When Alnylam Pharmaceuticals announced it would join the Alliance for Genomic Discovery (AGD), formed by Illumina and Nashville Biosciences, as the ninth biopharma member, the move signaled more than a new partnership. It marked another step toward reshaping precision medicine with large-scale, ancestrally diverse genomic data and detailed clinical records—resources long dominated by European cohorts.
“Genetic evidence is one of the most powerful tools we have to improve drug discovery,” Will J. Ferguson, vice president of pharmaceutical and biotech collaborations at Illumina, told Inside Precision Medicine. “AGD was designed to bring together all the pieces—sequencing infrastructure, informatics, and deep clinical data—to drive discoveries that can lead to better, faster treatments.”
A new kind of biobank
Traditional population biobanks like the UK Biobank have been invaluable but are limited in diversity. Ferguson credits UK Biobank’s leadership while noting that its roughly 500,000 participants are “96–97% European and primarily healthy volunteers with self-reported data.” AGD, by contrast, pulls samples from health systems across the Southeastern United States. African Americans account for about 20% of its non-European participants, and each de-identified record includes around 11 years of electronic medical records (EMRs).
One of Ferguson’s most emphatic points is that genomic diversity is not a matter of optics but of scientific necessity. “The lion’s share of genetic data in the field today comes from people of European descent. Full stop,” he said. “Ancestral diversity is a big driver for novel discovery—signals we haven’t seen before.” Ferguson predicts that biopharma companies will increasingly invest in underrepresented populations because they hold keys to understanding disease biology more fully. This shift could improve drug efficacy and equity: therapies developed and tested predominantly in European populations may not perform the same across ancestries.
Moreover, the combination of diversity and clinical depth allows for studying disease progression and associations at a level of granularity unavailable elsewhere. For example, African American populations in the Southeast have higher prevalence rates of hypertension and certain cardiometabolic conditions. By examining their genetic variants alongside long EMR histories, AGD researchers can probe the molecular underpinnings of these disparities. This combination—ancestral diversity, disease enrichment, and long-term clinical histories—allows scientists to ask questions that were previously out of reach: How do cardiometabolic disorders progress differently across ancestries? What genetic signals predict neurodegenerative disease trajectories? Can rare variants reveal entirely new drug targets?
AGD’s infrastructure makes those explorations possible. Illumina’s DRAGEN pipeline and Connected Analytics platform process and store the data, while deCODE genetics—an Amgen subsidiary renowned for population genomics—handled sequencing at record speed. “deCODE delivered ahead of schedule earlier this year,” Ferguson said. “It was one of the fastest whole genome projects on record.” Building and maintaining such a resource is not trivial. “Capital is absolutely a consideration,” Ferguson acknowledged. Sourcing samples, processing assays, and managing data at scale all require significant investment. Public-private partnerships, like the U.K. government’s backing of UK Biobank, are one approach. AGD, however, has been privately funded so far, with Illumina and its biopharma partners shouldering costs.
Diversity: the cornerstone of discovery
Ferguson believes this model works because the return on investment—faster, genetically validated drug targets—is tangible. Studies have repeatedly shown that drug programs supported by genetic evidence are more than twice as likely to succeed, including a milestone Nature Genetics paper in 2015 from Matt Nelson, PhD, who had a genetics role at GSK at the time and is now vice president, genetics and genomics, Deerfield Discovery and Development. Last year, Nelson provided an updated analysis in a Nature paper in April 2024 that demonstrated a 2.6-fold increase in likelihood of success when you have genetic evidence at the beginning of the drug discovery journey, with even higher rates for certain diseases. “That’s why biopharma companies are motivated to participate,” Ferguson said. “It’s about increasing the odds of success and reducing time to market for life-saving therapies.”
Speed is a recurring theme for Ferguson. Illumina built AGD as a “shovel-ready” project so partners can transition directly from sequencing to discovery. The recent Nature Communications paper on a rare FRS3 variant illustrates this agility: AGD data revealed a missense mutation associated with reduced body mass index and protection against obesity. Sequencing finished in Q1 2025, and the peer-reviewed study was published by May. “That timeline demonstrates what’s possible,” Ferguson said. “When you have the right partners, the right technology stack, and a diverse dataset, you can move from raw genomes to actionable insights in a matter of months.”
The obesity finding is not an isolated win. It is evidence that AGD’s design—combining deep clinical records with genetic diversity—can reveal signals invisible in conventional datasets. Ferguson expects more publications, especially as Alnylam’s involvement adds another tranche of genomes, which is already being utilized by AbbVie, Amgen, AstraZeneca, Merck, Bristol Myers Squibb, GSK (GlaxoSmithKline), and Novo Nordisk. Alnylam is best known as the pioneer of RNA interference (RNAi) therapeutics. Its recent success expanding its TTR amyloidosis treatment label underscores its interest in genetic validation. “For an RNAi company, the genetic sequence is literally the target,” Ferguson explained. “Alnylam saw AGD’s attributes as a strategic advantage.” By investing in AGD, Alnylam gains access to a dataset that could reveal novel genetic associations—especially those missed in European-heavy studies. Those insights could guide the design of small interfering RNA (siRNA) drugs that silence disease-causing genes more effectively, or point to entirely new therapeutic pathways.
Moving beyond genomics
Illumina’s ambitions go well beyond DNA. Ferguson described plans to layer proteomics and other “multi-omic” modalities onto AGD’s genomes. When protein measurements are combined with whole-genome sequences, researchers can identify protein quantitative trait loci (pQTLs)—links between genetic variants and protein expression levels. Those connections provide a functional bridge between genotype and disease. “You might find a loss-of-function variant and see directly how it alters protein abundance,” Ferguson said. “That’s incredibly valuable for drug developers because proteins are often the therapeutic targets.” UK Biobank has already expanded into proteomics, and Ferguson says AGD intends to follow suit. Adding single-cell transcriptomics is another step: Illumina’s 2023 acquisition of Fluent Biosciences, a single-cell platform company, sets the stage for integrating cell-level expression data into AGD’s resource. “Consortia-style projects are ideal for these technologies,” he noted.
Another pillar of AGD’s power is Illumina’s artificial intelligence expertise. Led by Kyle Farh, MD, PhD, the Illumina AI Lab has built deep learning tools like SpliceAI, PrimateAI, and PromoterAI to predict the effects of genetic variants across the genome. These models will be applied directly to AGD data, helping partners prioritize variants for functional validation and drug targeting. “We’re just scratching the surface,” Ferguson said. As sample numbers grow from hundreds of thousands to millions, statistical power will rise, allowing for finer associations between rare variants and disease. Such analyses could unearth previously unknown pathogenic variants or clarify the clinical significance of ambiguous mutations—critical information for both researchers and patients.
A biobank filled world
AGD’s early results, like the FRS3 obesity finding, suggest that approach works. Ferguson expects additional breakthroughs as more samples—bolstered by Alnylam’s investment—are sequenced by early next year. The alliance is also eyeing expansion into other underrepresented populations worldwide. Meanwhile, Illumina will continue to refine the technologies that underpin AGD. DRAGEN’s variant calling algorithms, Connected Analytics’ secure data sharing, and Fluent Biosciences’ single-cell tools are all part of a “full stack” Illumina can deploy rapidly. “We’ve essentially built a turnkey workflow,” Ferguson said. “That means biopharma partners can focus on discovery, not infrastructure.”
For patients, the promise of AGD is more personal. Faster, more effective drug development could mean better treatments for cardiometabolic disease, neurodegenerative disorders, rare genetic syndromes, and more. Genetic discoveries in diverse populations may lead to therapies that work across ancestries and avoid historical biases in clinical research. Moreover, detailed EMR data could help researchers understand not just which variants influence disease risk, but how those risks unfold over time. Such insights could improve screening guidelines, identify high-risk patients earlier, and tailor interventions more precisely.
Ferguson describes AGD as a “flagship project” requiring extensive coordination. Bringing Alnylam on board underscores its growing momentum. “We’re going full steam ahead,” he said. “With more genomes, more diversity, and more modalities, the next few years will be incredibly impactful for precision medicine.” The AGD’s collaborative spirit—academic medical centers, sequencing giants, AI experts, and drug developers—mirrors the complexity of modern biomedical challenges. No single entity can tackle them alone. But together, they can shorten the path from genetic discovery to clinical application.
The AGD is still young, but its trajectory is clear. As more companies like Alnylam join, the scale and diversity of the dataset will grow, and so will its potential to transform medicine. Ferguson envisions a future where AGD and similar initiatives feed into a global, interoperable network of genomic and multi-omic resources. “The more data we have—diverse, well-annotated data—the better we can understand human biology and develop therapies that truly work for everyone,” he said. Alnylam’s move is therefore more than a business decision. It’s a bet on a paradigm where diversity, data integration, and collaboration redefine what’s possible in drug development. For patients waiting on new treatments, that bet could pay dividends measured not just in discoveries, but in healthier, longer lives.
Illumina envisions a future where AGD data can be combined with other biobanks for meta-analyses across ancestries, diseases, and phenotypes. Using standardized variant calling (DRAGEN) and data storage (Connected Analytics) ensures compatibility. Such multi-biobank studies could amplify statistical power and reveal universal or ancestry-specific disease mechanisms. “Pulling together multiple sources is quite exciting,” Ferguson said. “It means discoveries won’t be siloed. Instead, they’ll be part of a global effort to understand the human genome and apply that knowledge clinically.”
