Automating Polygenic Score Calculation with pgsc_calc

Uncover the world of polygenic scores and learn about the PGS Catalog Calculator (pgsc_calc). Samuel Lambert introduces this Nextflow-developed tool that automates and reproducibly calculates polygenic scores, breaking barriers to their application by implementing genetic ancestry estimation and score normalisation.
Title: pgsc_calc: A reproducible workflow to calculate polygenic scores
Speaker: Samuel Lambert, University of Cambridge & EMBL-EBI
Abstract: Polygenic scores (PGS) have transformed human genetic research and have many potential clinical applications, including improved risk stratification for disease prevention, and predicting treatment response. PGS are now able to quantify the genetic predisposition of an individual to hundreds of common diseases and clinically relevant traits and are distributed via the PGS Catalog (the only FAIR repository of PGS). Calculating PGS requires significant bioinformatics expertise that is out of reach to many. Here we present the PGS Catalog Calculator (pgsc_calc), developed in Nextflow with the nf-core framework, to automate and reproducibly calculate PGS. pgsc_calc is scalable and portable, supporting deployment in high-performance computing clusters and airlocked trusted research environments that hold genetics data. Most importantly, pgsc_calc breaks barriers to the equitable application of PGS by implementing genetic ancestry estimation and score normalisation using reference data.