbal Overview of the data QC, code, and GWAS summary output from the 2017 UK Biobank data release - Nealelab/UK_Biobank_GWAS To be used with GWAS summary statistics from Biobank Japan, we also investigate three different LD reference panels. . This work generates mixed model associations and meta-analyses across genetic ancestry groups, inclusive of a larger fraction of the UKB than previous efforts, to produce freely-available summary statistics for 7,271 traits, and builds a quality control and analysis framework informed by genetic architecture. Here, we GWAS summary statistics for the largest GWAS to date on frailty were sourced from the European Bioinformatics Institute The Frailty Index mean in the UK Biobank GWAS was 0. Genetic variation in response to the environment, that is, genotype-by-environment interaction (GxE), is fundamental in the biology of complex traits and diseases. Derek Klarin, MD, 1, 2, 3 Connor A. Abstract. 10. Here we create summary statistics that have UK Biobank participants removed. Studies included from dbGaP, The UK Biobank (UKBB) project is a prospective cohort study with deep genetic and phenotypic data collected on almost 500,000 individuals from across the United Kingdom. To estimate R g with a range of publicly available GWAS summary statistics, Available from UK Biobank subject to standard procedures (www. Fasting glucose and 2-h glucose were not associated with any metabolite. 1 s. Because of the sample overlap between the GWAS and UK Biobank, we obtained genetic This study used data from UK biobank to search for additional loci. All the GWAS summary statistics can be browsed and downloaded at the fastGWA data portal. This effort is described in detail in 'Sexual differences in genetic architecture in UK Biobank' . The training set was used to perform genome-wide association analysis and the GWAS summary statistics were used to construct polygenic risk scores (PRSs) in the testing set, evaluated for the use of risk stratification for a variety of age-related outcomes. v5. Background: Brain iron deposition is common in dementia, but whether serum iron is a causal risk factor is unknown. phs001286. GWAS summary statistics are The NHGRI-EBI GWAS Catalog: a curated collection of all published genome-wide association studies, produced by a collaboration between EMBL-EBI and NHGRI. This document describes genome-wide association studies (GWAS) of pan-cancer and site-specific cancers in UK Biobank participants. UK Biobank is a prospective population-based project primarily including UK residents aged 40–69 years. The inverse variance weighted (IVW) method was the primary method for We used GWAS summary statistics from 2 publicly available biobank-scale cohorts: UK Biobank (UKB) and FinnGen (FG) . Through extensive This website releases genome-wide association study (GWAS) summary statistics of the BioBank Japan Project (BBJ). Despite being a cohort from the UK, this dataset is so large that it the GWAS summary statistics containing the allele frequencies of interest; 2/ match variants and alleles Moreover, we apply the newly developed method to the UK Biobank GWAS summary statistics from the XIII category with 70 related musculoskeletal system and connective tissue phenotypes. UK Biobank The UK Biobank (UKB), for example, includes information from approximately half a million participants 16. Population-specific GWAS summary statistics per protein measurement, as well as meta-data for annotating protein measurements and genetic variants. The inputs are female-specific GWAS summary statistics, male-specific GWAS summary statistics, and sex-agnostic GWAS summary statistics; PRS methods include PRScs, LDpred2, and PRScsx; validation samples are used to tune hyperparameters of PRSs and find the optimal weights of sex-specific PRSs; Objective To use genome-wide association study (GWAS) by subtraction, a method for deriving novel GWASs from existing summary statistics, to derive genome-wide summary statistics for paternal smoking. as well as downloading GWAS summary statistics for over 30 million imputed genetic variants (>23 billion phenotype In this study, a multi-trait analysis by the MTAG software and a two-stage transcriptome-wide association study (TWAS) with UTMOST and FUSION for seven upper GI diseases provided insights into the genetic nature of upperGI diseases. The GWAS summary statistics we used were sourced from the MRC Integrative Epidemiology Unit (IEU) Open GWAS database (https://gwas. However, individuals from diverse genetic ancestry groups are often excluded from association analyses due to concerns about population structure introducing false positive associations. For each SNP, the lowest P-value across the two traits was selected as the meta P-value. This Global Biobank Engine is a public browser Systematic analyses of GWAS summary statistics from UK Biobank identified novel susceptibility loci and genes for upper gastrointestinal diseases In the TWAS analysis, we revealed 5 susceptibility genes in known loci and identified 12 novel potential susceptibility genes, including HOXC9 at 12q13. Furthermore, the theoretical frameworks of GxEsum and VarExp Genetic variation in response to the environment, that is, genotype-by-environment interaction (GxE), is fundamental in the biology of complex traits and diseases. 1038/s41588-020-00725 A GWAS was first carried out using primary level data in the UK Biobank with ~9. The inputs are female-specific GWAS summary statistics, male-specific GWAS summary statistics, and sex-agnostic GWAS summary statistics; PRS methods include PRScs, LDpred2, and PRScsx; validation samples are used to tune hyperparameters of PRSs and find the optimal weights of sex-specific PRSs; The accuracy of polygenic risk scores (PRSs) to predict complex diseases increases with the training sample size. Association of UK Biobank inner retinal thickness-associated variants To gain more statistical power and further validate our results, we obtained the summary statistics from two recent insomnia GWAS, using data from UK Biobank or STARRS dataset 13,15. This section collects any data citations, data availability statements, or supplementary materials included in this article. The full GWAS summary statistics for the 23andMe discovery data-set will be made available through 23andMe to qualified researchers under an agreement with 23andMe that protects the privacy of the 23andMe participants. GWAS summary statistics (number of SNPs = 9,037,014) for 7050 ADGC samples can be accessed through the NIAGADS database (NG00076). These traits are distributed Genome-wide association study for osteoarthritis using data from UK Biobank identifies loci for knee- and hip-specific disease. Results: In a GWAS of MetS (binary) we found 93 independent loci with P < 5 × 10-8, of which 80 were not identified in previous GWASs GWAS datasets. Here we provide a detailed summary of The range of case numbers in biobank GWAS, summary statistics for which are often available in a uniformly processed and convenient format, do make such collections suitable for the construction of a test set of real GWAS on which to evaluate the performance of tests of shared genetic architecture across varied sample sizes. Additionally, we generated LDL-C polygenic scores from the meta-analyses. We calculated GWAS summary statistics from males (light purple) and females (orange) separately, so Heart failure (HF) is a leading cause of morbidity and mortality worldwide. 3. 47 , D1005–D1012 (2019). The association Download Citation | Systematic analyses of GWAS summary statistics from UK Biobank identified novel susceptibility loci and genes for upper gastrointestinal diseases | In recent decades, upper Please cite this reference when using the common factor model summary statistics and cite A genome-wide association study with 1,126,563 individuals identifies new risk loci for Alzheimer’s disease. UK Biobank is a major prospective epidemiological study, including multimodal brain imaging, genetics and ongoing health outcomes. & Kanai, M. This dataset includes summary results only. Pre-process of GWAS summary statistics Curated summary statistics on the database was pre-processed to standardise the format. Here, we conducted genome-wide association studies (GWAS) of 31 serum and urine biomarker quantitative traits in African (n = 9354), East Asian (n = 2559), and South Asian (n = 9823) ancestry UK FIGURE 1. Towards the end of 2021, UK Biobank released whole-genome sequencing (WGS) data on 200,000 individuals, Using data encompassing CNV-GWAS summary statistics submission, The NHGRI-EBI GWAS catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. They can also be accessed in the tables below (separate tables for the published and unpublished summary statistics). p2 and via the UK Biobank. bristol. Despite We download several genome-wide association study (GWAS) summary statistics for which allele frequencies are reported and apply this new method to them. [PMC free article] Associated Data. Here, we present an atlas of genetic associations for 118 non-binary and 660 binary traits of 452,264 UK Biobank participants of European ancestry. 05) in our analyses. 7) and subsequently calculated the gene set associations for 5,917 GO gene sets (C5). 27. If you think Studies with available summary statistics. The results are therefore a measure of ‘any insomnia’, and sample 1 is UK Biobank (our GWAS), This deposit contains summary statistics of genome-wide analysis for dental endpoints in GLIDE consortium, and UK Biobank as well as multi-trait analysis combining both GLIDE and UKBiobank. We include body mass index (BMI) as a covariate in the GWAS when As you may know, the UK Biobank released data on ~500,000 individuals to the scientific community to advance research on genetics. 1101/2021. The FinnGen study is a large-scale genomics initiative that has analyzed over 500,000 Finnish biobank samples and correlated genetic variation with health data to The GWAS summary statistics of factors and PD were acquired from the MRC IEU OpenGWAS database (https://gwas. We are thrilled to announce the release of GWAS summary statistics from the Pan-UK Biobank resource, which consists of genome-wide association analyses of 7,221 Here, we provide the summary statistics for our GWAS of self-reported risk-taking propensity amongst 436,236 white European participants of the UK Biobank (UKB) study, measured by In the current study, we systematically analyzed the GWAS summary statistics for 7 upper gastrointestinal diseases from UK Biobank at SNP level and gene level. This deposit contains summary statistics of genome-wide analysis for dental endpoints in GLIDE consortium, and UK Biobank as well as multi-trait analysis combining both GLIDE and UKBiobank. We'd love to hear from you! To provide feedback or ask a question, contact the GWAS Catalog team on gwas-info@ebi. As tag SNVs we used all SNVs except the focal SNV within a However, the analysis of huge cohorts, like UK Biobank, is challenging. MacArthur et al. However, these summary statistics, such 26 as those from the UK Biobank (UKB) provided by Neale’s lab, are often adjusted by a fixed set of covari- 27 ates to all traits (12 Summary statistics from the most recent MDD GWAS meta-analysis , with UK Biobank and 23andMe results removed, were harmonised with MCP GWAS summary statistics following guidelines as closely as possible with the available data. Derived phenotypic data for There is a GxE method that can use GWAS summary statistics, i. For summary statistics with non-hg19 genome coordinate, liftOver software was used to align to hg19. 27 The GWAS study included data from the UK Biobank, ICBP, and replication data from other smaller biobanks. A small proportion of HF cases are attributable to monogenic cardiomyopathies and existing genome-wide association We compare summary statistic prediction tools using 225 UK Biobank phenotypes; our new tool LDAK-BayesR-SS outperforms the existing tools lassosum, sBLUP, LDpred and SBayesR for 223 of the 225 The height GWAS summary statistics were provided by the GIANT Consortium and were from 82 cohorts (174 separate files) representing a total of 253 288 individuals, and ~2. Public sharing of GWAS SumStats received support through an update to the National Human Genome Research Institute (NHGRI) genomic data-sharing policy in 2018 (web resources). The UK Biobank (UKBB) project is a prospective cohort study with deep genetic and phenotypic data collected on almost 500 000 individuals from across the UK. 1 and European UK Biobank VTE meta-analyzed summary statistics and UK Biobank participants do not have a high-quality measure of intelligence or polygenic scores (PGSs) of intelligence to simultaneously examine the genetic and neural underpinnings of intelligence. ac. discovered in our study Through simulations and using 12 real case-control and quantitative traits from both iPSYCH and UK Biobank along with external GWAS summary statistics, we compare meta The UK Biobank (UKB) is a cohort of Standard PRSs were generated from 3 GWAS data sets external to the UKB, under default settings, to analyze the robust marginal, joint, a: Compression cost in British pound sterling (GBP) for converting the whole-chromosome polymorphisms from tabular formats (that is BGEN or BCF) to GRG, XSI and Genetic instruments were obtained from large genome-wide association studies (GWASs) from the UK Biobank and FinnGen Biobank. Here, we describe plasma nuclear magnetic resonance (NMR) biomarker data for 118,461 participants in the UK Biobank. We use either the 504 East Asian (including 104 Japanese) individuals from the 1000G, 400 Japanese-like UK Biobank plus the 104 Japanese 1000G individuals (also 504 in total), or 2,041 East Asian UK Biobank individuals (including Genome-wide association studies (GWAS) have revolutionized our understanding of the genetic architecture of complex traits and diseases. (2022) GSCAN dbGaP & UK Biobank. This research For each of the 25 traits analyzed in the UK Biobank and BioBank Japan, i-LDSC detects additional variation contributed by genetic interactions. This effort was led by Alicia Martin, Hilary Finucane, Mark Daly and Ben Neale, lead analysts Konrad Karczewski and Elizabeth Atkinson, with contributions from team members at ATGU. UK Biobank PRS data comes in BGEN v1. 05 to 0. Genome Biol. The methods used to perform the GWA analyses are described elsewhere 64,65 GxEsum: a novel approach to estimate the phenotypic variance explained by genome-wide GxE interaction based on GWAS summary statistics for biobank-scale data June 2021 Genome Biology 22(1) FIGURE 1. Variables within the UKB Returned Datasets Catalogue are available to researchers registered with the UK Biobank. NCBI dbGaP. uk. Genetics of 38 blood and urine biomarkers in the UK Biobank. camp of approaches is based on statistical models for ge-netic effects but is limited to the analysis of a small num-ber of traits due to computational demands. The UK Biobank recently released genome-wide association data on ~500,000 individuals. The utility of GWAS datasets has been vastly increased by SumStats sharing, This work relates to the UK Biobank application 15825: PI Dr Philip C Haycock. Sinnott-Armstrong*, Y. We calculated the approximated SKAT statistics using a range of values as threshold (from 0. 10–12 As more GWAS summary data become available in large biobanks,13–15 it is important to develop a scalable model-based approach that allows exploring the phe- In East Asian (EAS) populations, Biobank Japan (BBJ) 5, 12, 13, 14 has made important discoveries and publicly released genome-wide association summary statistics, thereby facilitating numerous other genetic studies. After running a GWAS of g on BD GWAS summary statistics were received for five external cohorts (iPSYCH 30, deCODE genetics 31, Estonian Biobank 32, Trøndelag Health Study (HUNT) 33 and UK Biobank 34), in which most cases In our analyses, we used GWAS summary statistics from the UK biobank, one of the largest genetic cohort in the world, to generate PRS for complex traits. The top plot represents the Manhattan plot from the nf-gwas pipeline in 375 278 UK Biobank participants of European ancestry GWAS summary output from the meta-analysis of UK Biobank and IGAP (sample size specified as 314,278 + 74,046 = 388,324) were included along with expression Quantitative Trait Loci (QTL) summary To evaluate whether there was evidence of colocalization across the VTE GWAS and PAI-1 pQTL studies, we used the European MVP v. A full Large biobanks, such as the UK Biobank (UKB), enable massive phenome by genome-wide association studies that elucidate genetic etiology of complex traits. Genetic predictors, or SNPs, of the BP traits were obtained from summary statistics of a large GWAS of BP traits with over 1 million people of European ancestry. We estimated heritability for all available traits in the UK biobank and only included traits with nominally significant heritability (p<0. Results Overview of GWAS Results We conducted a genome-wide association study using the 39,691 brain imaged samples in UK Biobank. The GWAS baseline box-plot is followed by the box-plots for the total numbers of significant loci after integrating the UK Biobank GWAS summary statistics with functional annotations using FINDOR New data & enhancements and future enhancements to UK Biobank New data are uploaded to the UK Biobank resource on a regular basis. We identify 1,857 loci associated with at least one trait, containing 3,374 fine-mapped associations and additional sets of large-effect (>0. Data Citations. These ancestry groups can serve as a global reference of worldwide populations, with a We used the UK Biobank-free GWAS results from the GWAS ATLAS as the source for the common variant-based associations. Using the UK Biobank as a global reference of worldwide populations: application to measuring ancestry diversity from GWAS summary statistics Florian Privé 1 National Centre for Register-based Research, Aarhus University, Aarhus 8210, Denmark The UK Biobank project is a prospective cohort study with deep genetic and phenotypic data collected on approximately 500,000 individuals from across the United Kingdom, aged between 40 and 69 at Summary statistics of a genome-wide association study of intracranial aneurysms in 10,754 cases and 306,882 controls. Panel A: Miami plot for the apoB GWAS. For UK Biobank data analysis (on 258 ordinal categorical phenotypes including 150 food and other preferences), we use a sparse GRM to adjust for sample relatedness. Defining cancer cases and controls GWAS was undertaken for pan-cancer or site-specific cancer diagnoses before 23 Abstract 24 Summary statistics derived from large-scale biobanks facilitate the sharing of genetic discoveries while 25 minimizing the risk of compromising individual-level data privacy. We use the UK Biobank data to highlight the usefulness and effectiveness of the proposed method in three applications that currently cannot be done with only GWAS summary data (for SNP-trait associations): marginal SNP-trait association analysis under non-additive genetic models, detection of SNP-SNP interactions, and genetic prediction of a Summary GWAS statistics will be made available at the UK Biobank web portal. 31, 38 In Figures 5 and S28-S32, we then provide 14 Department of Statistics, Stanford University, Stanford, CA, USA. v2. However, it is now common for researchers to have access to large individual-level data as well, such as the UK Biobank For insomnia, we used the GWAS summary statistics provided by the Neale lab (summary data code: ukb-a-13) and Philip et al. These GWAS are stored on the Data Ark in the GWAS-VCF format, which provides a consistent and robust approach to storing genetic variants, annotations and metadata enabling interoperability and reusability GWAS SumStats are defined as the aggregate p values and association data for every variant analyzed. This deposit contains summary statistics of genome-wide analysis for dental endpoints in GLIDE consortium, and UK Biobank as well as multi-trait analysis combining both GLIDE and Results: Using the UK Biobank data, a prospective cohort study with deep genetic and phenotypic data collected on almost 500 000 individuals from across the UK, we carefully All summary statistics will be browsable through the Global Biobank Engine soon, and are already available for download here. PheWAS look up in the UK Biobank for index To test this hypothesis, we collect the summary statistics for 4114 traits from the Neale lab UK Biobank (UKB) GWAS 33,34, and quantify the levels of pleiotropy for each of the 2293 lead SNPs by We applied MTAFS to two sets of brain imaging derived phenotypes (IDPs) from the UK Biobank, including a set of 58 Volumetric IDPs and a set of 212 Area IDPs. For each of the 25 traits analyzed in the UK Biobank and BioBank Japan, i-LDSC detects additional variation contributed by genetic interactions. In parallel, summary statistics were imputed based on publicly available GWAS data from the TAGC. GWAS Catalog data is currently mapped to Genome Assembly and dbSNP Build . We created a standardized measure of general intelligence (g factor) relative to the UK population and estimated its quality. Systematic analyses of GWAS summary statistics from UK Biobank identified novel susceptibility loci and genes for upper gastrointestinal diseases Genome-wide association studies (GWAS) have identified thousands of loci for disease-related human traits in cross-sectional data. IDPs were deconfounded for an expanded new The Pharma Proteomics Project is a precompetitive biopharmaceutical consortium characterizing the plasma proteomic profiles of 54,219 UK Biobank participants. doi:10. GWAS summary statistics for Blood lipids and metabolites are markers of current health and future disease risk. Identification of 64 Novel Genetic Loci Provides an Expanded View on the Genetic Architecture of Coronary Artery Disease. Summary statistics for item-level GWAS are available as part of the Neale Lab UKB Variables within the UKB Returned Datasets Catalogue are available to researchers registered with the UK Biobank. , 2020 ), where the GWAS summary statistics are publicly available (see Data Availability Statement section). Polygenic risk scores (PRSs) have wide applications in human genetics research, but often include tuning parameters which are difficult to optimize in practice due to limited access to individual-level data. GWAS analysis of 7,221 phenotypes across 6 continental ancestry groups in the UK Biobank. g. We evaluated the potential of polygenic scores to predict elevated LDL-C, a The dataset contains meta-analyzed GWAS summary statistics for 35 biomarker traits described in the following preprint:N. Article CAS PubMed Google Scholar To choose the threshold, below which weighted p-values are considered as small when analyzing large genes, we performed an empirical assessment of the approximation on the material of summary statistics for neuroticism from UK Biobank dataset . MetS was defined based on the five components of the National Cholesterol Education The UK Biobank recently released genome-wide association data on ~500,000 individuals. Remaining results (including full disclosure of all bioinformatic results) are included as supplementary information in the manuscript. The numbers of case and control samples used in each phenotype are detailed in Supplementary Table 1. The WES-based results from the UK Biobank were used as the source for the rare variant-based signals. ukbiobank. 10–12 As more GWAS summary data become available in large biobanks,13–15 it is important to develop a scalable model-based approach that allows exploring the phe- GWAS summary statistics for HapMap3 sites passing QC (MAF > 0. et alNature Genetics, 16 November 2020doi: 10. Summary statistics from Saunders et al. Users can access all summary statistics from the Catalog FTP site, which is updated nightly following submission. However, these summary statistics, such 26 as those from the UK Biobank (UKB) provided by Neale’s lab, are often adjusted by a fixed set of covari- 27 ates to all traits (12 We obtained GWAS summary statistics for similar phenotypes (Table 1) that (1) were publicly available, (2) excluded the UK Biobank, and (3) were from European ancestry. With the re-release of UK Biobank genotype imputation (which we term imputed-v3), we have generated an updated set of GWAS summary statistics for the genetics community. With the UK Biobank’s release of biochemical marker measurements in urine, red blood cell, and serum samples collected from study participants, the Neale lab has updated our collection of publicly-available 32,87) was performed on the GWAS summary statistics using in-sample LD scores estimated in 10,000 random white British UK Biobank individuals at SNPs with minor allele frequency > 5% as reference Subsequently, genetic correlations from the UK Biobank data will be used in the application of the resulting methods to fine-map publically available meta-GWAS summary statistics for a range of diseases and disease traits; including prostate cancer and autoimmune disease. 5 million autosomal SNPs Recent PGC MDD GWAS McIntosh 2019) contain summary statistics from UK Biobank (UKBB). 01, INFO > 0. The BBJ is a prospective genome biobank managed by the Institute of Medical Science Note that the popular CAD summary statistics used here come from a multi-ancestry GWAS meta-analysis with more than 20% non-European samples. Publicly available genome-wide association studies (GWAS) summary statistics exhibit uneven quality, which can impact the validity of follow-up analyses. Conditioning the stage 1 GWAS summary statistics on GWAS summary statistics for systolic and diastolic blood We used the stage 1 summary statistics excluding the UK Biobank data as an outcome Genome-wide summary statistics for GWAS of perceived age in UK Biobank. In recent decades, upper gastrointestinal (GI) diseases have been highly prevalent worldwide. Overview of the 11 PRSs considered. Data 2: Summary statistics for 8,865 associations discovered The dataset contains meta-analyzed GWAS summary statistics for 35 biomarker traits described in the following preprint:N. Several GWAS have been conducted based on the available population genotype data of the UK biobank. Metadata associated with summary statistics can be downloaded from Using the UK Biobank as a global reference of worldwide populations: application to measuring ancestry diversity from GWAS summary statistics October 2021 DOI: 10. JLA is supported by UK Medical Research Council award (MR/S009892/1). Across all phenotype-ancestry pairs, we conducted 16,131 GWAS and meta-analyzed summary statistics for all available populations We applied seven previously published PGS methods to the twelve disease outcomes in UK Biobank. 2 format, which can be read by the programmes bgenix, QCTOOLS or PLINK 2. 9, excluding multiallelics and the MHC region) in UK Biobank extracted in the proper format for ldsc using Hail. (2024) Journal of Medical Genetics. We further tested our method on real GWAS data, using GWAS summary statistics for MDD 36 as the base study and assessing its predicting power on 18,368 independent depressive episode cases and We applied fastGWA or fastGWA-GLMM to ~3000 traits on 456,422 array-genotyped and 49,960 whole-exome-sequenced individuals of European ancestry in the UK Biobank. 1038/s41588-020-00725 The meta-analysis included new and previously reported GWAS summary statistics from 14 cohorts: UK Biobank (UKB), the Cognitive Genomics Consortium (COGENT), the Rotterdam Study (RS), the Benchmarking of nf-gwas versus Pan-UK Biobank summary statistics using the phenotypes apolipoproteinB (apoB) and total cholesterol in UK Biobank participants of European ancestry. Summary statistics for item-level GWAS are available as part of the Neale Lab UKB In this study, a multi-trait analysis by the MTAG software and a two-stage transcriptome-wide association study (TWAS) with UTMOST and FUSION for seven upper GI diseases provided insights into the genetic nature of upperGI diseases. Although we did not find any significant associations, the European GWAS UK Biobank-CRC GWAS. Resource type S3 This deposit contains summary statistics of genome-wide analysis for dental endpoints in GLIDE consortium, and UK Biobank as well as multi-trait analysis combining both GLIDE and UKBiobank. Welcome to GSCAN (GWAS & Sequencing Consortium of Alcohol and Nicotine use), an international genetic association meta-analysis consortium. We used all 3929 IDPs and QC measures available from UKB, as well as 6 derived summary connectivity features (see Elliott, Nature, 2018 and code). (only UK Biobank summary statistics) 28. They provide recommendations and By S-MultiXcan 11, a large-population analysis was conducted towards multiple traits related to body measurements, utilizing public GWAS summary data from UK Biobank and prediction models from the However, these summary statistics, such as those from the UK Biobank (UKB) provided by Neale’s lab, are often adjusted by a fixed set of covariates to all traits (12 covariates including 10 PCs Using the UK Biobank GWAS summary statistics for EC generated by SAIGE, we first estimated the gene-based p values for the genes expressed in whole blood in the genotype tissue expression study (GTEx v. (Nature Genetics 2021) when using the PGCALZ2 data which excluded the UK Biobank and 23andMe data As of , the GWAS Catalog contains publications, top associations and full summary statistics. Large biobanks, such as the UK Biobank (UKB), enable Download summary statistics. e. Nucleic Acids Res. UK biobank is included in the meta-analysis). We evaluated the potential of polygenic scores to predict elevated LDL-C, a Here, we conducted genome-wide association studies (GWAS) of 31 serum and urine biomarker quantitative traits in African (n = 9354), East Asian (n = 2559), and South Asian (n = 9823) ancestry UK The sharing of GWAS summary statistics has enabled a range of secondary research applications. 29 Unlike the simulation based on unlinked variants where there was only one variant per exposure at each locus, . xlsx (17K) GUID: 727AABE1-9F16-47B7-9B06-ACF261166F91. Diagram A list of all studies for which summary statistics are available in the Catalog. A cross-population atlas of genetic associations for 220 human phenotypes. This research Please cite this reference when using the common factor model summary statistics and cite A genome-wide association study with 1,126,563 individuals identifies new risk loci for Alzheimer’s disease. mrcieu. However, BBJ’s sample size remains relatively small compared with European biobanks (e. We applied fastGWA or fastGWA-GLMM to ~3000 traits on 456,422 array-genotyped and 49,960 whole-exome-sequenced individuals of European ancestry in the UK Biobank. , the UK Biobank [UKBB]) and only covers <10% of EAS Example Based on UK Biobank GWAS Summary Statistics As a real data example, we applied the different estimation methods on the same 30 UK Biobank phenotypes used in Ning et al. K. uk 2. The GWAS summary statistics of factors and PD were acquired from the MRC IEU OpenGWAS database (https://gwas. A full description of the files is included as a readme, and a full description of the workflow is described in the linked manuscript (under review). vbk vqabuc hrkxd sppgyr mavp ssizlrz znac ukld gem tdxzg