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Grant Details

Grant Number: 5U24HG012542-02 Interpret this number
Primary Investigator: Parkinson, Helen
Organization: European Molecular Biology Laboratory
Project Title: Strengthening Community Knowledge Bases for Genetic Association Studies and Polygenic Scores, the Gwas and Pgs Catalogs
Fiscal Year: 2023


Abstract

PROJECT SUMMARY The Genome Wide Association Studies (GWAS) Catalog’s mission is to provide a comprehensive and complete resource of GWAS knowledge and to integrate the Catalog with appropriate resources, including those that translate GWAS knowledge to improve human health and improve our understanding of human variation in the context of complex disease and related traits. Over the next five years we will continue to provide the most complete, curated, standardised and FAIR resource of GWAS data for an international user community of biomedical researchers from academic and pharmaceutical companies. We will extend our resource activities to closely link the GWAS Catalog with a major cognate application, that of Polygenic Scores (PGS) and the Polygenic Score Catalog. We will continue to work with journals, consortia, charities and other funders to ensure that data is accessible, federating elements of the data where it cannot be shared due to ethical constraints. We will improve the data ingest, curation, visualisation and API components to ensure we scale to increasing data and user volumes. Automation of curation, user deposition and literature extraction will be automated and enhanced resulting in quality controlled, harmonised and FAIR knowledge for users. By integrating data flows with PGS and Mendelian Randomisation (MR) resources, we will make the data and necessary meta data readily accessible for analysis for a wider group of users and reduce redundancy in data flow and acquisition across resources, consolidating our resource as the world’s primary GWAS knowledge base. In Aim 1, we will deliver novel processes and support QC for author deposition of significant SNP-Trait associations enabling scaling and leveraging existing author relationships. Our work to acquire the community’s invaluable GWAS summary statistics will continue, with a target of 75% of all studies linked to summary statistics, emphasising non-European ancestries and under-represented disease areas. Aim 2 provides improvements for community uses of summary statistics by integrating data flows with PGS and Mendelian Randomisation (MR) resources. Aim 3 addresses performance improvements for the infrastructure ensuring it is portable and modular and enabling sharing of QC and harmonisation processes. Aim 4 improves our graphical user interfaces, visualisation and data exploration tools and APIs, ensuring they scale for unprecedented data volumes and are appropriate for evolving user needs. Together these aims will serve our growing user community to both enable and enhance the aetiological understanding, prevention and treatment of cardiovascular disease, diabetes, cancers, psychiatric disorders and other complex diseases.



Publications

The Polygenic Score Catalog: new functionality and tools to enable FAIR research.
Authors: Lambert S.A. , Wingfield B. , Gibson J.T. , Gil L. , Ramachandran S. , Yvon F. , Saverimuttu S. , Tinsley E. , Lewis E. , Ritchie S.C. , et al. .
Source: medRxiv : the preprint server for health sciences, 2024-05-31; , .
EPub date: 2024-05-31.
PMID: 38853961
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Genome-wide analyses of variance in blood cell phenotypes provide new insights into complex trait biology and prediction.
Authors: Xiang R. , Liu Y. , Ben-Eghan C. , Ritchie S. , Lambert S.A. , Xu Y. , Takeuchi F. , Inouye M. .
Source: medRxiv : the preprint server for health sciences, 2024-04-16; , .
EPub date: 2024-04-16.
PMID: 38699308
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Recent advances in polygenic scores: translation, equitability, methods and FAIR tools.
Authors: Xiang R. , Kelemen M. , Xu Y. , Harris L.W. , Parkinson H. , Inouye M. , Lambert S.A. .
Source: Genome medicine, 2024-02-19; 16(1), p. 33.
EPub date: 2024-02-19.
PMID: 38373998
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The Ontology of Biological Attributes (OBA)-computational traits for the life sciences.
Authors: Stefancsik R. , Balhoff J.P. , Balk M.A. , Ball R.L. , Bello S.M. , Caron A.R. , Chesler E.J. , de Souza V. , Gehrke S. , Haendel M. , et al. .
Source: Mammalian genome : official journal of the International Mammalian Genome Society, 2023 Sep; 34(3), p. 364-378.
EPub date: 2023-04-19.
PMID: 37076585
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The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource.
Authors: Sollis E. , Mosaku A. , Abid A. , Buniello A. , Cerezo M. , Gil L. , Groza T. , Güneş O. , Hall P. , Hayhurst J. , et al. .
Source: Nucleic acids research, 2023-01-06; 51(D1), p. D977-D985.
PMID: 36350656
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The Polygenic Score Catalog as an open database for reproducibility and systematic evaluation.
Authors: Lambert S.A. , Gil L. , Jupp S. , Ritchie S.C. , Xu Y. , Buniello A. , McMahon A. , Abraham G. , Chapman M. , Parkinson H. , et al. .
Source: Nature genetics, 2021 Apr; 53(4), p. 420-425.
PMID: 33692568
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