1
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Barrio-Hernandez I, Schwartzentruber J, Shrivastava A, Del-Toro N, Gonzalez A, Zhang Q, Mountjoy E, Suveges D, Ochoa D, Ghoussaini M, Bradley G, Hermjakob H, Orchard S, Dunham I, Anderson CA, Porras P, Beltrao P. Network expansion of genetic associations defines a pleiotropy map of human cell biology. Nat Genet 2023; 55:389-398. [PMID: 36823319 PMCID: PMC10011132 DOI: 10.1038/s41588-023-01327-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 01/30/2023] [Indexed: 02/25/2023]
Abstract
Interacting proteins tend to have similar functions, influencing the same organismal traits. Interaction networks can be used to expand the list of candidate trait-associated genes from genome-wide association studies. Here, we performed network-based expansion of trait-associated genes for 1,002 human traits showing that this recovers known disease genes or drug targets. The similarity of network expansion scores identifies groups of traits likely to share an underlying genetic and biological process. We identified 73 pleiotropic gene modules linked to multiple traits, enriched in genes involved in processes such as protein ubiquitination and RNA processing. In contrast to gene deletion studies, pleiotropy as defined here captures specifically multicellular-related processes. We show examples of modules linked to human diseases enriched in genes with known pathogenic variants that can be used to map targets of approved drugs for repurposing. Finally, we illustrate the use of network expansion scores to study genes at inflammatory bowel disease genome-wide association study loci, and implicate inflammatory bowel disease-relevant genes with strong functional and genetic support.
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Affiliation(s)
- Inigo Barrio-Hernandez
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
- Open Targets, Cambridge, UK
| | - Jeremy Schwartzentruber
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
- Open Targets, Cambridge, UK
- Wellcome Sanger Institute, Cambridge, UK
| | - Anjali Shrivastava
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
- Open Targets, Cambridge, UK
| | - Noemi Del-Toro
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
- Open Targets, Cambridge, UK
| | - Asier Gonzalez
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
- Open Targets, Cambridge, UK
| | - Qian Zhang
- Wellcome Sanger Institute, Cambridge, UK
| | - Edward Mountjoy
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
- Open Targets, Cambridge, UK
| | - Daniel Suveges
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
- Open Targets, Cambridge, UK
| | - David Ochoa
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
- Open Targets, Cambridge, UK
| | - Maya Ghoussaini
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
- Open Targets, Cambridge, UK
| | - Glyn Bradley
- Computational Biology, Genomic Sciences, GSK, Stevenage, UK
| | - Henning Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
- Open Targets, Cambridge, UK
| | - Sandra Orchard
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
- Open Targets, Cambridge, UK
| | - Ian Dunham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
- Open Targets, Cambridge, UK
- Wellcome Sanger Institute, Cambridge, UK
| | - Carl A Anderson
- Open Targets, Cambridge, UK
- Wellcome Sanger Institute, Cambridge, UK
| | - Pablo Porras
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
- Open Targets, Cambridge, UK
| | - Pedro Beltrao
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK.
- Open Targets, Cambridge, UK.
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland.
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2
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Ochoa D, Hercules A, Carmona M, Suveges D, Baker J, Malangone C, Lopez I, Miranda A, Cruz-Castillo C, Fumis L, Bernal-Llinares M, Tsukanov K, Cornu H, Tsirigos K, Razuvayevskaya O, Buniello A, Schwartzentruber J, Karim M, Ariano B, Martinez Osorio R, Ferrer J, Ge X, Machlitt-Northen S, Gonzalez-Uriarte A, Saha S, Tirunagari S, Mehta C, Roldán-Romero J, Horswell S, Young S, Ghoussaini M, Hulcoop D, Dunham I, McDonagh E. The next-generation Open Targets Platform: reimagined, redesigned, rebuilt. Nucleic Acids Res 2023; 51:D1353-D1359. [PMID: 36399499 PMCID: PMC9825572 DOI: 10.1093/nar/gkac1046] [Citation(s) in RCA: 57] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/14/2022] [Accepted: 10/27/2022] [Indexed: 11/19/2022] Open
Abstract
The Open Targets Platform (https://platform.opentargets.org/) is an open source resource to systematically assist drug target identification and prioritisation using publicly available data. Since our last update, we have reimagined, redesigned, and rebuilt the Platform in order to streamline data integration and harmonisation, expand the ways in which users can explore the data, and improve the user experience. The gene-disease causal evidence has been enhanced and expanded to better capture disease causality across rare, common, and somatic diseases. For target and drug annotations, we have incorporated new features that help assess target safety and tractability, including genetic constraint, PROTACtability assessments, and AlphaFold structure predictions. We have also introduced new machine learning applications for knowledge extraction from the published literature, clinical trial information, and drug labels. The new technologies and frameworks introduced since the last update will ease the introduction of new features and the creation of separate instances of the Platform adapted to user requirements. Our new Community forum, expanded training materials, and outreach programme support our users in a range of use cases.
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Affiliation(s)
- David Ochoa
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Andrew Hercules
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Miguel Carmona
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Daniel Suveges
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Jarrod Baker
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Cinzia Malangone
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Irene Lopez
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Alfredo Miranda
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Carlos Cruz-Castillo
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Luca Fumis
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Manuel Bernal-Llinares
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Kirill Tsukanov
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Helena Cornu
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Konstantinos Tsirigos
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Olesya Razuvayevskaya
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Annalisa Buniello
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Jeremy Schwartzentruber
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Mohd Karim
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Bruno Ariano
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Ricardo Esteban Martinez Osorio
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Javier Ferrer
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Xiangyu Ge
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Sandra Machlitt-Northen
- GlaxoSmithKline plc, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - Asier Gonzalez-Uriarte
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Shyamasree Saha
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Santosh Tirunagari
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Chintan Mehta
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Juan María Roldán-Romero
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Stuart Horswell
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Sarah Young
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Maya Ghoussaini
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - David G Hulcoop
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- GlaxoSmithKline plc, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - Ian Dunham
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Ellen M McDonagh
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
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3
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Gebresilase T, Finan C, Suveges D, Tessema TS, Aseffa A, Davey G, Hatzikotoulas K, Zeggini E, Newport MJ, Tekola-Ayele F. Replication of HLA class II locus association with susceptibility to podoconiosis in three Ethiopian ethnic groups. Sci Rep 2021; 11:3285. [PMID: 33558538 PMCID: PMC7870958 DOI: 10.1038/s41598-021-81836-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 12/29/2020] [Indexed: 11/25/2022] Open
Abstract
Podoconiosis, a debilitating lymphoedema of the leg, results from barefoot exposure to volcanic clay soil in genetically susceptible individuals. A previous genome-wide association study (GWAS) conducted in the Wolaita ethnic group from Ethiopia showed association between single nucleotide polymorphisms (SNPs) in the HLA class II region and podoconiosis. We aimed to conduct a second GWAS in a new sample (N = 1892) collected from the Wolaita and two other Ethiopian populations, the Amhara and the Oromo, also affected by podoconiosis. Fourteen SNPs in the HLA class II region showed significant genome-wide association (P < 5.0 × 10−8) with podoconiosis. The lead SNP was rs9270911 (P = 5.51 × 10−10; OR 1.53; 95% CI 1.34–1.74), located near HLA-DRB1. Inclusion of data from the first GWAS (combined N = 2289) identified 47 SNPs in the class II HLA region that were significantly associated with podoconiosis (lead SNP also rs9270911 (P = 2.25 × 10−12). No new loci outside of the HLA class II region were identified in this more highly-powered second GWAS. Our findings confirm the HLA class II association with podoconiosis suggesting HLA-mediated abnormal induction and regulation of immune responses may have a direct role in its pathogenesis.
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Affiliation(s)
- Tewodros Gebresilase
- Armauer Hansen Research Institute (AHRI), Addis Ababa, Ethiopia.,Unit of Health Biotechnology, Institute of Biotechnology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Chris Finan
- Institute of Cardiovascular Science, Faculty of Population Health, University College London, London, UK
| | - Daniel Suveges
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.,European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Tesfaye Sisay Tessema
- Unit of Health Biotechnology, Institute of Biotechnology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Abraham Aseffa
- Armauer Hansen Research Institute (AHRI), Addis Ababa, Ethiopia
| | - Gail Davey
- Brighton and Sussex Centre for Global Health Research, Brighton and Sussex Medical School, Brighton, UK
| | - Konstantinos Hatzikotoulas
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.,Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,TUM School of Medicine, Technical University of Munich and Klinikum Rechts Der Isar, Munich, Germany
| | - Eleftheria Zeggini
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.,Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,TUM School of Medicine, Technical University of Munich and Klinikum Rechts Der Isar, Munich, Germany
| | - Melanie J Newport
- Brighton and Sussex Centre for Global Health Research, Brighton and Sussex Medical School, Brighton, UK.
| | - Fasil Tekola-Ayele
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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4
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Ochoa D, Hercules A, Carmona M, Suveges D, Gonzalez-Uriarte A, Malangone C, Miranda A, Fumis L, Carvalho-Silva D, Spitzer M, Baker J, Ferrer J, Raies A, Razuvayevskaya O, Faulconbridge A, Petsalaki E, Mutowo P, Machlitt-Northen S, Peat G, McAuley E, Ong CK, Mountjoy E, Ghoussaini M, Pierleoni A, Papa E, Pignatelli M, Koscielny G, Karim M, Schwartzentruber J, Hulcoop DG, Dunham I, McDonagh EM. Open Targets Platform: supporting systematic drug-target identification and prioritisation. Nucleic Acids Res 2021; 49:D1302-D1310. [PMID: 33196847 PMCID: PMC7779013 DOI: 10.1093/nar/gkaa1027] [Citation(s) in RCA: 192] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/14/2020] [Accepted: 11/11/2020] [Indexed: 02/07/2023] Open
Abstract
The Open Targets Platform (https://www.targetvalidation.org/) provides users with a queryable knowledgebase and user interface to aid systematic target identification and prioritisation for drug discovery based upon underlying evidence. It is publicly available and the underlying code is open source. Since our last update two years ago, we have had 10 releases to maintain and continuously improve evidence for target-disease relationships from 20 different data sources. In addition, we have integrated new evidence from key datasets, including prioritised targets identified from genome-wide CRISPR knockout screens in 300 cancer models (Project Score), and GWAS/UK BioBank statistical genetic analysis evidence from the Open Targets Genetics Portal. We have evolved our evidence scoring framework to improve target identification. To aid the prioritisation of targets and inform on the potential impact of modulating a given target, we have added evaluation of post-marketing adverse drug reactions and new curated information on target tractability and safety. We have also developed the user interface and backend technologies to improve performance and usability. In this article, we describe the latest enhancements to the Platform, to address the fundamental challenge that developing effective and safe drugs is difficult and expensive.
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Affiliation(s)
- David Ochoa
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Andrew Hercules
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Miguel Carmona
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Daniel Suveges
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Asier Gonzalez-Uriarte
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Cinzia Malangone
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Alfredo Miranda
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Luca Fumis
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Denise Carvalho-Silva
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Michaela Spitzer
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Jarrod Baker
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Javier Ferrer
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Arwa Raies
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Olesya Razuvayevskaya
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Adam Faulconbridge
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Eirini Petsalaki
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Prudence Mutowo
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,GlaxoSmithKline plc, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Sandra Machlitt-Northen
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,GlaxoSmithKline plc, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Gareth Peat
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Elaine McAuley
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Chuang Kee Ong
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Edward Mountjoy
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Maya Ghoussaini
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Andrea Pierleoni
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Eliseo Papa
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Systems Biology, Biogen, Cambridge, MA 02142, USA
| | - Miguel Pignatelli
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Gautier Koscielny
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,GlaxoSmithKline plc, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Mohd Karim
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Jeremy Schwartzentruber
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - David G Hulcoop
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,GlaxoSmithKline plc, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Ian Dunham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Ellen M McDonagh
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
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5
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Ghoussaini M, Mountjoy E, Carmona M, Peat G, Schmidt E, Hercules A, Fumis L, Miranda A, Carvalho-Silva D, Buniello A, Burdett T, Hayhurst J, Baker J, Ferrer J, Gonzalez-Uriarte A, Jupp S, Karim M, Koscielny G, Machlitt-Northen S, Malangone C, Pendlington ZM, Roncaglia P, Suveges D, Wright D, Vrousgou O, Papa E, Parkinson H, MacArthur JAL, Todd J, Barrett JC, Schwartzentruber J, Hulcoop D, Ochoa D, McDonagh EM, Dunham I. Open Targets Genetics: systematic identification of trait-associated genes using large-scale genetics and functional genomics. Nucleic Acids Res 2021; 49:D1311-D1320. [PMID: 33045747 PMCID: PMC7778936 DOI: 10.1093/nar/gkaa840] [Citation(s) in RCA: 210] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/16/2020] [Accepted: 09/17/2020] [Indexed: 01/22/2023] Open
Abstract
Open Targets Genetics (https://genetics.opentargets.org) is an open-access integrative resource that aggregates human GWAS and functional genomics data including gene expression, protein abundance, chromatin interaction and conformation data from a wide range of cell types and tissues to make robust connections between GWAS-associated loci, variants and likely causal genes. This enables systematic identification and prioritisation of likely causal variants and genes across all published trait-associated loci. In this paper, we describe the public resources we aggregate, the technology and analyses we use, and the functionality that the portal offers. Open Targets Genetics can be searched by variant, gene or study/phenotype. It offers tools that enable users to prioritise causal variants and genes at disease-associated loci and access systematic cross-disease and disease-molecular trait colocalization analysis across 92 cell types and tissues including the eQTL Catalogue. Data visualizations such as Manhattan-like plots, regional plots, credible sets overlap between studies and PheWAS plots enable users to explore GWAS signals in depth. The integrated data is made available through the web portal, for bulk download and via a GraphQL API, and the software is open source. Applications of this integrated data include identification of novel targets for drug discovery and drug repurposing.
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Affiliation(s)
- Maya Ghoussaini
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Edward Mountjoy
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Miguel Carmona
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Gareth Peat
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Ellen M Schmidt
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Andrew Hercules
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Luca Fumis
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Alfredo Miranda
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Denise Carvalho-Silva
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Annalisa Buniello
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Tony Burdett
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - James Hayhurst
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Jarrod Baker
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Javier Ferrer
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Asier Gonzalez-Uriarte
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Simon Jupp
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Mohd Anisul Karim
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Gautier Koscielny
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- GlaxoSmithKline plc, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Sandra Machlitt-Northen
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- GlaxoSmithKline plc, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Cinzia Malangone
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Zoe May Pendlington
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Paola Roncaglia
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Daniel Suveges
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Daniel Wright
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Olga Vrousgou
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Eliseo Papa
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- Systems Biology, Biogen, Cambridge, MA 02142, USA
| | - Helen Parkinson
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Jacqueline A L MacArthur
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - John A Todd
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Oxford Biomedical Research Centre, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Jeffrey C Barrett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Jeremy Schwartzentruber
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - David G Hulcoop
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- GlaxoSmithKline plc, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - David Ochoa
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Ellen M McDonagh
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Ian Dunham
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
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6
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Gilly A, Southam L, Suveges D, Kuchenbaecker K, Moore R, Melloni GEM, Hatzikotoulas K, Farmaki AE, Ritchie G, Schwartzentruber J, Danecek P, Kilian B, Pollard MO, Ge X, Tsafantakis E, Dedoussis G, Zeggini E. Very low-depth whole-genome sequencing in complex trait association studies. Bioinformatics 2020; 35:2555-2561. [PMID: 30576415 PMCID: PMC6662288 DOI: 10.1093/bioinformatics/bty1032] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 11/17/2018] [Accepted: 12/17/2018] [Indexed: 12/31/2022] Open
Abstract
Motivation Very low-depth sequencing has been proposed as a cost-effective approach to capture low-frequency and rare variation in complex trait association studies. However, a full characterization of the genotype quality and association power for very low-depth sequencing designs is still lacking. Results We perform cohort-wide whole-genome sequencing (WGS) at low depth in 1239 individuals (990 at 1× depth and 249 at 4× depth) from an isolated population, and establish a robust pipeline for calling and imputing very low-depth WGS genotypes from standard bioinformatics tools. Using genotyping chip, whole-exome sequencing (75× depth) and high-depth (22×) WGS data in the same samples, we examine in detail the sensitivity of this approach, and show that imputed 1× WGS recapitulates 95.2% of variants found by imputed GWAS with an average minor allele concordance of 97% for common and low-frequency variants. In our study, 1× further allowed the discovery of 140 844 true low-frequency variants with 73% genotype concordance when compared to high-depth WGS data. Finally, using association results for 57 quantitative traits, we show that very low-depth WGS is an efficient alternative to imputed GWAS chip designs, allowing the discovery of up to twice as many true association signals than the classical imputed GWAS design. Availability and implementation The HELIC genotype and WGS datasets have been deposited to the European Genome-phenome Archive (https://www.ebi.ac.uk/ega/home): EGAD00010000518; EGAD00010000522; EGAD00010000610; EGAD00001001636, EGAD00001001637. The peakplotter software is available at https://github.com/wtsi-team144/peakplotter, the transformPhenotype app can be downloaded at https://github.com/wtsi-team144/transformPhenotype. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Arthur Gilly
- Department of Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.,Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Lorraine Southam
- Department of Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.,Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Daniel Suveges
- Department of Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Karoline Kuchenbaecker
- Department of Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Rachel Moore
- Department of Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Giorgio E M Melloni
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Konstantinos Hatzikotoulas
- Department of Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.,Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Aliki-Eleni Farmaki
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University of Athens, Athens, Greece
| | - Graham Ritchie
- Department of Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.,European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Jeremy Schwartzentruber
- Department of Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Petr Danecek
- Department of Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Britt Kilian
- Department of Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Martin O Pollard
- Department of Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Xiangyu Ge
- Department of Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - George Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University of Athens, Athens, Greece
| | - Eleftheria Zeggini
- Department of Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.,Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
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7
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Buniello A, MacArthur JAL, Cerezo M, Harris LW, Hayhurst J, Malangone C, McMahon A, Morales J, Mountjoy E, Sollis E, Suveges D, Vrousgou O, Whetzel PL, Amode R, Guillen JA, Riat HS, Trevanion SJ, Hall P, Junkins H, Flicek P, Burdett T, Hindorff LA, Cunningham F, Parkinson H. The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. Nucleic Acids Res 2020; 47:D1005-D1012. [PMID: 30445434 PMCID: PMC6323933 DOI: 10.1093/nar/gky1120] [Citation(s) in RCA: 2310] [Impact Index Per Article: 577.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 10/25/2018] [Indexed: 02/06/2023] Open
Abstract
The GWAS Catalog delivers a high-quality curated collection of all published genome-wide association studies enabling investigations to identify causal variants, understand disease mechanisms, and establish targets for novel therapies. The scope of the Catalog has also expanded to targeted and exome arrays with 1000 new associations added for these technologies. As of September 2018, the Catalog contains 5687 GWAS comprising 71673 variant-trait associations from 3567 publications. New content includes 284 full P-value summary statistics datasets for genome-wide and new targeted array studies, representing 6 × 109 individual variant-trait statistics. In the last 12 months, the Catalog's user interface was accessed by ∼90000 unique users who viewed >1 million pages. We have improved data access with the release of a new RESTful API to support high-throughput programmatic access, an improved web interface and a new summary statistics database. Summary statistics provision is supported by a new format proposed as a community standard for summary statistics data representation. This format was derived from our experience in standardizing heterogeneous submissions, mapping formats and in harmonizing content. Availability: https://www.ebi.ac.uk/gwas/.
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Affiliation(s)
- Annalisa Buniello
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jacqueline A L MacArthur
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Maria Cerezo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Laura W Harris
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - James Hayhurst
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Cinzia Malangone
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Aoife McMahon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Joannella Morales
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Edward Mountjoy
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.,JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Wellcome Centre for Human Genetics, University of Oxford, NIHR Oxford Biomedical Research Centre, Nuffield Department of Medicine, Oxford, UK
| | - Elliot Sollis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel Suveges
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Olga Vrousgou
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Patricia L Whetzel
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ridwan Amode
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jose A Guillen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Harpreet S Riat
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stephen J Trevanion
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Peggy Hall
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Heather Junkins
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Tony Burdett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Lucia A Hindorff
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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8
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Png G, Suveges D, Park Y, Walter K, Kundu K, Ntalla I, Tsafantakis E, Karaleftheri M, Dedoussis G, Zeggini E, Gilly A. Cover Image. Genet Epidemiol 2020. [DOI: 10.1002/gepi.22219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Grace Png
- Wellcome Sanger InstituteWellcome Genome Campus Hinxton United Kingdom
- Department of Medical GeneticsUniversity of Cambridge Cambridge United Kingdom
- Institute of Translational GenomicsHelmholtz Zentrum München—German Research Center for Environmental Health Neuherberg Germany
| | - Daniel Suveges
- Wellcome Sanger InstituteWellcome Genome Campus Hinxton United Kingdom
- European Bioinformatics InstituteWellcome Genome Campus Hinxton United Kingdom
| | - Young‐Chan Park
- Wellcome Sanger InstituteWellcome Genome Campus Hinxton United Kingdom
- Department of Medical GeneticsUniversity of Cambridge Cambridge United Kingdom
| | - Klaudia Walter
- Wellcome Sanger InstituteWellcome Genome Campus Hinxton United Kingdom
| | - Kousik Kundu
- Wellcome Sanger InstituteWellcome Genome Campus Hinxton United Kingdom
| | - Ioanna Ntalla
- William Harvey Research Institute, Barts and The London School of Medicine and DentistryQueen Mary University of London London United Kingdom
| | | | | | - George Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and EducationHarokopio University of Athens Athens Greece
| | - Eleftheria Zeggini
- Wellcome Sanger InstituteWellcome Genome Campus Hinxton United Kingdom
- Institute of Translational GenomicsHelmholtz Zentrum München—German Research Center for Environmental Health Neuherberg Germany
| | - Arthur Gilly
- Wellcome Sanger InstituteWellcome Genome Campus Hinxton United Kingdom
- Institute of Translational GenomicsHelmholtz Zentrum München—German Research Center for Environmental Health Neuherberg Germany
- Department of Public Health and Primary CareUniversity of Cambridge Cambridge United Kingdom
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9
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Png G, Suveges D, Park YC, Walter K, Kundu K, Ntalla I, Tsafantakis E, Karaleftheri M, Dedoussis G, Zeggini E, Gilly A. Population-wide copy number variation calling using variant call format files from 6,898 individuals. Genet Epidemiol 2019; 44:79-89. [PMID: 31520489 PMCID: PMC8653900 DOI: 10.1002/gepi.22260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/31/2019] [Accepted: 08/28/2019] [Indexed: 11/10/2022]
Abstract
Copy number variants (CNVs) play an important role in a number of human diseases, but the accurate calling of CNVs remains challenging. Most current approaches to CNV detection use raw read alignments, which are computationally intensive to process. We use a regression tree-based approach to call germline CNVs from whole-genome sequencing (WGS, >18x) variant call sets in 6,898 samples across four European cohorts, and describe a rich large variation landscape comprising 1,320 CNVs. Eighty-one percent of detected events have been previously reported in the Database of Genomic Variants. Twenty-three percent of high-quality deletions affect entire genes, and we recapitulate known events such as the GSTM1 and RHD gene deletions. We test for association between the detected deletions and 275 protein levels in 1,457 individuals to assess the potential clinical impact of the detected CNVs. We describe complex CNV patterns underlying an association with levels of the CCL3 protein (MAF = 0.15, p = 3.6x10-12 ) at the CCL3L3 locus, and a novel cis-association between a low-frequency NOMO1 deletion and NOMO1 protein levels (MAF = 0.02, p = 2.2x10-7 ). This study demonstrates that existing population-wide WGS call sets can be mined for germline CNVs with minimal computational overhead, delivering insight into a less well-studied, yet potentially impactful class of genetic variant.
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Affiliation(s)
- Grace Png
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom.,Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom.,Institute of Translational Genomics, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Daniel Suveges
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom.,European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Young-Chan Park
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom.,Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Klaudia Walter
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Kousik Kundu
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Ioanna Ntalla
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | | | | | - George Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University of Athens, Athens, Greece
| | - Eleftheria Zeggini
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom.,Institute of Translational Genomics, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Arthur Gilly
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom.,Institute of Translational Genomics, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.,Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
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10
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Gilly A, Suveges D, Kuchenbaecker K, Pollard M, Southam L, Hatzikotoulas K, Farmaki AE, Bjornland T, Waples R, Appel EVR, Casalone E, Melloni G, Kilian B, Rayner NW, Ntalla I, Kundu K, Walter K, Danesh J, Butterworth A, Barroso I, Tsafantakis E, Dedoussis G, Moltke I, Zeggini E. Cohort-wide deep whole genome sequencing and the allelic architecture of complex traits. Nat Commun 2018; 9:4674. [PMID: 30405126 PMCID: PMC6220258 DOI: 10.1038/s41467-018-07070-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 10/08/2018] [Indexed: 11/08/2022] Open
Abstract
The role of rare variants in complex traits remains uncharted. Here, we conduct deep whole genome sequencing of 1457 individuals from an isolated population, and test for rare variant burdens across six cardiometabolic traits. We identify a role for rare regulatory variation, which has hitherto been missed. We find evidence of rare variant burdens that are independent of established common variant signals (ADIPOQ and adiponectin, P = 4.2 × 10-8; APOC3 and triglyceride levels, P = 1.5 × 10-26), and identify replicating evidence for a burden associated with triglyceride levels in FAM189B (P = 2.2 × 10-8), indicating a role for this gene in lipid metabolism.
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Affiliation(s)
- Arthur Gilly
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, CB10 1SA, United Kingdom
| | - Daniel Suveges
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, CB10 1SA, United Kingdom
| | - Karoline Kuchenbaecker
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, CB10 1SA, United Kingdom
- Division of Psychiatry, University College of London, London, W1T 7NF, United Kingdom
- UCL Genetics Institute, University College London, London, WC1E 6BT, United Kingdom
| | - Martin Pollard
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, CB10 1SA, United Kingdom
- Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Hills Road, Cambridge, CB2 0QQ, United Kingdom
| | - Lorraine Southam
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, CB10 1SA, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom
| | - Konstantinos Hatzikotoulas
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, CB10 1SA, United Kingdom
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, D-85764, Germany
| | - Aliki-Eleni Farmaki
- Department of Health Sciences, College of Life Sciences, University of Leicester, Leicester, LE1 6TP, United Kingdom
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University of Athens, Athens, 176-71, Greece
| | - Thea Bjornland
- Department of Mathematical Sciences, Norwegian Institute of Science and Technology, Trondheim, 7491, Norway
| | - Ryan Waples
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Emil V R Appel
- Section for Metabolic Genetics, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, 2200, Denmark
| | | | - Giorgio Melloni
- Department of Biomedical Informatics, Harvard Medical School, Boston, 02115, MA, USA
| | - Britt Kilian
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, CB10 1SA, United Kingdom
| | - Nigel W Rayner
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, CB10 1SA, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Old Road, Headington, Oxford, OX3 7LE, United Kingdom
| | - Ioanna Ntalla
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, United Kingdom
| | - Kousik Kundu
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, CB10 1SA, United Kingdom
- Department of Haematology, Cambridge Biomedical Campus, University of Cambridge, Long Road, Cambridge, CB2 0PT, United Kingdom
| | - Klaudia Walter
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, CB10 1SA, United Kingdom
| | - John Danesh
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, CB10 1SA, United Kingdom
- The National Institute for Health Research Blood and Transplant Unit (NIHR BTRU) in Donor Health and Genomics at the University of Cambridge, Strangeways Research Laboratory, Wort's Causeway, University of Cambridge, Cambridge, CB1 8RN, United Kingdom
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, Wort's Causeway, University of Cambridge, Strangeways Research Laboratory, Cambridge, CB1 8RN, United Kingdom
| | - Adam Butterworth
- The National Institute for Health Research Blood and Transplant Unit (NIHR BTRU) in Donor Health and Genomics at the University of Cambridge, Strangeways Research Laboratory, Wort's Causeway, University of Cambridge, Cambridge, CB1 8RN, United Kingdom
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, Wort's Causeway, University of Cambridge, Strangeways Research Laboratory, Cambridge, CB1 8RN, United Kingdom
- British Heart Foundation Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, United Kingdom
| | - Inês Barroso
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, CB10 1SA, United Kingdom
| | | | - George Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University of Athens, Athens, 176-71, Greece
| | - Ida Moltke
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Eleftheria Zeggini
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, CB10 1SA, United Kingdom.
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, D-85764, Germany.
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11
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Zengini E, Hatzikotoulas K, Tachmazidou I, Steinberg J, Hartwig FP, Southam L, Hackinger S, Boer CG, Styrkarsdottir U, Gilly A, Suveges D, Killian B, Ingvarsson T, Jonsson H, Babis GC, McCaskie A, Uitterlinden AG, van Meurs JBJ, Thorsteinsdottir U, Stefansson K, Davey Smith G, Wilkinson JM, Zeggini E. Genome-wide analyses using UK Biobank data provide insights into the genetic architecture of osteoarthritis. Nat Genet 2018; 50:549-558. [PMID: 29559693 PMCID: PMC5896734 DOI: 10.1038/s41588-018-0079-y] [Citation(s) in RCA: 175] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 01/29/2018] [Indexed: 12/19/2022]
Abstract
Osteoarthritis is a common complex disease imposing a large public-health burden. Here, we performed a genome-wide association study for osteoarthritis, using data across 16.5 million variants from the UK Biobank resource. After performing replication and meta-analysis in up to 30,727 cases and 297,191 controls, we identified nine new osteoarthritis loci, in all of which the most likely causal variant was noncoding. For three loci, we detected association with biologically relevant radiographic endophenotypes, and in five signals we identified genes that were differentially expressed in degraded compared with intact articular cartilage from patients with osteoarthritis. We established causal effects on osteoarthritis for higher body mass index but not for triglyceride levels or genetic predisposition to type 2 diabetes.
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Affiliation(s)
- Eleni Zengini
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
- 5th Psychiatric Department, Dromokaiteio Psychiatric Hospital, Athens, Greece
| | | | - Ioanna Tachmazidou
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
- GSK, R&D Target Sciences, Medicines Research Centre, Stevenage, UK
| | - Julia Steinberg
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
- Cancer Research Division, Cancer Council NSW, Sydney, New South Wales, Australia
| | - Fernando P Hartwig
- Postgraduate Program in Epidemiology, Federal University of Pelotas, Pelotas, Brazil
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Lorraine Southam
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Cindy G Boer
- Departments of Internal Medicine and Epidemiology, Erasmus MC, Rotterdam, the Netherlands
| | | | - Arthur Gilly
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Daniel Suveges
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Britt Killian
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Thorvaldur Ingvarsson
- Department of Orthopaedic Surgery, Akureyri Hospital, Akureyri, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- Institution of Health Science, University of Akureyri, Akureyri, Iceland
| | - Helgi Jonsson
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- Department of Medicine, Landspitali, National University Hospital of Iceland, Reykjavik, Iceland
| | - George C Babis
- 2nd Department of Orthopaedic Surgery, Konstantopouleio General Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Andrew McCaskie
- Division of Trauma & Orthopaedic Surgery, Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Andre G Uitterlinden
- Departments of Internal Medicine and Epidemiology, Erasmus MC, Rotterdam, the Netherlands
| | - Joyce B J van Meurs
- Departments of Internal Medicine and Epidemiology, Erasmus MC, Rotterdam, the Netherlands
| | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Kari Stefansson
- deCODE genetics/Amgen, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - George Davey Smith
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, University of Bristol, Bristol, UK
- National Institute for Health Research, Bristol Biomedical Research Centre, University Hospitals Bristol, NHS Foundation Trust and University of Bristol, Bristol, UK
| | - Jeremy M Wilkinson
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
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12
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Casalone E, Tachmazidou I, Zengini E, Hatzikotoulas K, Hackinger S, Suveges D, Steinberg J, Rayner NW, Wilkinson JM, Panoutsopoulou K, Zeggini E. A novel variant in GLIS3 is associated with osteoarthritis. Ann Rheum Dis 2018; 77:620-623. [PMID: 29436472 PMCID: PMC5890630 DOI: 10.1136/annrheumdis-2017-211848] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 12/08/2017] [Accepted: 12/10/2017] [Indexed: 11/25/2022]
Abstract
OBJECTIVES Osteoarthritis (OA) is a complex disease, but its genetic aetiology remains poorly characterised. To identify novel susceptibility loci for OA, we carried out a genome-wide association study (GWAS) in individuals from the largest UK-based OA collections to date. METHODS We carried out a discovery GWAS in 5414 OA individuals with knee and/or hip total joint replacement (TJR) and 9939 population-based controls. We followed-up prioritised variants in OA subjects from the interim release of the UK Biobank resource (up to 12 658 cases and 50 898 controls) and our lead finding in operated OA subjects from the full release of UK Biobank (17 894 cases and 89 470 controls). We investigated its functional implications in methylation, gene expression and proteomics data in primary chondrocytes from 12 pairs of intact and degraded cartilage samples from patients undergoing TJR. RESULTS We detect a genome-wide significant association at rs10116772 with TJR (P=3.7×10-8; for allele A: OR (95% CI) 0.97 (0.96 to 0.98)), an intronic variant in GLIS3, which is expressed in cartilage. Variants in strong correlation with rs10116772 have been associated with elevated plasma glucose levels and diabetes. CONCLUSIONS We identify a novel susceptibility locus for OA that has been previously implicated in diabetes and glycaemic traits.
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Affiliation(s)
- Elisabetta Casalone
- Department of Medical Sciences, University of Turin, Turin, Italy
- Italian Institute for Genomic Medicine, IIGM, Turin, Italy
| | | | - Eleni Zengini
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
- 5th Psychiatric Department, Dromokaiteio Psychiatric Hospital of Athens, Athens, Greece
| | | | | | - Daniel Suveges
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Julia Steinberg
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Nigel William Rayner
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
- Wellcome Trust Centre for Human Genetics, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
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13
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Grarup N, Moltke I, Andersen MK, Dalby M, Vitting-Seerup K, Kern T, Mahendran Y, Jørsboe E, Larsen CVL, Dahl-Petersen IK, Gilly A, Suveges D, Dedoussis G, Zeggini E, Pedersen O, Andersson R, Bjerregaard P, Jørgensen ME, Albrechtsen A, Hansen T. Loss-of-function variants in ADCY3 increase risk of obesity and type 2 diabetes. Nat Genet 2018; 50:172-174. [PMID: 29311636 PMCID: PMC5828106 DOI: 10.1038/s41588-017-0022-7] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 11/29/2017] [Indexed: 01/08/2023]
Abstract
We have identified a variant in ADCY3 (encoding adenylate cyclase 3) associated with markedly increased risk of obesity and type 2 diabetes in the Greenlandic population. The variant disrupts a splice acceptor site, and carriers have decreased ADCY3 RNA expression. Additionally, we observe an enrichment of rare ADCY3 loss-of-function variants among individuals with type 2 diabetes in trans-ancestry cohorts. These findings provide new information on disease etiology relevant for future treatment strategies.
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Affiliation(s)
- Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ida Moltke
- Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Mette K Andersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Maria Dalby
- Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kristoffer Vitting-Seerup
- Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Timo Kern
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Yuvaraj Mahendran
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Emil Jørsboe
- Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Christina V L Larsen
- National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark
- Greenland Centre for Health Research, University of Greenland, Nuuk, Greenland
| | - Inger K Dahl-Petersen
- National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark
| | - Arthur Gilly
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Daniel Suveges
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - George Dedoussis
- Department of Nutrition and Dietetics, Harokopio University of Athens, Athens, Greece
| | - Eleftheria Zeggini
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Robin Andersson
- Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Peter Bjerregaard
- National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark
- Greenland Centre for Health Research, University of Greenland, Nuuk, Greenland
| | - Marit E Jørgensen
- National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark.
- Greenland Centre for Health Research, University of Greenland, Nuuk, Greenland.
- Steno Diabetes Center Copenhagen, Gentofte, Denmark.
| | - Anders Albrechtsen
- Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
- Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark.
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