Gentropy is out today!

In the last few months, the Open Targets team has been working on a new foundational pipeline to facilitate the interpretation and analysis of GWAS and functional genomic studies for target identification.

Today, we are delighted to announce that we have released Gentropy, a Python package to help with different tasks associated with harmonisation, statistical analysis and target prioritisation.

Gentropy is released as an open-source project and is expected to define the foundation of the future iterations of Open Targets Genetics, with an ambition also to allow scientists to perform their analysis using the same toolkit. The Python package is available through Pypi.

The current implementation already includes:

  • Datasource harmonisation
    • FinnGen R10
    • GWAS Catalog w or w/o sumstats
    • GnomAD v4 variant annotation
    • GTEx eQTLs (eQTL Catalogue)
    • Intervals
  • Methods:
    • Window-based clumping
    • LD clumping
    • Coloc (from credible sets)
    • eCAVIAR
    • LDannotator (using GnomAD LD v2.1.1)
    • PICS finemapping
    • Locus-to-gene (new training strategy limited to available features)
    • CARMA (outlier detection)

For a full explanation of the available features and more information on the next stages of development please visit our documentation page.

As always, we welcome feedback or contributions to the codebase. Let us know how you plan to use this tool, to help inform our future directions.

We look forward to hearing from you!


Congratulations Gentropy team!! Gentropy has been used in latest Open Targets platform, correct? Can we expect more GWAS will be curated to the platform?

Hi Shicheng,

Gentropy is primarily a post GWAS analysis toolkit to provide a scalable solution for OpenTargets Genetics. As such, the same pipeline will provide various input for the Platform as well (eg. disease to target evidence based on locus to gene scores). At this point, we are in the phase of doing a thorough quality control and planning how to phase the newly generated data into production.

Once this question is sorted, the released data will include the full set of harmonised summary statistics from the GWAS Catalog, the most recent Finngen release (r10) and many more.