"NGS-based proteomics provides critical speed, accuracy, reproducibility, and scalability to power large studies and accelerate the drug discovery pipeline for our ecosystem partners in biopharma," said Steve Barnard, chief technology officer of Illumina. "Proteomics is essential to advancing our understanding of disease and is a central pillar of multiomics. Illumina Protein Prep will help deliver multiomics at scale to transform biologic discovery."
Proteomics offers a view into proteins and their functions in biologic processes. Understanding their roles in gene expression and how proteins change throughout disease states is critical to biomarker discovery and precision therapy development. Illumina Protein Prep is powered by SOMAmer™ technology and can measure 9500 unique human protein targets, the most with an NGS readout; offering the greatest insights into protein biology.
Combining Illumina Protein Prep with the power and scalability of Illumina NovaSeq™ sequencing platforms enables the simultaneous interrogation of thousands of proteins in a single experiment, maximizing the discovery power of proteomics studies. After sequencing, Illumina DRAGEN™ Protein Quantification and Connected Multiomics software work together to turn complex proteomic data into clear insights. This powerful combination helps researchers streamline analysis and accelerate progress from discovery to therapeutic development, supporting pharma, contract research organizations, and translational research worldwide.
Early access customers commend scale, high consistency, and easy workflow
Since 2024, Illumina has worked with nearly 40 early collaborators to pilot Illumina Protein Prep, informing development and leading to an optimized customer experience. Since the inception of early access, about 30,000 samples have been processed with the Illumina Protein Prep 6K assay and over 6000 samples with the Illumina Protein Prep 9.5K assay, which was made available through early access this March.
Illumina Protein Prep accelerates global discovery initiative in rare disease
Proteomic studies bridge the gap between genotype and phenotype, providing a real-time snapshot of cellular activity between healthy and disease states. Large-scale proteomic studies can accelerate the discovery of biomarkers for the early detection and monitoring of cancer and other diseases. Proteogenomics studies, which combine proteomic, genomic, and transcriptomic data, identify critical links between gene variants and protein expression that can be used to guide drug discovery.
Researchers leading Genomics England's 100,000 Genomes Project have implemented a multiomics program aimed at improving upon the 2019 diagnostic yield of about 25% for the rare disease cohort. As part of that, they've leveraged Illumina Protein Prep to profile more than 7800 participants. Data from the initial 500-sample pilot study showed a significant 7.5% increase in diagnostic yield.
"Until now, proteomics has been considered as a standalone research test, and what this study shows is it will have a much bigger clinical impact on both rare and common diseases," said Professor Matthew Brown, chief scientific officer of Genomics England. "I am confident based on our pilot that proteomics will have significant clinical value in the not-too-distant future."
The findings stemmed from the discovery of abundant differential proteins in specific disease categories, which supports the diagnostic potential of proteomics to advance rare genetic disease research by revealing disease-associated genes and pathways.
"The large content and high analytical sensitivity of Illumina Protein Prep is a big advantage to identify the differentially abundant proteins that link strongly with known factors involved in the disease category concerned, especially with rare disease," said Brown.
Leveraging proteomics to understand rare melanomas
Immunotherapy has changed how oncologists treat cutaneous melanomas—a common and aggressive form of skin cancer. Unfortunately, these therapies are less effective against rare melanomas, such as ocular, acral, and mucosal. Kasey Couts, PhD, codirector of the CU Center for Rare Melanomas at the University of Colorado Anschutz Medical Campus, is working to understand why this happens and investigating new ways to improve melanoma care.
Illumina Protein Prep is giving Couts's research team a powerful, unbiased tool to interrogate these unique conditions. Other proteomic technologies the lab has used were limited to 92 proteins.
"Illumina Protein Prep can help us identify as many as 9500 proteins," Couts said. "This scale is tremendously useful, as we try to dissect the mechanisms that are making these rare tumors resistant to immunotherapy."
The team is using Illumina Protein Prep to investigate how cutaneous and rare melanomas can generate different proteomic signatures. Once identified, these biomarkers could eventually lead to new diagnostics and therapies.
"We are looking at what's happening in the tumor cells, as well as the types of immune cells inside tumors and the overall tumor microenvironment," Couts continued. "Illumina Protein Prep is helping us broaden our analyses to systemically investigate circulating proteins and the different factors that could be impacting the immune response."
More proteomics news from Illumina
In January, Illumina announced a pilot proteomics program with UK Biobank and a consortium of biopharma collaborators to analyze 50,000 samples with Illumina Protein Prep, the NovaSeq X Plus System, and the DRAGEN Protein Quantification pipeline. The study will generate a new collection of high-quality, NGS-based proteomics data for the research community and pharma partners to advance biological insights.
In June, Illumina announced a definitive agreement with Standard BioTools (NASDAQ: LAB) under which Illumina will acquire SomaLogic, a leader in data-driven proteomics technology. The move enhances Illumina's presence in the expanding proteomics market, advances the company's multiomics strategy, and reinforces the value of the NovaSeq X Series as an enabler of the next generation of multiomic applications.
Once the transaction closes, Illumina platforms will continue to support all NGS-based proteomics solutions. Illumina will also continue to support SomaLogic's currently offered array-based proteomics solutions. Until that time, Illumina and SomaLogic remain and will continue to operate as separate entities.
Early-access collaborators will be presenting at upcoming conferences, including the American Society of Human Genetics Annual Meeting in October, visit the event page, and the Human Proteome Organization World Congress in November.
To learn more, visit illumina.com/proteinprep.
Use of forward-looking statements
This release may contain forward-looking statements that involve risks and uncertainties. Among the important factors to which our business is subject that could cause actual results to differ materially from those in any forward-looking statements are: (i) challenges inherent in developing and launching new products and services, including modifying and scaling manufacturing operations, and reliance on third-party suppliers for critical components; (ii) our ability to manufacture robust instrumentation and consumables; and (iii) the acceptance by customers of our newly launched products, which may or may not meet our and their expectations, and (iv) our ability to obtain any required regulatory clearances to close our acquisition of SomaLogic, together with other factors detailed in our filings with the Securities and Exchange Commission, including our most recent filings on Forms 10-K and 10-Q, or in information disclosed in public conference calls, the date and time of which are released beforehand. We undertake no obligation, and do not intend, to update these forward-looking statements, to review or confirm analysts' expectations, or to provide interim reports or updates on the progress of the current quarter.
About Illumina
Illumina is improving human health by unlocking the power of the genome. Our focus on innovation has established us as a global leader in DNA sequencing and array-based technologies, serving customers in the research, clinical, and applied markets. Our products are used for applications in the life sciences, oncology, reproductive health, agriculture, and other emerging segments. To learn more, visit illumina.com and connect with us on X, Facebook, LinkedIn, Instagram, TikTok, and YouTube.
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