PGS Catalog Calculator

PGS Catalog Calculator implements an open-source, scalable and portable Nextflow pipeline to reproducibly calculate polygenic scores (PGS) with genetic ancestry estimation and score normalization using reference data.

Key Features:

• Reproducible PGS Calculation: The pipeline enables reproducible calculation of polygenic scores from the PGS Catalog repository.
• Genetic Ancestry Estimation: The pipeline implements genetic ancestry estimation to support equitable PGS applications.
• Score Normalization: The pipeline performs score normalization using reference data.
• Scalable and Portable Architecture: The pipeline is built as a Nextflow workflow for scalability and portability across computing environments.
• FAIR Data Integration: The pipeline connects to the PGS Catalog, the largest findable, accessible, interoperable, and reusable repository of polygenic scores.

Scientific Applications:

• Disease Risk Stratification: Users can quantify an individual's genetic predisposition for hundreds of common diseases to support disease prevention strategies.
• Treatment Response Prediction: The calculated scores enable prediction of treatment response based on genetic profiles.
• Clinical Trait Assessment: Users can evaluate genetic predisposition for clinically relevant traits across diverse populations.
• Clinical Integration Research: The tool facilitates clinical studies necessary to identify where PGS may be integrated into clinical practice.

Methodology:

The PGS Catalog Calculator is implemented as a Nextflow pipeline that calculates polygenic scores using data from the PGS Catalog, with genetic ancestry estimation and score normalization performed using reference data.