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The SOMAscan® assay: a novel biomarker discovery tool now available at Erasmus MC

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The SOMAscan® assay is a highly multiplexed, sensitive, quantitative, and reproducible proteomic tool for discovering previously undetected biomarkers for drug discovery, pre-clinical and clinical drug development, and clinical diagnostics, across a wide range of important diseases and conditions. The SOMAscan assay measures 1,310 protein analytes in only 150 μL of serum, plasma or cerebrospinal fluid, or equally small amounts of a variety of other biological matrices. The assay offers exceptional dynamic range, quantifying proteins that span over 8 logs in abundance (from femtomolar to micromolar), with excellent reproducibility [1].The SOMAscan® assay has been developed by SomaLogic, currently based at Boulder, CO. Recently, the SOMAscan® assay has been deployed at the department of Immunology of the Erasmus MC, University Medical Center Rotterdam. As a result, researchers at Erasmus MC can now access the SOMAscan® assay for their own investigations at their own institution. Furthermore, researchers outside Erasmus MC can access the SOMAscan® assay as well, in collaboration with Erasmus MC’s department of Immunology.

 Technique

At the heart of SomaLogic's proteomic platform are SOMAmer (Slow Off-rate Modified Aptamer) protein-binding reagents, each of which combine the best properties of antibodies (range of target proteins) and traditional aptamers (durability and reliability), and each of which is highly specific for its respective cognate protein.  A SOMAmer reagent consists of a unique short DNA sequence that incorporates several bases that have been modified to include "protein-like" side chains, and a 5'-linker optimized for use in the SOMAscan® assay (figure 1). To date, SomaLogic has developed SOMAmer reagents to a broad array of more than 1,300 different protein targets  critical to normal and disease biology, and they continue to expand their SOMAmer reagent library at regular intervals.


SOMAscan® assay highlights:

  • powerful, highly multiplexed platform for biomarker discovery
  • measures 1.310 proteins in 150 µl of biological material
  • highly sensitive with 5 log range
  • first automated, high throughput facility including bioinformatics in Europe at Erasmus MC

 

  
 

 

 

Figure 1: The crystal structure of a SOMAmer-protein pair  reveals the unique binding properties of SOMAmer reagents compared to antibodies or traditional aptamers (base modifications are in purple).

 Facility

The SOMAscan® assay facility created at the department of Immunology utilizes a fully automated assay procedure using state-of-the-art equipment (figure 2). The facility is closely associated with the department’s ISO 15189 certified Laboratory of Medical Immunology (LMI). The stringent quality management operational at the LMI is currently being implemented at the SOMAscan® assay facility, to ensure performance of the assay at the highest level possible. Furthermore, the facility is associated with Erasmus MC’s department of Bioinformatics to support data analysis.

Figure 2: State-of-the-art equipment for automated SOMAscan® assay high throughput procedure at Erasmus MC. From left to right: Freedom EVO200 Liquid Handler (Tecan), Little Dipper Processor for Agilent Arrays (SciGene), SureScan Microarray Scanner (Agilent)

 Contact

For further information on the SOMAscan® assay, its facility at the department of Immunology or potential research collaboration, please contact:

 References

1) Gold, L. et al. Aptamer-Based Multiplexed Proteomic Technology for Biomarker Discovery. PLoS ONE (2010); 5(12): e15004.