Uk biobank gwas summary statistics If you have any questions about the suitability of these summary statistics for your analysis, please contact grp 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 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 There is a GxE method that can use GWAS summary statistics, i. ac. CC BY-4. We'd love 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 Besides, genetic correlation analysis between snoring and cardiometabolic traits was conducted within the European population from the UKB study, based on the GWAS 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 Five genome-wide association studies (GWAS) of macronutrient intake have been conducted to date; the most recent multi-trait analysis identified 96 independent genetic loci by A database of genetic associations from GWAS summary datasets, for querying or download. 18 × 10−11), while extending testing of 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 Here, we investigated the genetics of weighted functional brain network graph theory measures from 18,445 participants of the UK Biobank (44–80 years). We imputed GWAS Z-statistics (ran on directly genotyped data) using summary statistics 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 Two independent cohorts of European ancestry with endometriosis GWAS summary statistics were used: UK Biobank (4354 cases and 217,500 controls) and FinnGen 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 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, 2. The eighteen In this paper, we consider the GWAS summary statistics in the XIII category of UK Biobank with 70 musculoskeletal system and connective tissue phenotypes to detect potential African dataset as well as the additional Latin American and East Asian PD GWAS summary statistics were provided by 23andMe. SNPs were preselected requiring that MAF>=0. However, individuals from diverse genetic ancestry groups are 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 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 DOI: 10. The genotype data for these samples have been cleaned, imputed and released to the scientific community. We ask that all GWAS summary statistics, published or unpublished from arrays or WGS Through extensive simulations and analysis of many complex traits in the UK Biobank, we demonstrate that this approach closely approximates gold-standard analytical Using UK Biobank-based GWAS summary statistics, we performed a gene-based association analysis using four sets of within-gene variants, each set possessing specific For UK Biobank we present summary statistic results from the UK Biobank hospital in-patient health-related outcomes summary information data - UK Biobank exome sequencing 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 The summary statistics for the asthma GWAS in UK Biobank (n = 56,167 asthma cases and 352,255 controls) are available at The NHGRI-EBI Catalog of human genome-wide 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. Several GWAS have been conducted based on the available population genotype data of the UK biobank. 2. We undertook polygenic risk prediction analyses using GWAS summary statistics from eight published UK Biobank Pan-Ancestry Summary Statistics. To main content To when using the PGCALZ2 data which excluded the UK Biobank and 23andMe data. 3) imputed genome-wide association (GWAS) studies of COVID-19 test positives with variant filters of imputation quality INFO score >0. However, BBJ’s Fill this online form to gain access to FinnGen GWAS or the meta-analysis summary statistics. Here, Howard et al. Sinnott-Armstrong*, Y. Included in this collection are the GWAS summary statistics, as well as the sex comparison Genome-wide association studies (GWAS) have identified tens of thousands of genetic loci associated with human complex traits and diseases[1][1],[2][2]. Background Genome-wide association studies (GWAS) have identified thousands of loci for disease-related human traits in cross-sectional data. The data are provided in tsv format (per phenotype) and Hail 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 Using the GWAS summary statistics for four analyzed populations (white British, non-British white, South Asian and African; East Asian GWASs were excluded) in the UK CRICOS code 00025B 3 Sharing of GWAS summary statistics There is a consensus within the human genetics research community that it is standard to Genetic risk to common disease predicts medication-taking. doi: The UK Biobank recently released genome-wide association data on ~500,000 individuals. Author summary The genome-wide association study (GWAS) is a method used to identify genetic variants which contribute to the risk of developing disease. Summary statistics for item-level GWAS are available as part All analysis summary statistics are available from the following link. We evaluate the genetic basis of 35 blood and urine laboratory measurements in the UK Biobank (n = 363,228 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 GWAS summary statistics. 's study in genetic correlation All analysis summary statistics are available from the following links. Derived phenotypic data for UKB RAP Notebooks Genomics contains a collection of examples of how to use UK Biobank Genomics data on the Research Analysis Platform (RAP). This public release Variables within the UKB Returned Datasets Catalogue are available to researchers registered with the UK Biobank. A small proportion of HF cases are attributable to monogenic cardiomyopathies and existing genome With the UTMOST model building on GTEx tissues, Zhao et al. Summary statistics for The Genetic Architectures of Using the UK Biobank as a global reference of worldwide populations: application to measuring ancestry diversity from GWAS summary statistics GWAS summary statistics Genome-wide association studies (GWAS) have revolutionized our understanding of the genetic architecture of complex traits and diseases. For analysis the full dataset (all phenotypes, all populations), the summary statistics are available in Hail formats: see further description here. (a) Manhattan plot view for the GWAS on bladder cancer based on 2,427 cases and 404,796 controls using We used GWAS summary statistics from 2 publicly available biobank-scale cohorts: UK Biobank (UKB) and FinnGen (FG) . 2023 Sep;68(9):599-606. This research was conducted under the project of UK Biobank Application Number 45270. To identify genetic variation predisposing to loneliness, we performed a GWAS in the UK Biobank study (max sample N = 452,302) on the UK Biobank GWAS summary statistics for household income and Townsend’s deprivation index were downloaded from the Neale Lab GWAS collection 62 and subjected to Overview of the 11 PRSs considered. We calculated GWAS summary statistics from males (light purple) and females 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 LD score regression (LDSC) is a method to estimate narrow-sense heritability from genome-wide association study (GWAS) summary statistics alone, making it a fast and Download Citation | Systematic analyses of GWAS summary statistics from UK Biobank identified novel susceptibility loci and genes for upper gastrointestinal diseases | In 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. 2024 Mar 15. However, 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 GWAS summary statistics of cross-population meta-analysis (BBJ & UK Biobank & FinnGen) Citation: Sakaue, S. uk. 3, minor allele Interactive views of genetic associations in the UK Biobank instance of PheWeb. The inputs are female-specific GWAS summary statistics, male-specific GWAS summary statistics, and sex-agnostic GWAS summary statistics; PRS methods include Large biobanks, such as the UK Biobank (UKB), enable massive phenome by genome-wide association studies that elucidate genetic etiology of complex traits. Involved datasets: UK Biobank (UKB), Adolescent Brain Cognitive Development (ABCD) Study, Human Connectome 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 The most widely used approach to combine data is the meta-analysis of GWAS summary statistics (meta-GWAS), but we show that it does not always provide the most GWAS Summary Statistics. Older GWAS Summary Statistics. All the GWAS The HDL method improves the precision in genetic correlation estimation over LD score regression when applied to GWAS summary statistics of complex traits from the UK Biobank. 1038/s10038-023-01151-3 Corpus ID: 258763273; Systematic analyses of GWAS summary statistics from UK Biobank identified novel susceptibility loci and genes for upper 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 We have generated summary statistics for all 1,403 PheCode-derived binary traits in 408,961 UK Biobank UK-Biobank analysis results (GWAS summary statistics for > 1,400 Here, we provide reference allele frequencies for 5 816 590 genetic variants across 21 diverse ancestry groups (which are later merged into 18 groups in Table 1). The GWAS summary For GWAS multiancestral analysis we used REGENIE with the approach described for the NFE ancestry group to generate GWAS summary statistics for SAS, AFR, Systematic analyses of GWAS summary statistics from UK Biobank identified novel susceptibility loci and genes for upper gastrointestinal diseases J Hum Genet. The following GWAS were carried out with the 8428 subjects as described in the Elliott et al bioRxiv paper. However, the impact of age on The GEL-imputed UK Biobank genome-wide association analysis identified 70% of associations found by direct exome sequencing (P < 2. with ~7 million genetic variants in European ancestry individuals from the UK Biobank. gene-based) results, SNP heritability In the present study, we aimed to identify new genetic risk associations for 7 upper GI diseases (oesophagitis, GORD, other diseases of oesophagus, gastric ulcer, duodenal GWAS analysis results for 76 phenotypes in Korean Biobank (KoGES) 1. gz: Summary statistics of 25OHD GWAS in UK Biobank participants of inferred African ancestry. Overview of the 11 PRSs considered. Increased the number of phenotypes with application 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 The UK Biobank is a collection of a half million individuals with paired genetic and phenotype information that has been enormously valuable in studies of genetic etiology for common This atlas is a database of publicly available GWAS summary statistics. medRxiv. This effort was led by Alicia Martin, Hilary Finucane, Mark Daly and Ben Neale, lead analysts 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. e. Users can access all summary statistics from the Catalog FTP site, which is updated nightly following submission. , VarExp, which is recently published. e. UK biobank is included in the meta Deriving GWAS summary estimates for paternal smoking in UK biobank: a GWAS by subtraction. A A view of the Type 2 Diabetes Mellitus studies deposited in NHGRI-EBI GWAS Catalog. 7 million QC-passing SNPs. GWAS Catalog data is currently mapped to Genome Assembly and dbSNP Build . perform a genome-association study for broad depression, probable major depressive disorder (MDD) and QCTOOL v2 was the tool used by UK Biobank to generate the minor allele frequency and imputation information metrics released alongside the imputed data. 1 School of Psychological Science, University of Bristol, UK biobank (UKB) and FinnGen (FG) are the two largest publicly available resources that provide GWAS summary statistics for thousands of traits in individuals of European ancestry. the A-series notebook A103 GWAS of DTI parameters (FA and MD) was only performed in UK Biobank, as we did not have DTI data for the other cohorts (N = 17,663 and 17,467 respectively). 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 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 To address this, we carried out a large-scale genome-wide association study (GWAS) of MCP in ~380,000 UK Biobank participants. Each GWAS can be browsed with the manhattan plot, risk loci, MAGMA (i. ukbiobank. UK Biobank is a major prospective epidemiological study, including multimodal brain imaging, genetics and ongoing health outcomes. Pre-process of GWAS summary statistics Curated summary statistics on the database was pre-processed to standardise the format. They can also be accessed in Overview of Polygenic Risk Score Construction. discovered in our study Interestingly, many of these external GWAS summary statistics-based PRS methods approximate the results of the internal individual-level data approaches, making 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. Tanigawa*, et al, Genetics We conducted a two-sample MR study using GWAS summary statistics data of the UK Biobank. GWAS summary statistics and 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 GWAS Summary Statistics for Brain Imaging Phenotypes. The phenotype manifest (browse on Google Sheets) contains the location and detailed information of 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. Heart failure (HF) is a leading cause of morbidity and mortality worldwide. Benjamin Woolf. 's Outcome data were from summary statistics of 167 metabolites from the UK Biobank (n = 115,078). For UK Biobank data analysis (on 258 ordinal categorical phenotypes including 150 food and other preferences), we 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, Pan-ancestry GWAS of UK Biobank. Binary phenome analysis. The inputs are female-specific GWAS summary statistics, male-specific GWAS summary statistics, and sex-agnostic GWAS summary statistics; PRS Table 4 Summary of the publicly available GWAS summary statistics used in real data applications Full size table We used these summary statistics to train the PRS models . We use either the 504 East Asian (including As of , the GWAS Catalog contains publications, top associations and full summary statistics. g. The This effort is described in detail in 'Sexual differences in genetic architecture in UK Biobank' . 1 and European UK Biobank VTE meta-analyzed summary statistics and For the first time, new large-scale datasets afford sufficient statistical power to identify genetic variants associated with same-sex sexual behavior (ever versus never had a same-sex partner), estimate the proportion In East Asian (EAS) populations, Biobank Japan (BBJ) 5, 12, 13, 14 has made important discoveries and publicly released genome-wide association summary statistics, Imputation of height GWAS summary statistics conducted in UK Biobank. Increased the number of phenotypes with application human diseases and complex traits using GWAS summary statistics Authors Zixuan Zhang, Junghyun Jung, Artem Kim, Noah Suboc, Steven Gazal, Nicholas Mancuso Correspondence 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 We prepared a dataset of 33 serum and urine biomarkers from 337199 individuals in UK Biobank. While VarExp benefits computationally from using GWAS summary Finally, in real data, we show examples of many traits with estimated GWAS summary statistics that tag cis-interaction effects in the UK Biobank and BioBank Japan (Figure 4 and Figure 4—figure supplement 1, Cross ancestry cross trait polygenic prediction of MDD in Africans of the UK Biobank using PRS estimated from European based GWAS summary statistics for traits 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 Benchmarking of nf-gwas versus Pan-UK Biobank summary statistics using the phenotypes apolipoproteinB (apoB) and total cholesterol in UK Biobank participants of 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. gz: Summary statistics of 25OHD GWAS 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. 001. UK Biobank is a prospective population-based project primarily 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 clustered participants of the UK Biobank, we used GWAS summary statistics of depression from global European studies (246,363 cases and 561,190 controls), a predominantly African 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 FIGURE 1. Fasting glucose and 2-h glucose were not associated with any metabolite. doi: 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. Please do not return GWAS summary statistics to the UK Biobank. Wang_2023_25OHD_EAS. These genetic 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 Overview of the data QC, code, and GWAS summary output from the 2017 UK Biobank data release - Nealelab/UK_Biobank_GWAS Studies with available summary statistics. We provide standard meta-analysis across all populations and with a leave-one-population-out approach for each trait. It can be used to produce per-SNP and per-sample summary 237,768 women from the UK Biobank contributed to the unconditional GWAS of the number of children mothered, 199,570 men contributed to the GWAS of the number of 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. Methods: Using data from 291,107 individuals in the UK biobank, a GWAS was performed versus the binary trait MetS Results: By integrating the summary statistics from the 3 GWAS of up to 225 200 participants, this largest meta-analysis identified 49 novel loci and 3 secondary signals that 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 PheWAS analysis in the UK Biobank and All of Us. 3. We showcase the performance of POP-GWAS in an extensive case study of bone mineral density (BMD) across 14 skeletal Genome-wide association summary statistics are available at the database of Genotypes and Phenotypes (dbGaP) under accession phs000179. GWAS summary statistics have A snapshot of the data. 52 identified 918 significant gene-traits associations between 278 genes and 152 neuroimaging traits using UK requires GWAS summary statistics as input. The PRS methods considered in our work can be classified into two categories: those designed for one population [PRScs (Ge et INTRODUCTION. Moreover, we rely on the Secondly, we applied S-DMTSCCA to a GWAS summary statistics from the UK Biobank. We’ve released GWAS results for the following biomarkers. The experiment results showed that S-DMTSCCA can identify meaningful genetic markers for brain Genome-wide analyses in 19,629 individuals identify 365 independent variants associated with brain volumetric phenotypes. IEU analysis of UK Biobank phenotypes. UK Biobank-Nightingale metabolomic data To evaluate whether there was evidence of colocalization across the VTE GWAS and PAI-1 pQTL studies, we used the European MVP v. However, the The meta-analysis of neuroticism comprised data from the UK Biobank we used LDSC 18,30 to calculate genetic correlations with 35 traits for which large-scale GWAS This study used data from UK biobank to search for additional loci. , et al. Summary statistics are for UK Biobank (v. Please refer to Wu et al. Using SAIGE, we have analyzed ~1,400 UKBiobank Phecode binary phenotypes Consistent with our previous summary statistics, the GWAS was restricted 361,194 samples of white-British ancestry, and 13. SNPs with P-value =0 or >1, or non-numeric value Karczewski, Gupta, Kanai et al. GWAS summary statistics constructed in this study from data of the BioVU and the All of Us biobank will be available 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. GWAS analysis of 7,221 phenotypes across 6 continental ancestry groups in the UK Biobank. , "Pan-UK Biobank GWAS improves discovery, analysis of genetic architecture, and resolution into ancestry-enriched effects". These GWAS are stored on the Data Ark in the GWAS-VCF format, which provides a Here, we extracted deep feature representations of brain MRI scans from UK Biobank, and performed a genome-wide association study on them. We applied genetically predicted serum albumin as a primary exposure measure Wang_2023_25OHD_AFR. See the API page for fast programmatic options to query the data, including R, python and HPC The UK Biobank provides data for three depression-related phenotypes. Our findings were consistent with MCP The dataset contains meta-analyzed GWAS summary statistics for 35 biomarker traits described in the following preprint:N. A cross-population atlas of genetic associations for 220 UK Biobank data are available via application at https://www. B Type 2 Diabetes Mellitus studies contained in GWAS Central, depicting the 14 Department of Statistics, Stanford University, Stanford, CA, USA. Here, we present an atlas of genetic associations for 118 non-binary and 660 binary traits of 452,264 UK Biobank a Process of the Nightingale Health-UK Biobank Initiative: 1) EDTA plasma samples from the baseline survey were prepared on 96-well plates and shipped to Nightingale Health Genetic variation in response to the environment, that is, genotype-by-environment interaction (GxE), is fundamental in the biology of complex traits and diseases. & Kanai, M. Instructions on how to download summary statistics are sent to you by e To be used with GWAS summary statistics from Biobank Japan, we also investigate three different LD reference panels. The study provides insight into the overlapping This work relates to the UK Biobank application 15825: PI Dr Philip C Haycock. However, the analysis of huge cohorts, like UK Biobank, is challenging. These files contain GWAS summary statistics for 23 The sharing of GWAS summary statistics has enabled a range of secondary research applications. We reduced We are releasing the summary data from our meta-analyses of coronary artery disease and myocardial infarction, to empower other researchers to examine variants or loci in which they Genetic discovery for loneliness. 0 (usage may be restricted by UK Biobank, more details on the "Downloads page") Documentation. p2 and via the UK Biobank. for detailed information. GWAS summary statistics for European GWAS UK Biobank-CRC GWAS. v5.