Illumina, Inc. has launched the Illumina Billion Cell Atlas, the world’s largest genome-wide genetic perturbation dataset, designed to accelerate AI-enabled drug discovery across the pharmaceutical industry. The Atlas marks the first phase of Illumina’s broader ambition to build a 5 billion-cell atlas over three years, creating one of the most comprehensive maps of human disease biology to date.

Developed under an alliance framework with AstraZeneca, Merck, and Eli Lilly and Company as founding partners, the Atlas is already being generated across a curated set of disease-relevant cell lines. The dataset is intended to support drug target validation, train large-scale AI models, and deepen understanding of disease mechanisms that have historically been difficult to study.

“We believe the cell atlas is a critical step toward scaling AI for drug discovery,” said Jacob Thaysen, chief executive officer of Illumina. “By building an unprecedented biological dataset, we aim to enable the next generation of AI models for precision medicine and target identification, ultimately helping decode the pathways behind complex and devastating diseases.”

The Atlas captures how one billion individual cells respond to genetic perturbations using CRISPR technology, spanning more than 200 disease-relevant human cell lines. These include models relevant to cancer, immune disorders, cardiometabolic and neurological diseases, as well as rare genetic conditions. By systematically switching genes on and off across key cell types, researchers can study the functional consequences of nearly all 20,000 human genes.

Pharma partners will use the dataset to explore disease mechanisms, validate genetically supported targets, and identify new therapeutic indications. Merck plans to apply the data to train proprietary AI and machine-learning models, enabling the development of virtual cell systems to improve disease prediction and precision medicine strategies.

“Grounding AI models in real biological variation rather than text-based knowledge alone allows us to translate genomic insight into actionable targets and biomarkers,” said Iya Khalil, vice president and head of Data, AI & Genome Sciences at Merck.

AstraZeneca highlighted the Atlas’s potential to convert genetic signals into experimentally testable biology, improving confidence in early drug development decisions, while Eli Lilly emphasized the importance of large-scale, diverse biological datasets as the foundation for the next generation of AI-driven research.

The Billion Cell Atlas is the first major data product from Illumina’s newly launched BioInsight business, which aims to deliver large-scale biological datasets and enabling technologies for AI-powered drug discovery. The initiative is supported by Illumina’s Single Cell 3’ RNA sequencing platform, capable of capturing millions of cells in a single experiment, and advanced analytics infrastructure capable of processing tens of petabytes of transcriptomic data annually.

Illumina plans to continue expanding the Atlas in collaboration with industry partners, steadily building toward its multi-billion-cell vision and establishing a new foundation for AI-enabled discovery across the pharmaceutical ecosystem.