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Prioritizing and interpreting disease-associated genetic variants remains one of the greatest challenges in human genetics. Today, we’re thrilled to introduce AlphaGenome Atlas 🧬, a genome-wide platform providing precomputed predictions for the regulatory effects of all ~9 billion possible single-letter changes and >100M observed indels in the human genome.
Here is what Atlas delivers:
1. Variant Prioritization via AVI
To prioritize variants, we developed the AlphaGenome Variant Impact (AVI) score. AVI predicts a unified score per variant, where higher values indicate greater disruption. It achieves state-of-the-art performance across diverse benchmarks. As a proof-of-concept with our collaborators at @broadinstitute, AVI prioritized a deep-intronic variant in DNM1, helping solve a previously unexplained rare epileptic encephalopathy case by revealing a brain-specific cryptic splice site.
2. Multi-Layer Molecular Interpretation
Variant prioritization is only half the battle; researchers also need to understand why a variant matters. Atlas decomposes variant effects across multiple interpretable layers:
•Feature Attributions which decompose each variant’s score into specific biological modalities driving the impact.
•Cell-Type Specificity: Precomputed predictions with AlphaGenome across hundreds of biosamples reveal the exact cellular context in which a variant acts.
•Regulatory Grammar: Over 2,600 de novo DNA motifs (and >250B genome-wide instances) show when variants directly disrupt critical regulatory binding "words".
Explore the resource:
🌐 Interactive browser & precomputed data: alphagenome.google/atlas
- 🎥 Video: youtu.be/U0aToL5C-bQ
- 📖 Blog: goo.gle/4heuCvn
- 📄 Preprint: storage.googleapis.com/deepmind-media…
Here is what Atlas delivers:
1. Variant Prioritization via AVI
To prioritize variants, we developed the AlphaGenome Variant Impact (AVI) score. AVI predicts a unified score per variant, where higher values indicate greater disruption. It achieves state-of-the-art performance across diverse benchmarks. As a proof-of-concept with our collaborators at @broadinstitute, AVI prioritized a deep-intronic variant in DNM1, helping solve a previously unexplained rare epileptic encephalopathy case by revealing a brain-specific cryptic splice site.
2. Multi-Layer Molecular Interpretation
Variant prioritization is only half the battle; researchers also need to understand why a variant matters. Atlas decomposes variant effects across multiple interpretable layers:
•Feature Attributions which decompose each variant’s score into specific biological modalities driving the impact.
•Cell-Type Specificity: Precomputed predictions with AlphaGenome across hundreds of biosamples reveal the exact cellular context in which a variant acts.
•Regulatory Grammar: Over 2,600 de novo DNA motifs (and >250B genome-wide instances) show when variants directly disrupt critical regulatory binding "words".
Explore the resource:
🌐 Interactive browser & precomputed data: alphagenome.google/atlas
- 🎥 Video: youtu.be/U0aToL5C-bQ
- 📖 Blog: goo.gle/4heuCvn
- 📄 Preprint: storage.googleapis.com/deepmind-media…
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