Google DeepMind's AlphaGenome AI tackles the 98% of human genome that doesn't code for proteins

Reviewed byNidhi Govil

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Google DeepMind unveiled AlphaGenome, a deep-learning AI model that predicts how mutations in non-coding DNA affect gene expression across sequences up to one million base pairs long. The tool outperforms existing models in 25 out of 26 tasks and is already being used by nearly 3,000 scientists worldwide to investigate rare diseases, cancer mutations, and design new gene therapies.

AlphaGenome Addresses Biology's Grand Challenge

Google DeepMind has released AlphaGenome, a deep-learning AI model designed to decode the 98% of the human genome that doesn't produce proteins

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. Described in Nature on January 28, this research tool can analyze DNA sequences up to one million base pairs in length and predict how mutations in non-coding DNA affect gene expression and other biological processes

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. The model represents what researchers call a "Swiss Army knife for exploring non-coding DNA," offering unprecedented precision in modeling intricate genomic processes

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Source: Digit

Source: Digit

Deciphering non-coding regions has long been one of biology's most stubborn challenges. Once dismissed as "junk DNA," these sequences are now understood to be crucial for determining when, where, and how genes are turned on and off

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. Mutations in these areas are especially vexing to researchers seeking to uncover the genetic basis for rare, often fatal genetic diseases. "These are variants that, to be quite honest, often get triaged," says Eric Klee, a bioinformatician at the Mayo Clinic who tested AlphaGenome at the Undiagnosed Hackathon in September 2025

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How AlphaGenome Predicts Genetic Changes Across Multiple Tasks

AlphaGenome takes a DNA sequence as input and predicts 11 types of biological signals that help determine how genes function inside cells

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. These include whether a gene is activated or silenced, where gene activity begins, how genetic messages are edited, how tightly DNA is packed, which regulatory proteins bind to it, and how distant regions of the genome interact. The model can pinpoint biologically important spots down to single base resolution, a significant improvement over its predecessor Borzoi, which identified points of biological interest in 32 base-pair bins

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Source: ET

Source: ET

The tool matched or outperformed other state-of-the-art models in 25 out of 26 tasks predicting the effects of genetic variations

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. For example, AlphaGenome identified gene activity changes in certain cell types 14.7 percent better than Borzoi2

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. The team also successfully simulated known DNA mutations responsible for a type of leukemia, predicting the same results observed in laboratory experiments

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From AlphaFold to AlphaGenome: Building a Molecular Prediction Platform

AlphaGenome extends Google DeepMind's growing stable of biological models, which includes the Nobel Prize-winning AlphaFold for protein structure prediction, AlphaMissense for analyzing mutations in protein-coding regions, and AlphaProteo for designing proteins that bind to specific molecular targets

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. "The genome is the recipe and understanding the effect of changing any part of the recipe is what AlphaGenome looks at," explains Pushmeet Kohli, vice president of science at Google DeepMind

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Source: IEEE

Source: IEEE

While AlphaMissense focused on the small fraction of the genome that codes for proteins, AlphaGenome tackles the far larger regulatory landscape

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. This vertical integration across genomics creates a comprehensive platform for molecular prediction that could unlock new diagnostic capabilities and therapeutic strategies. "All these different models are solving key problems that are relevant for understanding biology," Kohli notes

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Real-World Applications in Rare Disease Diagnosis

Nearly 3,000 scientists in 160 countries have already used AlphaGenome since Google DeepMind released a preview for non-commercial research in June last year, submitting around one million requests daily

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. At the Undiagnosed Hackathon, where more than 100 researchers tackled 29 undiagnosed conditions, AlphaGenome was deployed to investigate several cases

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. The event, organized by the Wilhelm Foundation—a charity founded by parents who lost three of their four children to an undiagnosed disease—aims to help the approximately 350 million people worldwide living with undiagnosed rare conditions.

Klee tested AlphaGenome's predictions on a variant his team had linked to an individual's diagnosis before the hackathon. Experimental work showed the mutation altered gene expression in cardiac cells but not neural cells, aligning with the patient's symptoms. AlphaGenome's predictions supported this conclusion

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. While none of the AlphaGenome predictions at the September 2025 hackathon led directly to a diagnosis, six of the 29 conditions were diagnosed using other approaches, demonstrating how AI tools complement traditional methods.

Limitations and Future Directions in Genomics Research

Despite its advances, AlphaGenome faces notable constraints. The model's training data draw largely from bulk tissue datasets, limiting reliability in rare cell types or specific developmental stages. "Generalization to new cell types is a huge limitation," notes Christina Leslie, a computational biologist at Memorial Sloan Kettering Cancer Center

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. The tool also struggles to capture distant effects when regulatory regions are hundreds of thousands to millions of DNA letters away from their target genes.

Additionally, while the model makes accurate predictions, it doesn't always directly inform researchers of the underlying biological processes, explains Jian Zhou, a genomics machine learning researcher at the University of Chicago

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. Robert Goldstone, head of genomics at the Francis Crick Institute, describes AlphaGenome as "a foundational, high-quality tool that turns the static code of the genome into a decipherable language for discovery," but cautions it "is not a magic bullet for all biological questions"

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. Researchers suggest the next leap will come from generating new types of data for the model to analyze, as AlphaGenome has "maxed out" what this type of architecture can achieve

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