PGS-Depot

PGS-Depot aggregates 5,585 GWAS summary statistics and executes a standardized suite of 11 polygenic score (PGS) methods to generate and compare PGS performance for quantitative and binary traits across European and East Asian populations.

Key Features:

• Extensive Database: Houses 5,585 high-quality GWAS summary statistics covering 1,564 traits across European and East Asian populations, including 1,933 quantitative and 3,652 binary trait statistics.
• Standardized Pipeline: Implements a standardized best-practice pipeline to execute 11 different PGS methods based on summary statistics, enabling direct comparison across methods with varying model assumptions and estimation procedures.
• Cross-Ancestry Analysis: Enables evaluation of predictive accuracy within and across European and East Asian ancestral groups to assess transferability of PGS.
• Custom PGS Generation: Generates custom polygenic scores from user-provided summary statistics using the implemented PGS methods.

Scientific Applications:

• Prediction of Complex Traits: Enables prediction of quantitative and binary complex traits using generated polygenic scores.
• Cross-Population Genetic Analysis: Supports assessment of PGS transferability and comparative performance across European and East Asian populations.
• Disease Genetics and Risk Stratification: Facilitates investigation of genetic influences on diseases and applications in personalized medicine through PGS-based risk models.
• Method Benchmarking: Provides a framework to compare and benchmark 11 PGS methods for improving predictive models.

Methodology:

Uses a standardized best-practice pipeline to run 11 PGS methods on GWAS summary statistics, with methods that vary in model assumptions and estimation procedures to compare prediction performance across populations.