Google DeepMind releases AlphaGenome 2 API for single-cell DNA variant prediction

Google DeepMind released AlphaGenome 2 on 11 November 2026 through its updated alphagenome Python package (alphagenome.models.v2) and free non-commercial research API, alongside the zero-code and programmatic AlphaGenome Atlas covering pre-computed in silico mutagenesis and AlphaGenome Variant Impact (AVI) prioritisation scores across 9 billion human coding and non-coding variants. Whereas AlphaGenome 1 scored variants across fixed reference assays simultaneously, AlphaGenome 2 zooms into specific cellular contexts to model why identical single-letter DNA mutations trigger disease in certain cell types, such as heart muscle or immune cells, while sparing others.

Single-cell expression conditioning and imputed modalities

AlphaGenome 2 pairs a 1-megabase (1 Mb) conditional U-Net and transformer sequence backbone with a dedicated cell expression encoder (encode_cells). Researchers can select composite ontology reference conditions or pass their own raw human single-cell RNA-seq (scRNA-seq) unique molecular identifier count matrices (up to 256 cells per API call via cell_conditioning) to generalise regulatory predictions to previously unseen cell states.

The v2 release adds predicted single-cell chromatin accessibility (SC_ATAC), denoised and protocol-specific single-cell gene expression, CpG methylation variant scoring (MethylationScorer), cross-modality imputation for unmeasured biosample tracks, and batched input-gradient calls (predict_interval_gradients_batch) for enhancer-to-gene attribution across human and mouse genomes. Google DeepMind has not announced commercial API pricing tiers.