Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Comment
  • Published:

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

Nature Genetics volume 53, pages 420–425 (2021)Cite this article

Subjects

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.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

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.

References

  1. Lambert, S. A., Abraham, G. & Inouye, M. Hum. Mol. Genet. 28, R133–R142 (2019).

    Article  CAS  Google Scholar 

  2. Torkamani, A., Wineinger, N. E. & Topol, E. J. Nat. Rev. Genet. 19, 581–590 (2018).

    Article  CAS  Google Scholar 

  3. Chatterjee, N., Shi, J. & García-Closas, M. Nat. Rev. Genet. 17, 392–406 (2016).

    Article  CAS  Google Scholar 

  4. Wray, N. R., Kemper, K. E., Hayes, B. J., Goddard, M. E. & Visscher, P. M. Genetics 211, 1131–1141 (2019).

    Article  Google Scholar 

  5. Evans, D. M., Visscher, P. M. & Wray, N. R. Hum. Mol. Genet. 18, 3525–3531 (2009).

    Article  CAS  Google Scholar 

  6. International Schizophrenia Consortium. Nature 460, 748–752 (2009).

  7. Kathiresan, S. et al. N. Engl. J. Med. 358, 1240–1249 (2008).

    Article  CAS  Google Scholar 

  8. Ripatti, S. et al. Lancet 376, 1393–1400 (2010).

    Article  Google Scholar 

  9. Khera, A. V. et al. Cell 177, 587–596.e9 (2019).

    Article  CAS  Google Scholar 

  10. Kuchenbaecker, K. et al. Nat. Commun. 10, 4330 (2019).

    Article  Google Scholar 

  11. Lee, J. J. et al. Nat. Genet. 50, 1112–1121 (2018).

    Article  CAS  Google Scholar 

  12. Inouye, M. et al. J. Am. Coll. Cardiol. 72, 1883–1893 (2018).

    Article  Google Scholar 

  13. Khera, A. V. et al. Nat. Genet. 50, 1219–1224 (2018).

    Article  CAS  Google Scholar 

  14. Mavaddat, N. et al. Am. J. Hum. Genet. 104, 21–34 (2019).

    Article  CAS  Google Scholar 

  15. Zheutlin, A. B. et al. Am. J. Psychiatry 176, 846–855 (2019).

    Article  Google Scholar 

  16. Abraham, G. et al. Nat. Commun. 10, 5819 (2019).

    Article  CAS  Google Scholar 

  17. Mavaddat, N. et al. J. Natl. Cancer Inst. 107, djv03 (2015).

    Article  Google Scholar 

  18. Natarajan, P. J. Am. Coll. Cardiol. 72, 1894–1897 (2018).

    Article  Google Scholar 

  19. Tada, H. et al. Eur. Heart J. 37, 561–567 (2016).

    Article  CAS  Google Scholar 

  20. Abraham, G. et al. Eur. Heart J. 37, 3267–3278 (2016).

    Article  CAS  Google Scholar 

  21. Seibert, T. M. et al. Br. Med. J. 360, j5757 (2018).

    Article  Google Scholar 

  22. Li, H. et al. Genet. Med. 19, 30–35 (2017).

    Article  CAS  Google Scholar 

  23. Sharp, S. A. et al. Diabetes Care 42, 200–207 (2019).

    Article  CAS  Google Scholar 

  24. Natarajan, P. et al. Circulation 135, 2091–2101 (2017).

    Article  Google Scholar 

  25. Wand, H. et al. Nature https://doi.org/10.1038/s41586-021-03243-6 (2021).

  26. Choi, S. W., Mak, T. S.-H. & O’Reilly, P. F. Nat. Protoc. 15, 2759–2772 (2020).

    Article  CAS  Google Scholar 

  27. ICDA Organizing Committee and Working Groups. International Common Disease Alliance Recommendations and White Paper v.1.0 (ICDA, 2020); https://drive.google.com/file/d/16SVJ5lbneN9hB9E03PZMhpescAN527HO/view.

  28. Wünnemann, F. et al. Circ. Genom. Precis. Med. 12, e002481 (2019).

    Article  Google Scholar 

  29. Dikilitas, O. et al. Am. J. Hum. Genet. 106, 707–716 (2020).

    Article  CAS  Google Scholar 

  30. Martin, A. R. et al. Nat. Genet. 51, 584–591 (2019).

    Article  CAS  Google Scholar 

  31. Reisberg, S., Iljasenko, T., Läll, K., Fischer, K. & Vilo, J. PLoS ONE 12, e0179238 (2017).

    Article  Google Scholar 

  32. Duncan, L. et al. Nat. Commun. 10, 3328 (2019).

    Article  CAS  Google Scholar 

  33. Wilkinson, M. D. et al. Sci. Data 3, 160018 (2016).

    Article  Google Scholar 

  34. Morales, J. et al. Genome Biol. 19, 21 (2018).

    Article  Google Scholar 

  35. Buniello, A. et al. Nucleic Acids Res. 47, D1005–D1012 (2019). (D1).

    Article  CAS  Google Scholar 

  36. Chang, C. C. et al. Gigascience 4, 7 (2015).

    Article  Google Scholar 

  37. Bycroft, C. et al. Nature 562, 203–209 (2018).

    Article  CAS  Google Scholar 

  38. Fritsche, L. G. et al. Am. J. Hum. Genet. 107, 815–836 (2020).

    Article  CAS  Google Scholar 

  39. Richardson, T. G., Harrison, S., Hemani, G. & Davey Smith, G. eLife 8, e43657 (2019).

    Article  Google Scholar 

  40. Rosenberg, N. A., Edge, M. D., Pritchard, J. K. & Feldman, M. W. Evol. Med. Public Health 2019, 26–34 (2018).

    Article  Google Scholar 

  41. Malone, J. et al. Bioinformatics 26, 1112–1118 (2010).

    Article  CAS  Google Scholar 

  42. Jupp, S., Burdett, T., Leroy, C. & Parkinson, H.E. In Proc. 8th International Conference on Semantic Web Applications and Tools for Life Sciences (eds. Malone, J. et al.) 1546, 118–119 (CEUR Workshop Proceedings, 2015).

  43. Mills, M. C. & Rahal, C. Commun. Biol. 2, 9 (2019).

    Article  Google Scholar 

Download references

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.

Author information

Authors and Affiliations

  1. Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK

    Samuel A. Lambert, Scott C. Ritchie, Yu Xu, Gad Abraham & Michael Inouye

  2. British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK

    Samuel A. Lambert, Laurent Gil, Scott C. Ritchie, Yu Xu, Michael Chapman, John Danesh & Michael Inouye

  3. Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK

    Samuel A. Lambert, Laurent Gil, Michael Chapman, Helen Parkinson, John Danesh & Michael Inouye

  4. European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK

    Samuel A. Lambert, Simon Jupp, Annalisa Buniello, Aoife McMahon, Helen Parkinson & Jacqueline A. L. MacArthur

  5. Wellcome Sanger Institute, Hinxton, UK

    Laurent Gil, Michael Chapman & John Danesh

  6. National Institute for Health Research Cambridge Biomedical Research Centre at the Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK

    Scott C. Ritchie, John Danesh & Michael Inouye

  7. British Heart Foundation Cambridge Centre of Research Excellence, Department of Clinical Medicine, University of Cambridge, Cambridge, UK

    Scott C. Ritchie, John Danesh & Michael Inouye

  8. Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia

    Gad Abraham & Michael Inouye

  9. NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK

    John Danesh

  10. The Alan Turing Institute, London, UK

    Michael Inouye

Authors
  1. Samuel A. Lambert
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Laurent Gil
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Simon Jupp
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Scott C. Ritchie
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Yu Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Annalisa Buniello
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Aoife McMahon
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Gad Abraham
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Michael Chapman
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Helen Parkinson
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. John Danesh
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Jacqueline A. L. MacArthur
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Michael Inouye
    View author publications

    You can also search for this author in PubMed Google Scholar

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.

Ethics declarations

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

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

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

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41588-021-00783-5

This article is cited by

Search

Advanced search

Quick links

Nature Briefing: Translational Research

Sign up for the Nature Briefing: Translational Research newsletter — top stories in biotechnology, drug discovery and pharma.

Get what matters in translational research, free to your inbox weekly. Sign up for Nature Briefing: Translational Research