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Predicting non-coding variant effects with AlphaGenome

Alan E. Murphy^1,† , Masayuki Nagai^1,† , Peter K. Koo^1,*

¹Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
^†These authors contributed equally: Alan E. Murphy, Masayuki Nagai
* Correspondence: Peter K. Koo(koo@cshl.edu)

Most genetic variants associated with human traits and disease lie outside protein-coding regions and influence gene expression through regulatory elements. AlphaGenome is a recently developed sequence-to-function model that leverages megabase-scale genomic context to predict diverse regulatory activities and variant effects, with the potential to guide experimental prioritization and provide mechanistic insights.

https://doi.org/10.1038/s41422-026-01249-1

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