Powering protein discovery with NGS
Proteomics workflows have long faced technical challenges that have kept them trailing behind equivalent genomics workflows, including inefficient protocols, low coverage and limited sensitivity for low abundance proteins. SomaLogic, now part of Illumina®, introduced a novel approach to protein measurement using modified DNA aptamers, known as SOMAmer Reagents®, to enable NGS-based analysis. Building on this foundation, Illumina has worked closely with Tecan to develop an automated proteomics solution capable of quantifying more than 9,500 human proteins in just 2.5 days from sample to analysis.
Proteomics technologies have advanced significantly in recent years, and are now used across a wide range of applications, including the discovery and validation of disease-specific biomarkers. Illumina’s Protein Prep solution is at the forefront of these technologies, enabling large-scale, sensitive and highly multiplexed quantification of proteins as an alternative to mass spectrometry or antibody-based approaches. This innovative platform was the result of combining SomaLogic’s SOMAmer Reagents with Illumina sequencing and Tecan automation to deliver a high throughput platform with the potential to accelerate proteomics research worldwide.
Finding the right automation partner
Michael Dorwart, Director of Research at Illumina, played a pivotal role in the project’s development from the start, and outlined its aims: “Our goal was to develop a single workflow that seamlessly integrated SomaLogic’s technology with our NGS capabilities. To achieve this, we needed a partner with deep automation expertise to help us automate the Illumina Protein Prep assay in a robust and flexible way. We selected Tecan based on the company’s extensive OEM automation experience, collaborative approach to product development and ability to support complex and evolving workflows.”
Overcoming technical challenges together
The Illumina Protein Prep assay uses SOMAmer reagents with human serum or plasma samples, followed by a series of binding, washing and elution steps prior to conversion into sequencing-ready libraries. A key differentiator of the workflow is the replacement of a conventional enzymatic cleavage step with a light-based process operating at a unique wavelength, which requires precise control within an automated environment. In collaboration with Illumina, Tecan developed an automated workflow based on a Fluent® Automation Workstation, equipped with a Multiple Channel Arm 96™, a Robotic Gripper Arm™ and a Fluent ID™ barcode scanner, together with several custom modules designed specifically to support this process. Tecan also assisted with the design and implementation of the automated light-based cleavage step, ensuring consistent performance across high throughput runs. Michael stated: “Proteomics is a fast-paced field, so we needed to remain agile throughout the project, adapting the system as requirements changed. Tecan helped us to modify instrument features right through development, which was essential to the success of the platform. The result is a highly streamlined workflow with only around four hours of total hands-on time. From running the assay through to NGS library preparation, sequencing and analysis, the complete workflow takes approximately 2.5 days.”
Delivering consistency at scale
Automation plays a critical role in delivering the reproducibility required for large-scale proteomics studies, particularly when working with blood-based samples, where protein concentrations can span more than 10 orders of magnitude. The Translational Genomics Research Institute (TGen) – part of City of Hope, a non-profit biomedical research institute in Phoenix, Arizona – was one of the first laboratories to implement the platform through Illumina’s early access program. Patrick Pirrotte, Associate Professor and Director of the Integrated Mass Spectrometry Facility at TGen, described the benefits of the automated workflow: “Once the samples are transferred from the vials onto the assay plate, the workstation takes over. The automation ensures a level of consistency that is extremely difficult to achieve manually. From plate to plate, even when runs are spaced out by months, we are achieving coefficient of variations of three to four percent or lower for most analytes. This level of reproducibility is something specific to the platform, and is simply not achievable with traditional mass spectrometry workflows at this scale.”
Enabling new applications in translational research
The ability to rapidly quantify thousands of proteins in parallel with high sensitivity has enabled the exploration of new applications at TGen. “We have already run thousands of plasma samples across multiple studies,” Patrick explained. “One example is an early detection pan-cancer assay designed to rule in or out the presence of a malignancy, followed by staging if the result is positive. The Illumina solution has been very successful in the discovery phase, and we’re now expanding into validation studies with a greater number of samples. The consistency of the Tecan automation, combined with a very well refined assay, gives us confidence in the data and allows us to scale our studies efficiently.”
Tecan’s OEM expertise enabled Illumina to package the entire workflow – from automated sample preparation through to library preparation, sequencing and analysis – into a single, integrated solution for its customers. “Working with Tecan was an extremely positive experience. The internal teams are clearly very good at what they do, on both the business and technical sides. Overall, I do not know how it could have gone better,” Michael concluded.
M-AMR-02060
