Illumina unveils massive cell atlas to speed up drug discovery

Illumina on Tuesday unveiled what it calls the world’s largest functional cell dictionary that, when paired with artificial intelligence, will help accelerate drug discovery. 

Dubbed the Billion Cell Atlas, the data set shows how cells react to specific alterations. The company calls it the “most comprehensive map of human disease biology to date.”

Illumina is partnering with pharmaceutical giants AstraZeneca, Merck and Eli Lilly to help train the AI model. Within hours of the announcement, other pharma and tech companies were calling, eager to tap the data set for drug discovery, said Rami Mehio, senior vice president of Illumina’s BioInsight, the newly launched business that focuses on AI, software, and data to accelerate discovery across life sciences.

Pharma companies want to know their targets, explained Mehio. “‘If you do this, what happens? If you do that, what happens?’ They need to do endless experiments, most of which fail,” he said.

Traditionally, researchers study diseases by perturbing individual genes — switching the code “on and off” using CRISPR technology — to study how the body responds. But these alterations don’t work in isolation: Each change cascades across the entire genome.

Understanding a disease requires understanding the whole system rather than toying with “specific switches.”

That’s where Atlas comes in. “The future of drug discovery isn’t about doing more experiments. It’s about doing the right ones,” said Mehio.

Atlas will measure how 1 billion individual cells respond to genetic changes across more than 200 disease-relevant cell types, according to Illumina.

By working with pharmaceutical giants to train AI models, Atlas aims to accelerate disease research — helping scientists to understand the impact of specific drugs, identify new treatments, and confirm promising genetic targets.

“There is not a single big, serious pharma company that isn’t trying to build a data set like this,” said Mehio.

Some big technology companies have come out of the woodwork and expressed interest in Illumina’s Atlas. “It’s interesting,” said Mehio. “You’re going to see a world where traditional pharma and tech start to compete,” he said.

Illumina’s biggest competitors are its clients: pharmaceutical companies. “Some players who are within pharma have better domain knowledge of the needs of pharma,” said Mehio.

“There are a lot of people entering the data space, but Illumina is uniquely positioned in our understanding of biology, our full software stack, and our cost structure to generate the data,” he said.

Illumina’s most recent financial filings show third-quarter revenue of $1.08 billion, flat compared to the same period last year. Net income declined 76%, falling to $150 million in the third quarter from $642 million in the same quarter last year. The company expects to report its full fourth-quarter and fiscal year 2025 results at the close of the market on Feb. 5.