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Functional Molecular Units for Guiding Biomarker Panel Design

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Biomedical Literature Mining

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1159))

Abstract

The field of biomarker research has experienced a major boost in recent years, and the number of publications on biomarker studies evaluating given, but also proposing novel biomarker candidates is increasing rapidly for numerous clinically relevant disease areas. However, individual markers often lack sensitivity and specificity in the clinical context, resting essentially on the intra-individual phenotype variability hampering sensitivity, or on assessing more general processes downstream of the causative molecular events characterizing a disease term, in consequence impairing disease specificity. The trend to circumvent these shortcomings goes towards utilizing multimarker panels, thus combining the strength of individual markers to further enhance performance regarding both sensitivity and specificity. A way of identifying the optimal composition of individual markers in a panel approach is to pick each marker as representative for a specific pathophysiological (mechanistic) process relevant for the disease under investigation, hence resulting in a multimarker panel for covering the set of pathophysiological processes underlying the frequently multifactorial composition of a clinical phenotype.

Here we outline a procedure of identifying such sets of disease-specific pathophysiological processes (units) delineated on the basis of disease-associated molecular feature lists derived from literature mining as well as aggregated, publicly available Omics profiling experiments. With such molecular units in hand, providing an improved reflection of a specific clinical phenotype, biomarker candidates can then be assigned to or novel candidates are to be selected from these units, subsequently resulting in a multimarker panel promising improved accuracy in disease diagnosis as well as prognosis.

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Acknowledgements

The research leading to these results has received funding from the European Community’s Seventh Framework Programme under the grant agreement no. 2782494 (EU-MASCARA).

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Authors and Affiliations

  1. emergentec biodevelopment GmbH, Gersthofer Strasse 29-31, 1180, Vienna, Austria

    Andreas Heinzel, Irmgard Mühlberger, Raul Fechete, Bernd Mayer & Paul Perco

  2. Institute for Theoretical Chemistry, University of Vienna, Währinger Strasse 17, 1090, Vienna, Austria

    Bernd Mayer

Authors
  1. Andreas Heinzel
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  2. Irmgard Mühlberger
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  3. Raul Fechete
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  4. Bernd Mayer
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  5. Paul Perco
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Corresponding author

Correspondence to Paul Perco .

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Editors and Affiliations

  1. GlaxoSmithKline, King of Prussia, Pennsylvania, USA

    Vinod D. Kumar

  2. GlaxoSmithKline, Hitchin, Hertfordshire, United Kingdom

    Hannah Jane Tipney

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Heinzel, A., Mühlberger, I., Fechete, R., Mayer, B., Perco, P. (2014). Functional Molecular Units for Guiding Biomarker Panel Design. In: Kumar, V., Tipney, H. (eds) Biomedical Literature Mining. Methods in Molecular Biology, vol 1159. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-0709-0_7

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  • DOI: https://doi.org/10.1007/978-1-4939-0709-0_7

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-0708-3

  • Online ISBN: 978-1-4939-0709-0

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