David Peoples
CFO, CBO
Ultima Genomics
Multiomics is in vogue and several sequencing companies have taken notice. Rather than building capabilities for things like single-cell sequencing, spatial transcriptomics, and proteomics themselves, some established vendors have opted to acquire existing companies or partner with current providers of these emerging technologies. “What you need to look for has expanded dramatically,” David Peoples, Ultima Genomics CFO and CBO, told GEN. Nowadays, to really understand biology, the scientific community needs to merge DNA with data from the transcriptome, methylome, proteome, and more.
Proteomics in particular has seen a lot of activity, especially in recent efforts to combine gene sequencing and proteomics technologies in a single assay run. Three years ago, Ultima Genomics announced a collaborative effort to pair its sequencer with the Explore HT proteomics platform from Olink Proteomics, a Thermo Fisher Scientific company. That same year, Illumina signed a co-development agreement with SomaLogic, now part of Standard BioTools, to integrate its SomaScan proteomics assays with Illumina’s next-generation sequencing platforms and informatics toolsets. Both proteomics technologies are built so that existing DNA sequencing technologies can also be used to also measure protein identities and expression.
Olink’s proximity extension assay (PEA) technology uses an antibody-based immunoassay that features matched antibodies with unique DNA tags and couples these constructs with a polymerase chain reaction to measure thousands of proteins in a single sample. Meanwhile SomaLogic’s SomaScan technology uses so-called slow off-rate modified aptamers (SOMAmers), which rely on modified nucleotides to bind to proteins and form complexes that can be captured and quantified using established DNA sequencing technologies.
Fundamentally, sequencing technology can be “an extremely powerful reader of genetic signatures,” Peoples said. That capability is turning out to be important for the readouts from these emerging proteomics technologies. And, if the scientific community continues the trend towards multiomics, Peoples believes that sequencers could have a central role in reading the output from other kinds of omics tools beyond the proteome.
A population-scale perspective on proteins
In 2019, neuroscientist and geneticist Chris Whelan, PhD, (currently the director of neuroscience, data science, and digital health at Johnson & Johnson Innovative Medicine) was studying the dynamics of protein biomarkers like neurofilament light chain (NfL) and growth-associated protein 43 (GAP-43) in neurodegenerative diseases. Increased levels of these proteins in the blood and cerebrospinal fluid are biomarkers for the progression of disorders like Alzheimer’s disease and Parkinson’s disease. Whelan’s challenge was reliably measuring the levels of biomarkers on a large scale. To do that, he would need a population-sized dataset and tools for measuring thousands of proteins easily and efficiently.
Chris Whelan, PhD
Director of Neuroscience
Johnson & Johnson Innovative Medicine
Around this time, Whelan began using new proteomics tools from Olink and SomaLogic in his research and was impressed with the results. The confluence of those two activities led to something of a “lightbulb moment,” he tells GEN. Could affinity-based technologies be applied to study proteins in the UK Biobank? And would other biopharmaceutical companies be interested in partnering and funding this kind of broad-scale study?
Whelan’s instinct was right. In 2020, the U.K. Biobank Pharma Proteomics Project (UKB-PPP), a consortium of some of the biggest biopharma companies in the world, launched with 10 partners. As of January 2025, four more companies have joined the consortium. The current partners are Alden Scientific, Amgen, AstraZeneca, Bristol Myers Squibb, Calico Life Sciences, Roche, GSK, Isomorphic Labs, Johnson & Johnson, MSD, Novo Nordisk, Pfizer, Regeneron, and Takeda.
As a feasibility study, the UKB-PPP conducted a pilot project with a subset of the UK Biobank data that started in spring 2021 and concluded in winter 2022. The group analyzed nearly 3,000 circulating proteins from 54,000 UK Biobank participants. They have published several papers about their work, including in Nature in 2023.1
Ray Chen, Olink’s senior director for global strategic accounts, presented some of the findings from that pilot study and the Nature paper at the 2025 annual meeting of the U.S. Human Proteome Organization (US HUPO). In a conversation with GEN, Chen explained how Olink’s PEA technology identified more than 14,000 protein quantitative trait loci, linking common genetic variants to changes in protein expression levels. Eighty-one percent of these links were previously unknown, providing fodder for new studies into potential targets for new therapies or diagnostics. The consortium has since published two more papers based on the pilot data and has had their work cited in hundreds of scientific papers.
In a pilot study of 54,000 UK Biobank participants, members of the UKB-Pharma Proteomics Project linked over 14,000 genetic variants to expression changes in 3,000 circulating proteins. [Fan / iStock / Getty Images Plus]
“We’ve identified probably hundreds of new therapeutic targets [that are] starting points from which we can build new drug programs,” Whelan says, including targets for Parkinson’s, Alzheimer’s, and schizophrenia. “We’re applying AI on the proteins directly to find new insights into different kinds of complex diagnoses like major depressive disorders.” For example, “We are finding evidence that there may be an immuno-metabolic subtype of depression, but also one that involves dampened mitochondrial activity and one that involves heightened mitochondrial activity.”
Buoyed by the success of the pilot, the partners are now moving on to a much larger study of about 600,000 samples, which covers all the people currently in the U.K. Biobank cohort plus some repeat sampling, to examine how protein levels change over time. “It’s going to be around 500,000 participants at baseline, but then about 100,000 of those people will have follow-up samples taken somewhere between 7-10 years after that initial visit,” Whelan explains. This time, scientists will measure 5,400 protein markers across all samples.
The larger study will use Ultima’s sequencing technology paired with Olink’s protein detection and measurement platform. After considering biological breadth, throughput, scalability and other insights from their experiences with both platforms in the pilot, about half of the consortium members wanted to proceed with Illumina Protein Prep and the other half wanted to proceed with Olink’s offering. Ultimately, the decision to go with Ultima and Olink’s technologies came down largely to the complementarity of the Olink PEA technology with the UG 100 sequencer, Whelan says. It also made sense to continue using Olink’s assays, as these were also used for the pilot study.
Furthermore, some consortium members felt that working with a different partner could foster a more competitive sequencing market that would only benefit the scientific community. Ultima’s Peoples echoes those sentiments regarding healthy competition among tool providers. “I think it’s a really good thing for the community that there’s competition now out there for these types of projects,” he says.
“To be clear, both Illumina and Ultima were very strong partners during the negotiation process and the consortium was happy with the data that Illumina delivered during the pilot phase of the project,” Whelan stresses. “As the project leader, it’s paramount to me that everything is done in a highly democratic and fair way. It is funny that, on at least two major decisions, we’ve come to a tie where we need to have a tiebreaker vote. Often it comes down to just very minor factors that help us lean more towards one technology or one path forward, versus the other.”
Dalia Daujotyte, PhD
Senior Product Manager
Illumina
Dalia Daujotyte, PhD, senior director, product management at Illumina, notes that at the time the UKB-PPP consortium was assessing proteomics partners for the broader project, Illumina’s protein assay was still in early testing and could only detect 6,000 proteins rather than the 9,500 it can measure now. They had some internal verification data on the assay but nothing they could show externally at the time. “It was basically a year too soon for Illumina Protein Prep,” she says. Also, the consortium had already worked with Olink on the initial 50,000 sample pilot study so it was understandable that they wanted to continue with the technology they began with.
Members of the UKB-PPP consortium were expecting to get the first batch of samples shipped from the UK Biobank in March 2025. They expect to receive the first tranche of proteomic data from 150,000 samples by September 2025, with a second batch of data from another 150,000 samples anticipated in the first half of 2026. The third and final tranche of 300,000 samples will be delivered later. “That’s primarily because the consortium has secured funding for those first 300,000 samples,” Whelan explained. “We are looking for additional commercial or philanthropic or public partners to help fund the generation of data for the last 300,000 samples.”
As the data comes in, members of the consortium will have a limited time to take a first crack at analyzing it for projects they are interested in—they had six months with the pilot data before it was made available to the broader scientific community. They will do joint analysis projects with the data as well, Whelan tells GEN, although exactly what those will look like is still being discussed.
Illumina’s proteomics play
Illumina has initiated a separate pilot project to also analyze proteins from 50,000 UK Biobank samples using Illumina Protein Prep and the NovaSeq X Plus
sequencer. Collaborators with Illumina are deCODE Genetics, Standard BioTools, Tecan, GSK, Johnson & Johnson, and Novartis. “We wanted to set our own standard using Illumina Protein Prep,” Daujotyte says. “The U.K. Biobank is a trendsetting biobank. A lot of scientists reuse their data for many different applications so it’s a very important biobank to work with.”
Like the UKB-PPP, this pilot will analyze 50,000 samples that span different disease types and health statuses. The partners have agreed that deCODE Genetics will process the samples using the Illumina Protein Prep solution and NovaSeq X Plus system and run analysis using Illumina’s DRAGEN Protein Quantification pipeline.
The first 30,000 samples are funded through co-investment from Illumina, deCODE Genetics, and Standard BioTools, with automation support from Tecan. The data from this initial batch of samples will be available immediately to the scientific research community once the data has passed quality control. This is expected to happen in the second half of 2025. Data from the remaining 20,000 samples will initially be available to the pharma partners for a limited period before being made available more broadly.
For Illumina, moving into proteomics now makes sense given the growing interest in a multi-omics approach to biologics development. “This is part of the broader strategy to lead the next wave biologics discovery,” says Daujotyte. Illumina Protein Prep is the sequencing vendor’s first proteomics solution. A key differentiator is the fact that Illumina is offering an end-to-end solution for protein discovery from sample collection through sequencing and data analysis.
As of press time, Illumina Protein Prep was in early-access testing with a full launch planned for later this year. The technology uses the SOMAmer technology developed by SomaLogic, which currently measures 9,500 unique proteins in a single assay, the most of any other affinity-based proteomic platform. Illumina is positioning it as a solution for protein discovery that includes sequencing and data analysis capabilities, which Daujotyte says sets it apart from the competition.
Fiona Kaper, PhD
Vice President and Head, Assay R&D
Illumina
Another differentiator is the aptamer technology. There are benefits to using oligonucleotides, says Fiona Kaper, PhD, vice president, head of assay research and development at Illumina. “These can be made and remade over and over again, very reproducibly,” she explains. “So, you get that continued reproducibility over different batches.”
Furthermore, “you don’t have to start splitting up your sample into multiple reactions because you can do it all in one go,” which contributes to its reproducibility, she continues. That’s important because “the more you split up samples, the more variability you insert in the assay.”
Reference
1. Sun, B.B., Chiou, J., Traylor, M. et al. Plasma proteomic associations with genetics and health in the UK Biobank. Nature 622, 329–338 (2023). https://doi.org/10.1038/s41586-023-06592-6
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