Illumina Launches Protein Prep Assay to Accelerate Drug Discovery Through Large-Scale Proteomics
核心洞察
Illumina has launched Protein Prep, an NGS-based proteomics assay capable of measuring 9,500 unique human protein targets to accelerate drug discovery and biomarker identification.
Early access data from Genomics England (搜索)'s 100,000 Genomes Project showed a significant 7.5% increase in diagnostic yield for rare diseases when proteomics was added to genomic analysis.
The platform has processed over 36,000 samples during early access testing and enables researchers to investigate protein signatures in cancer, cardiovascular, metabolic, and immunologic diseases.
Illumina Inc. has officially launched Illumina Protein Prep (搜索), a next-generation sequencing-based proteomics assay designed to transform drug discovery and biomarker identification through large-scale protein analysis. The platform, which can measure 9,500 unique human protein targets, represents the most comprehensive NGS-based proteomics solution available and has already demonstrated significant clinical impact in early studies.
Platform Capabilities and Technology
Illumina Protein Prep (搜索) is powered by SOMAmer™ technology and offers researchers the ability to simultaneously interrogate thousands of proteins in a single experiment. The platform integrates with Illumina's NovaSeq™ sequencing systems and utilizes DRAGEN™ Protein Quantification and Connected Multiomics software to convert complex proteomic data into actionable insights.
"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."
The assay addresses a critical gap in biomedical research by bridging genotype and phenotype, providing real-time snapshots of cellular activity between healthy and disease states. This capability is particularly valuable for biomarker discovery and precision therapy development across cancer, cardiovascular, metabolic, and immunologic diseases.
Clinical Validation and Early Results
Since 2024, Illumina has collaborated with nearly 40 early access partners to validate the platform's performance. During this period, approximately 30,000 samples were processed using the Illumina Protein Prep (搜索) 6K assay, with an additional 6,000 samples analyzed using the 9.5K assay introduced in March 2025.
The most significant clinical validation comes from Genomics England (搜索)'s 100,000 Genomes Project, where researchers implemented a multiomics program to improve diagnostic yields for rare diseases. The project, which had achieved approximately 25% diagnostic yield in 2019 using genomics alone, leveraged Illumina Protein Prep (搜索) to profile more than 7,800 participants.
Data from an initial 500-sample pilot study revealed a substantial 7.5% increase in diagnostic yield when proteomics was added to genomic analysis. "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 (搜索).
The diagnostic improvements stemmed from the discovery of abundant differential proteins in specific disease categories, supporting the potential of proteomics to advance rare genetic disease research by revealing disease-associated genes and pathways.
Research Applications in Oncology
The platform's clinical utility extends to cancer research, particularly in understanding treatment resistance mechanisms. Kasey Couts, PhD, codirector of the CU Center for Rare Melanomas at the University of Colorado Anschutz Medical Campus, is using Illumina Protein Prep (搜索) to investigate why immunotherapies are less effective against rare melanomas compared to cutaneous melanomas.
"Illumina Protein Prep (搜索) can help us identify as many as 9,500 proteins," Couts explained. "This scale is tremendously useful, as we try to dissect the mechanisms that are making these rare tumors resistant to immunotherapy." Previously, the research team was limited to analyzing only 92 proteins with other proteomic technologies.
The team is investigating how different melanoma types generate distinct proteomic signatures, with the goal of identifying biomarkers that could 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 noted.
Strategic Partnerships and Market Expansion
The launch coincides with Illumina's broader multiomics strategy, including a definitive agreement to acquire SomaLogic (搜索), a leader in data-driven proteomics technology. This acquisition will enhance Illumina's presence in the expanding proteomics market and advance the company's multiomics capabilities.
In January, Illumina announced a pilot proteomics program with UK Biobank (搜索) and a consortium of biopharma collaborators to analyze 50,000 samples using Illumina Protein Prep (搜索), the NovaSeq X Plus System, and the DRAGEN Protein Quantification pipeline. This study aims to generate high-quality, NGS-based proteomics data for the research community and pharmaceutical partners.
Clinical Impact and Future Applications
The platform's ability to identify differentially abundant proteins has particular significance for rare disease research. "The large content and high analytical sensitivity of Illumina Protein Prep (搜索) 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," Brown emphasized.
Professor Brown expressed confidence in the clinical potential of proteomics, stating, "I am confident based on our pilot that proteomics will have significant clinical value in the not-too-distant future."
The technology supports pharmaceutical companies, contract research organizations, and translational research institutions worldwide by streamlining the path from discovery to therapeutic development. Early access customers have particularly commended the platform's scale, high consistency, and streamlined sample-to-insights workflow.
As proteogenomics studies continue to identify critical links between gene variants and protein expression, Illumina Protein Prep (搜索) positions researchers to guide drug discovery with unprecedented protein-level insights across multiple disease areas.