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Partnering to translate population-scale signals
into mechanistic insights for faster drug discovery
Building on its leadership in sequencing and data insights, Illumina is uniting pharma R&D
around large-scale datasets to accelerate therapeutic discovery.
C
omplex diseases involve networks of genes, proteins, cells,
and clinical phenotypes — far beyond what any single
data modality can capture. Large-scale multiomic datasets
now offer a more integrated and efficient way to understand disease mechanisms, identify drug targets, and uncover
therapeutic opportunities. Through cross-industry collaboration,
these resources are becoming more accessible and central to
modern drug discovery.
Illumina, known for the sequencing tools that power genomics
research worldwide, is now actively building and expanding partnerships that elevate its role as a scientific collaborator. Together
with pharmaceutical, biotechnology, and academic partners, the
company has already made several highly impactful datasets and
analytical frameworks available to collaborators, who can engage
directly with Illumina to access and apply them in ongoing research.
Building the first real-world GLP-1 multiomic
dataset
Today, millions of people take glucagon-like peptide-1 (GLP-1)
receptor agonists to manage diabetes or weight, yet nearly 40
percent of individuals with type 2 diabetes do not respond effectively. Understanding the molecular basis of that variation could
improve treatment selection and reveal new drug targets.
To investigate these mechanisms, Illumina and Ovation.io are
developing a first-of-its-kind multiomic dataset that integrates
genomic, proteomic, and clinical information from 25,000 patients
treated with GLP-1 therapies. The project uses Illumina’s sequencing platform, the Illumina Protein Prep assay, and the DRAGEN and
Connected Multiomics analysis tools to create a comprehensive
molecular view of treatment response (1).
The collaboration’s next phase will introduce proteomic sampling
before or after therapy, laying the groundwork for longitudinal analyses of protein expression changes associated with drug exposure.
These data are expected to support the discovery of biomarkers
that predict therapeutic response, resistance, or adverse effects,
and to reveal pathways that could guide next‑generation metabolic
treatments. They also offer previously uncharacterized insights
into GLP‑1 combination therapies and comorbid indications that
are often excluded from clinical trials. Together, this collaboration
generates one of the largest real‑world multiomic resources for
metabolic disease, offering a foundation for both biological discovery and therapeutic development.
Expanding the Alliance for Genomic Discovery
Across the life sciences, large-scale genomics projects are changing how drug targets are identified and validated. Pharmaceutical
companies increasingly recognize that targets supported by human
genetic data are more likely to lead to successful drug approvals.
Illumina is helping drive this shift through the Alliance
for Genomic Discovery (AGD), a multiyear partnership with
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Nashville Biosciences and a rapidly growing group of nine global
biopharma companies. Launched in 2022, the alliance has already
generated more than 250,000 whole genomes linked to longitudinal
phenotypic data, creating one of the world’s most comprehensive
genomic datasets for clinical research (2).
Paired with Illumina’s field-leading analytics and interpretation
tools, the dataset gives members a comprehensive view of disease pathways and is already powering target discovery across
autoimmune, fibrotic, liver, and metabolic disorders. A key strength
of the dataset is its ancestral diversity, still uncommon in large
genomic resources, which significantly expands its ability to reveal
biologically and clinically meaningful associations.
This has been demonstrated in recent analyses. A study of
35,024 predominantly African-ancestry AGD participants revealed
disease-causing variants and associations missed in Eurocentric
datasets (3), while another multi-ancestry meta-analysis using
AGD genomes identified rare missense variants influencing body
mass index, pointing to potential pathways to obesity treatment (4).
Building on this momentum, the alliance will sequence an additional
31,000 genomes and integrate proteomic and phenotypic layers to
deliver even richer insights into disease biology.
Scaling single-cell analysis
One of the most powerful advances accelerating modern drug
discovery is the shift from narrow, low-throughput gene studies to
genome-wide screens that systematically probe both gene activation and inhibition. These approaches replace time- and resource-intensive targeted assays with scalable, unbiased methods capable
of surveying entire pathways and regulatory networks at once.
Perturb-seq exemplifies this transformation. By pairing CRISPR-based activation and inhibition with single-cell RNA sequencing,
it enables massively parallel profiling of how individual gene perturbations reshape cellular programs. The result is a high-resolution,
genome-wide map of the causes and consequences of altering gene
function, captured at the level where biology actually unfolds: individual cells representing clinically relevant cellular heterogeneity.
Illumina has been at the forefront of Perturb-seq, launching
a major project in mid-2025 to generate a billion-cell atlas built
from hundreds of cell lines derived from diverse, disease-relevant
tissues (5). A functional screen of this scale is unprecedented in
the industry and is purpose-built to help collaborators tackle key
facets of drug discovery. These include efficient identification of
new drug targets, accurate characterization of disease mechanisms
and mechanisms of action, exploration of new therapeutic areas
for existing drugs, assessment of off-target effects, and more, all
paired with analytical tools to derive actionable insights.
Illumina’s Billion Cell Atlas uses CRISPR-based gene activation and
inhibition across 20,000 genes and 250 disease-relevant human cell
types, generating over 10 million perturbations to build a highresolution, mechanistic map of disease biology.
Toward an integrated research ecosystem
Together, these collaborations point to a more connected model of
scientific discovery. Illumina and its partners are not only linking
large-scale genomic, single-cell, and multiomic datasets, but also
equipping researchers with analysis tools that transform large-scale
data into meaningful insight. This creates an integrated ecosystem
where population-level signals and molecular mechanisms reinforce one another and feed directly into drug discovery pipelines.
As genomics continues to evolve, collaboration will remain
central to progress. Through its technologies, data platforms, and
partnerships, Illumina is helping to unify the tools and expertise
needed to turn complex biological data into practical advances
for precision health.
REFERENCES
1. Illumina and Ovation.io. Illumina and Ovation.io launch first-of-its-kind GLP-1 dataset to
accelerate new therapy development. https://www.illumina.com/content/illumina-marketing/
amr/en_US/company/news-center/press-releases/2025/68501611-1012-4650-be64-
81a0f863a688.html (2025).
2. Alnylam Pharmaceuticals joins Alliance for Genomic Discovery, expanding diverse
clinical genomic dataset to drive precision medicine. https://www.illumina.com/company/
news-center/press-releases/press-release-details.html?newsid=65116392-fb5c-4513-a1feb36f8f8a4ea5 (2025).
3. Avery, C. et al. Genome sequencing of 35,024 predominantly African ancestry
persons addresses gaps in genomics and healthcare. bioRxiv https://doi.
org/10.1101/2025.10.30.25338549 (2025).
4. Jonsdottir, A. B. et al. Missense variants in FRS3 affect body mass index in populations of
diverse ancestries. Nat Commun 16, 2694 (2025).
5. Illumina and Broad Clinical Labs usher in new era of drug discovery with collaboration to
rapidly scale single-cell solutions. https://www.illumina.com/company/news-center/pressreleases/press-release-details.html?newsid=383b9322-6cef-4fdd-8099-05a6f6904872 (2025).
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