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The Polygenic Score Catalog as an open database for reproducibility and systematic evaluation

We present the Polygenic Score (PGS) Catalog (https://www.PGSCatalog.org), an open resource of published scores (including variants, alleles and weights) and consistently curated metadata required for reproducibility and independent applications. The PGS Catalog has capabilities for user deposition, expert curation and programmatic access, thus providing the community with a platform for PGS dissemination, research and translation.

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Fig. 1: Common aspects of PGS analyses that are captured and displayed in the PGS Catalog.
Fig. 2: Benchmarking the association of nine colorectal cancer PGSs in UKB.

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Acknowledgements

We wish to thank all the authors of publications in the PGS Catalog for making their data available and indexable in our database, and all those who responded to our inquiries and requests for data. We thank P. L. Whetzel for implementing the links from the NHGRI-EBI GWAS Catalog publication, study and trait pages to the PGS Catalog. We also wish to acknowledge E. Tinsley, S. Saverimuttu and members of the laboratory of M.I. for curation support. This work makes use of data from UK Biobank Project no. 7439.

This work was supported by core funding from the UK Medical Research Council (MR/L003120/1), the British Heart Foundation (RG/13/13/30194 and RG/18/13/33946) and the National Institute for Health Research (Cambridge Biomedical Research Centre at the Cambridge University Hospitals NHS Foundation Trust). This work was also supported by Health Data Research UK, which is funded by the UK Medical Research Council, Engineering and Physical Sciences Research Council, Economic and Social Research Council, Department of Health and Social Care (England), Chief Scientist Office of the Scottish Government Health and Social Care Directorates, Health and Social Care Research and Development Division (Welsh Government), Public Health Agency (Northern Ireland), British Heart Foundation and Wellcome. M.I. was supported by the Munz Chair of Cardiovascular Prediction and Prevention. This study was supported by the Victorian Government’s Operational Infrastructure Support (OIS) program. Research reported in this publication was supported by the National Human Genome Research Institute of the National Institutes of Health under award U41HG007823. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. In addition, we acknowledge funding from the European Molecular Biology Laboratory. J.D. holds a British Heart Foundation Professorship and is funded by a National Institute for Health Research Senior Investigator Award. M.I. and S.R. are supported by the National Institute for Health Research (Cambridge Biomedical Research Centre at the Cambridge University Hospitals NHS Foundation Trust). S.A.L. is supported by a Canadian Institutes of Health Research postdoctoral fellowship (MFE-171279). This work was performed by using resources provided by the Cambridge Service for Data Driven Discovery (CSD3) operated by the University of Cambridge Research Computing Service (http://www.csd3.cam.ac.uk), provided by Dell EMC and Intel, by using Tier-2 funding from the Engineering and Physical Sciences Research Council (capital grant EP/P020259/1) and DiRAC funding from the Science and Technology Facilities Council (http://www.dirac.ac.uk). The views expressed are those of the authors and not necessarily those of the NHS, the NIHR or the Department of Health and Social Care.

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Authors and Affiliations

Authors

Contributions

S.A.L., J.A.L.M. and M.I. conceived the PGS Catalog, led its development and cowrote the manuscript. S.A.L. and L.G. developed the PGS Catalog interface and computational infrastructure, with critical support from S.J. and H.P. S.A.L., J.A.L.M., M.I., A.B., A.M., S.J., G.A., M.C. and J.D. contributed to the definition of relevant PGS metadata. S.A.L., A.B., A.M. and S.C.R. curated data for inclusion in the Catalog. S.A.L. performed the colorectal cancer PGS benchmarking analysis, with contributions from Y.X. and S.C.R. All authors reviewed and contributed edits to the final manuscript.

Corresponding authors

Correspondence to Samuel A. Lambert, Jacqueline A. L. MacArthur or Michael Inouye.

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Competing interests

J.D. is part of the International Cardiovascular and Metabolic Advisory Board for Novartis (since 2010); the Steering Committee of UK Biobank (since 2011); the MRC International Advisory Group (ING), London (since 2013); the MRC High Throughput Science Omics Panel, London (since 2013); the Scientific Advisory Committee for Sanofi (since 2013); the International Cardiovascular and Metabolism Research and Development Portfolio Committee for Novartis; and the Astra Zeneca Genomics Advisory Board (2018).

Additional information

Peer review information Nature Genetics thanks Melinda Mills and Pradeep Natarajan for their contribution to the peer review of this work.

Supplementary information

Supplementary Information

Supplementary Notes 1–5, Figs. 1–3 and Tables 1–3

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Lambert, S.A., Gil, L., Jupp, S. et al. The Polygenic Score Catalog as an open database for reproducibility and systematic evaluation. Nat Genet 53, 420–425 (2021). https://doi.org/10.1038/s41588-021-00783-5

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