Our understanding of the molecular biology of degenerative diseases has made great strides with the emergence of genomics (the study of an organism's entire genome) and proteomics (the large scale study of an organism's proteins). Clinical proteomics and clinical genomics are emerging segments in the field of molecular diagnostics. Molecular diagnostics is focused on the ability to understand diseases at the molecular level providing better, patient specific, diagnostic information to clinicians facilitating better-informed treatment decisions.

Today, there are many new diagnostic products entering the clinic based on 'genomic' tools (mutation analysis or gene expression). These will continue to expand and provide clinical value. But, compared to mRNA expression, protein expression is more representative of the functional and interactive endpoints of biological systems and potential drug targets. Drugs often work through a combination of methods and their effectiveness can be a function of the integrated 'state' of the patient and the stage of the disease at the time of therapy. Because protein expression levels provide a better view of which molecules are actually interacting in the body at a given time they can be a better tool then genomic techniques for certain clinical challenges. In addition, the measurement of an individual's ability to express specific proteins provides greater insight into a drug's ability to regulate specific physiological processes whether these processes are distant or immediate targets of the drug in the molecular pathway. A measure of a particular proteomic phenotype can provide this information closer to the target than mRNA expression, allele copy number or mutation analysis.

Diagnostic measurements that can inform clinicians about real time physiology or the potential for actually demonstrating a particular physiological response are valuable tools in the treatment of disease.

There are many tools used today for assaying proteins in biological samples. The most common is the use of specific labeled capture agents (typically antibodies) and there are many such assays for the measurement of a single protein used in the clinic today. Further, significant efforts are being made to measure multiple proteins in a single assay through the use of 'protein arrays', though these are not yet available in the clinic. However, these techniques require two non-trivial tasks: first the identification of the differentiating proteins and then the creation of the capture agent(s). This is time consuming and presents many difficulties. Further, there are a number of tools for protein analysis which are used extensively in research (such as two dimensional gel electrophoresis (2DGE and high performance liquid chromatography (HPLC)) which are also often used with mass spectrometry (MS) but are very difficult to use in the clinic because of cost, lack of reproducibility, and technical complexity.

Worldwide, the leading method for high-throughput, label-free detection of proteins (without the use of capture agents) is mass spectrometry (MS). The technology has evolved rapidly as a tool for biologic research and is now emerging as a promising - if challenging - platform for clinical diagnostics.

Biodesix has cracked one of the most difficult analysis problems in diagnostics by creating tools which enable the coherent and reliable use of mass spectrometry (MS) as a diagnostic instrument. The Company has developed a set of tools and a methodology—the ProTS Platform—for the analysis and creation of diagnostic tests and for use in biomarker discovery. See Biodesix Technology

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