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Discovery and validation of protein biomarkers

10 July 2012  •  Author(s): Péter Horvatovich & Rainer Bischoff, Analytical Biochemistry, Department of Pharmacy, University of Groningen

Biomarkers are biological characteristics that are objectively measured and evaluated as indicators of normal biological processes, pathogenic processes or pharmacological responses to a therapeutic intervention1. Biomarkers can be used to determine disease onset, progression, efficacy of drug treatment, patient susceptibility to develop a certain type of disease or predict efficacy of treatment at a particular disease stage2. Protein molecular biomarkers are particularly popular due to the availability of a large range of analytical instrumentation, which can identify and quantify proteins in complex biological samples.

Proteins are key compounds in biosynthesis, cell, tissue and organ signalling and provide cell and tissue structural stability in living organisms. The primary protein sequences are encoded in the genome; however, their complex posttranslational modifications (PTMs) and three dimensional structures are fairly unpredictable from genomic information. In this mini-review, we will provide an overview of the current state, challenge and important aspects of protein biomarker discovery and validation.

Biomarker research should start with defining the target normal biological processes, pathogenic processes, or pharmacological responses to a therapeutic intervention, what the biomarker should highlight. This is followed by setting up a team with medical, analytical and bioinformatics partners (Figure 1).

The medical partner is responsible for sample collection, storage and pre-classification of samples based on accurate clinical data (disease phenotype), and store samples and clinical information in biobanks. The analytical participant is responsible for the development of an analytical platform both for the discovery stage comprehensively measuring a low number of samples and for validation. Validation includes the targeted analysis of a preselected list of biomarker candidates in a large sample cohort. The bioinformatics partner is responsible for management, processing and accurate evaluation of all data acquired during the study. All of the three parties need to collaborate closely, and the work requires careful planning before starting the sample collection and analytical work3.

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