Illumina Unveils Billion Cell Atlas to Revolutionize Drug Discovery

On January 13, 2026, Illumina, Inc. (NASDAQ: ILMN) announced the launch of the Billion Cell Atlas, a groundbreaking initiative aimed at accelerating drug discovery through artificial intelligence (AI) across the pharmaceutical landscape. This ambitious project marks the first phase of an overall plan to create a comprehensive 5 billion cell atlas over the next three years, positioning itself as the most extensive map of human disease biology to date.

The Billion Cell Atlas is set to be developed in collaboration with leading pharmaceutical companies, including AstraZeneca, Merck, and Eli Lilly and Company, who are participating as founding partners. This strategic alliance aims to leverage a curated set of cell lines to enhance drug target validation, scale AI model training, and advance research into previously elusive disease mechanisms.

Jacob Thaysen, CEO of Illumina, emphasized the significance of the cell atlas, stating, “We believe the cell atlas is a key development that will enable us to significantly scale AI for drug discovery.” He further elaborated that the initiative will create an unparalleled resource for training advanced AI models for precision medicine and drug target identification.

Merck plans to utilize the Billion Cell Atlas to enhance its precision medicine strategies within its drug discovery pipelines. The dataset will support the training of Merck's proprietary AI/machine learning foundation models and the creation of virtual cell models, thereby refining the prediction of disease indications.

Iya Khalil, Vice President and Head of Data, A.I. & Genome Sciences at Merck, highlighted the initiative's potential impact, stating, “By harnessing advanced genomic patient datasets, Merck scientists are building and leveraging AI models grounded in real biological variation — not just literature text.” This collaboration aims to create a scalable connection between genomic insights and therapeutic outcomes, expediting the transition from discovery to clinical applications.

The Billion Cell Atlas will focus on capturing data on how 1 billion individual cells respond to genetic alterations via CRISPR technology across over 200 disease-relevant cell lines. These selected cell lines are critical for understanding complex diseases historically challenging to decode, including immune disorders, cancer, and other cardiometabolic, neurological, and rare genetic diseases.

Slavé Petrovski, Vice President of the Centre for Genomics Research at AstraZeneca, commented on the challenges of translating genetic information into medicines, noting the Atlas's role in providing clarity to drug development decisions by elucidating how genetic perturbations manifest in human cells.

Ruth Gimeno, Group Vice President of Cardiometabolic Research at Eli Lilly and Company, echoed this sentiment, asserting, “The next generation of AI-driven drug discovery will depend on biological data at a scale never before achieved.”

The Billion Cell Atlas represents the first product from Illumina’s newly established BioInsight business, designed to provide the foundational technologies and datasets necessary for the next generation of drug discovery and AI in pharmaceuticals. Utilizing the Illumina Single Cell 3' RNA prep platform, the Atlas will generate an impressive 20 petabytes of single-cell transcriptomic data annually.

To manage this vast amount of data, Illumina employs its DRAGEN pipeline with hardware acceleration, allowing for efficient processing. The data will be hosted on the Illumina Connected Analytics cloud platform, facilitating scalable analysis for researchers.

Illumina is committed to expanding its multi-billion cell atlases in collaboration with its partners. The Billion Cell Atlas builds on a prior initiative announced in February 2025, which aims to ultimately create a 5 billion single-cell resource.

CEO Jacob Thaysen will present further details on this innovative project at the 44th Annual J.P. Morgan Healthcare Conference, emphasizing Illumina's commitment to improving human health through genomic advancements.

The Illumina Billion Cell Atlas represents a significant leap forward in the integration of AI and genomics in drug discovery. By fostering collaboration with major pharmaceutical players and harnessing cutting-edge technologies, Illumina is poised to enhance our understanding of complex diseases and revolutionize the paths from discovery to therapeutic applications. As the industry watches closely, the potential for transformative impacts on patient care and precision medicine is immense.