Google DeepMind releases AlphaGenome 2, a DNA model that predicts variant effects one cell type at a time, through its API for non-commercial research

Google DeepMind announced AlphaGenome 2 at 15:00 UTC on November 11. The model reads a DNA sequence up to a million letters long and predicts how genetic variants change gene activity in one specific human cell type or state at a time. It is available from today for non-commercial research through the AlphaGenome API, and in private preview for commercial research.

WHAT CHANGED FROM ALPHAGENOME

• The first AlphaGenome, launched last year, predicted thousands of readouts across broad tissues at once. AlphaGenome 2 is conditional: it takes a tissue, cell type or state as input alongside the DNA sequence and predicts for that one condition.
• DeepMind says it trained the model on bulk and single-cell data from human and mouse samples, including more than 107 million individual cell profiles from 68 tissues.
• It predicts the same readouts as AlphaGenome (gene expression, histone modifications and chromatin accessibility) and adds DNA methylation.
• Scientists can upload a single-cell RNA-seq snapshot from a few dozen cells to describe a new cell state, and the model predicts for that state without retraining.

DEEPMIND'S OWN RESULTS

• On TenK10K, a single-cell map of 28 primary immune cell types, DeepMind says AlphaGenome 2 identified 30% of causal variants against 16% for the original AlphaGenome fine-tuned on single-cell data and other specialized tools, and 43% of directional gene effects against 23%.
• DeepMind says the model reproduced a published finding that a variant behind inflammatory bowel disease boosts the ETS2 gene in gut macrophages, while leaving other cell types and genes largely unaffected.
• These are Google DeepMind's own figures. No independent benchmark has scored the model yet.

AVAILABILITY

• The AlphaGenome API serves AlphaGenome 2 for non-commercial research, with Colab tutorials. Commercial research is in private preview.
• DeepMind says 'AlphaGenome 2 Skills' are coming soon to Google Antigravity, its agentic development platform.
• DeepMind says AlphaGenome and AlphaGenome 2 are for research use only and are not validated or approved for clinical or diagnostic use.

WHAT WE DO NOT KNOW

What the API charges or allows per researcher, when commercial access opens beyond the private preview, and when the Antigravity skills ship. DeepMind's post gives no dates for either.