PolyGenie: a reproducible Nextflow pipeline for phenome-wide association studies using polygenic risk scores
Xavier Farré, Mireia Gasco, Natalia Blay, Rafael de Cid · 2026
Read PolyGenie: a reproducible Nextflow pipeline for phenome-wide association studies using polygenic risk scores by Xavier Farré, Mireia Gasco, Natalia Blay, Rafael de Cid (2026) in the Tower of Babel, a free online library of public-domain works preserved in clean, searchable text. No sign-up. The full text is served as a plain-text file at a predictable URL, where text is present: https://antarctic-labs.com/tower-of-babel/pmc-13247587.txt.
Description
Farré, Gasco, and Blay present open-source software for scanning genetic risk across the whole phenome, in this 2026 NAR Genomics and Bioinformatics brief report. A phenome-wide association study tests whether polygenic risk scores, summaries of a person's many small genetic effects, connect to hundreds of traits at once. No standard, portable pipeline existed for running such scans in any cohort, so the team built PolyGenie on the Nextflow workflow system.
The pipeline takes ready-made risk scores and phenotype data, runs regressions across binary and continuous outcomes, stores results in a database, and serves them through an interactive web app. Their demonstration applied one hundred thirty-five risk scores to the Catalan GCAT cohort's clinical, molecular, and lifestyle traits. Because configuration is metadata-driven, other cohorts can adopt it without code changes.
Catalog record
| CREATOR | Xavier Farré, Mireia Gasco, Natalia Blay, Rafael de Cid |
|---|---|
| YEAR | 2026 |
| COLLECTION | PAPERS |
| FORMAT | TXT |
| FILE SIZE | 26 KB |
| VERSION | 1.0 |
| LICENSE | CC BY 4.0 |
| RIGHTS | CC BY |
| SOURCE | Europe PMC |