The Polygenic Score Catalog increases the diversity and usability of genetic data

An article highlighting changes to the Polygenic Score (PGS) catalog for predicting genetic disease risk for people from different genetic backgrounds has been published in a leading journal Natural genetics.

In the work, supported by the NIHR Cambridge BRC and other funders, the researchers added data from multi-ancestry and non-European populations and introduced a new software tool to make calculating the PGS easier and more reproducible.

This work was carried out as part of the Cambridge Baker Systems Genomics Initiative, a research partnership between the Baker Heart and Diabetes Institute and the University of Cambridge to significantly expand access to big data and related expertise to inform targeted approaches in disease prediction and personalized medicine to reach.

Other collaborators involved in the work include the EMBL European Bioinformatics Institute GWAS Catalog (EMBL-EBI).

Mike Inouye, senior professor of data science and population health, who is also leader of the Cambridge Baker Systems Genomics Initiative and Munz Chair in Cardiovascular Prediction and Prevention, said: “The PGS catalog is the largest open database of polygenic scores, with around 27,000 users. “Last year alone over 140 countries.

“These scores estimate an individual’s genetic predisposition to a particular trait or disease by summarizing the effect of many different genetic variants across the genome.

“Polygenic scores are particularly useful for predicting complex health conditions such as heart disease, diabetes and certain cancers, where multiple genetic variants contribute to the overall risk.

“Integrating these results into clinical practice could help scientists and clinicians understand genetic influences on health, potentially leading to better prevention strategies and tailored treatments.”

About the PGS

The Polygenic Score (PGS) Catalog is an open source resource created to make this genetic prediction method more accessible to the research community. It includes over 4500 scores to predict over 600 traits (including common diseases and laboratory measurements) and is widely used in research and industry for applications such as disease prediction. It launched in 2019 and attracted 27,000 users from over 140 countries last year alone.

Due to the lack of genetic data from populations of non-European ancestry, the data in early publications of the PGS catalog consisted largely of assessments that used data from individuals of European ancestry. More PGS have now been added from studies that use data from Africa, Asia, and often multiple ancestries to develop and evaluate PGS.

Via the PGS catalog calculator

The PGS Catalog Calculator is a new addition to the PGS Catalog. This open source software tool automates the process of PGS calculation and allows users to apply polygenic scores to new genomic data, simplifying tasks such as formatting genotype data and variant matching.

The calculator also implements methods for genetic similarity analysis and ancestry matching, an important step to ensure that calculated polygene scores are more interpretable across populations. This could help optimize the use of PGS in research and clinical trials.