PGS Catalog metadata (i.e. traits, authors, methods, performance metrics, cohort, etc...) is available through:
PGS Catalog scoring files (i.e. variants, weights, etc...) are available in the PGS Catalog FTP, however links to these files are available in the web interface and REST API.
The PGS Catalog development is led by Samuel Lambert under the supervision of Michael Inouye (University of Cambridge & Baker Institute) in collaboration with Health Data Research - UK (Laurent Gil) and the EBI Samples, Phenotypes and Ontologies team / NHGRI-EBI GWAS Catalog (Helen Parkinson, Aoife McMahon, Laura Harris).
The Catalog is under active development, and we continue to add new features and curate new data. If you use the Catalog or Calculator in your research we ask that you cite our below flagship publications:
Samuel A. Lambert, Benjamin Wingfield, Joel T. Gibson, Laurent Gil, Santhi Ramachandran, Florent Yvon, Shirin Saverimuttu, Emily Tinsley, Elizabeth Lewis, Scott C. Ritchie, Jingqin Wu, Rodrigo Canovas, Aoife McMahon, Laura W. Harris, Helen Parkinson, Michael Inouye
Enhancing the Polygenic Score Catalog with tools for score calculation and ancestry normalization
Nature Geneticsdoi: 10.1038/s41588-024-01937-x (2024).
Samuel A. Lambert, Laurent Gil, Simon Jupp, Scott C. Ritchie, Yu Xu, Annalisa Buniello, Aoife McMahon, Gad Abraham, Michael Chapman, Helen Parkinson, John Danesh, Jacqueline A. L. MacArthur, Michael Inouye
The Polygenic Score Catalog as an open database for reproducibility and systematic evaluation
Nature Genetics volume 53, pages420–425doi: 10.1038/s41588-021-00783-5 (2021).
Individual PGS obtained from the database should also be cited appropriately, and used in accordance with any licensing restrictions set by the authors (see our Terms of Use for more information).
Published or preprinted polygenic score data meeting our inclusion criteria can be indexed in the Catalog. Please see the About page for a guide for authors looking to submit their data to the Catalog.
Pre-publication data can also be submitted and embargoed until publication to meet journal requirements.
The PGS Catalog and all its contents are made available through the standard EMBL-EBI terms of use.
Some scores have a known specific license (e.g. Creative Commons or specific non-commercial terms). These licenses are listed in the scoring file header, API/metadata and web display.
Type your query, e.g. “breast carcinoma”, into the search box and hit return or click the search icon . You can type any text you wish into the search bar.
| Data type | Example |
|---|---|
| Ontology identifier | EFO_0001645, EFO:0001645 |
| Ontology term | coronary artery disease |
| Ontology synomym | CAD |
| Ontology mapped terms | ICD10:I25, OMIM:608901 |
| Trait category | Cardiovascular disease |
More information about the Trait data in the PGS Catalog can be found here.
| Data type | Example |
|---|---|
| PGS Catalog Publication identifier (PGP ID) | PGP000007 |
| Publication title | Genomic Risk Prediction of Coronary Artery Disease in 480,000 Adults: Implications for Primary Prevention. |
| Publication authors | Inouye |
| PubMed identifier | 30309464 |
| DOI | 10.1016/j.jacc.2018.07.079 |
More information about the Publication data in the PGS Catalog can be found here.
| Data type | Example |
|---|---|
| PGS Catalog Score identifier (PGP ID) | PGS001530 |
| Score name | GBE_INI4103 |
| Score reported trait | Speed of sound through heel (L) |
More information about the Score data in the PGS Catalog can be found here.
The search then returns any Traits (marked with the letter ), Publications () or Scores () in the Catalog that contain a string match within a number of data fields.
By default all the results are showed. However you can use the buttons at the top of the page results to show only Traits, Publications or Scores, e.g.:
Each result is displayed as a card, with different information whether it is a Trait, a Publication or a Score, e.g.:
The buttons "Show PGS" display the list of Polygenic Score(s) associated with the Trait or the Publication.
| PGS ID | PGS Name | Reported Trait |
|---|---|---|
| PGS000002 | PRS77_ERpos | ER-positive Breast Cancer |
| PGS000005 | PRS313_ERpos | ER-positive Breast Cancer |
| PGS000008 | PRS3820_ERpos | ER-positive Breast Cancer |
| PGS000046 | BCPRS_ER+ | Estrogen receptor [ER]-positive breast cancer |
| PGS000347 | PRS287_ERpos | Estrogen receptor positive breast cancer |
| PGS000774 | PRS179_ERpos | Estrogen receptor positive breast cancer |
| PGS ID | PGS Name | Reported Trait | Developed | Evaluated |
|---|---|---|---|---|
| PGS000004 | PRS313_BC | Breast Cancer | ||
| PGS000007 | PRS3820_BC | Breast Cancer | ||
| PGS000001 | PRS77_BC | Breast Cancer | - | |
| PGS000006 | PRS313_ERneg | ER-negative Breast Cancer | ||
| PGS000009 | PRS3820_ERneg | ER-negative Breast Cancer | ||
| PGS000003 | PRS77_ERneg | ER-negative Breast Cancer | - | |
| PGS000005 | PRS313_ERpos | ER-positive Breast Cancer | ||
| PGS000008 | PRS3820_ERpos | ER-positive Breast Cancer |
For further information about the PGS Catalog scoring files (e.g. file format), please look at the documentation in the Download page.
https://www.pgscatalog.org/rest/score/PGS000001
{...
"ftp_scoring_file": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000001/ScoringFiles/PGS000001.txt.gz",
...}
We wrote pgsc_calc: a reproducible workflow to calculate both PGS Catalog and custom polygenic scores. The workflow automates PGS downloads from the Catalog, reading custom scoring files, variant matching between scoring files and target genotyping samplesets, and the parallel calculation of multiple PGS. See the full documentation here.
By default the download of the metadata and scoring files uses the protocol HTTPS, e.g.:
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000001/ScoringFiles/PGS000001.txt.gz
However our FTP server is having some intermittent issues with the HTTPS protocol.
If the downloads don't work with HTTPS, we recommend to replace it by one of the following protocols:
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000001/ScoringFiles/PGS000001.txt.gz
ftp://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000001/ScoringFiles/PGS000001.txt.gz