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Integrating Biomolecular and Clinical Data for Cancer Research: Concepts and Challenges

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Abstract

In this review we describe current concepts and future challenges for integrating biomolecular and clinical data for cancer research. We first highlight the various sources for generating data with specific focus on medium- and large-scale omics approaches as well as relevant public databases. We then give an overview of the computational methods necessary to analyze primary data as well as bioinformatics tools for using databases, extracting pathway information, and reconstructing biomolecular networks. The main focus of this work is on current methodological concepts for data integration as well as integrative data analyses. Using a case study in cancer immunology, we demonstrate the power and the limitations of the used methods. Finally we discuss future challenges and suggest how a combined computational/experimental approaches can lead to new insights into the molecular mechanisms of cancer, and improved diagnosis and prognosis of the disease.

Pornpimol Charoentong and Hubert Hackl contributed equally to this work.

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Abbreviations

FACS:

Fluorescence-activated cell sorter

GO:

Gene ontology

miRNA:

MicroRNA

MSI:

Microsatellite instability

PH:

Proportional hazards

qPCR:

Quantitative real-time polymerase chain reaction

SNP:

Single nucleotide polymorphism

TMA:

Tissue microarray

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Authors and Affiliations

  1. Biocenter, Section for Bioinformatics, Innsbruck Medical University, Innsbruck, Austria

    Pornpimol Charoentong & Hubert Hackl

  2. INSERM, Integrative Cancer Immunology Team, INSERM U872, Cordeliers Research Center, Paris, France

    Bernhard Mlecnik & Gabriela Bindea

  3. INSERM, Integrative Cancer Immunology Team, INSERM U872, Cordeliers Research Center, 15 rue de l’Ecole de Médecine, 75006, Paris, France

    Jerome Galon

  4. Biocenter, Division of Bioinformatics, Innsbruck Medical University, Innrain 80, 6020, Innsbruck, Austria

    Zlatko Trajanoski

Authors
  1. Pornpimol Charoentong
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  2. Hubert Hackl
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  3. Bernhard Mlecnik
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  4. Gabriela Bindea
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  5. Jerome Galon
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  6. Zlatko Trajanoski
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Corresponding authors

Correspondence to Jerome Galon or Zlatko Trajanoski .

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Editors and Affiliations

  1. , Section for Bioinformatics, Medical University of Innsbruck, Innrain 80, Innsbruck, 6020, Austria

    Zlatko Trajanoski

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Charoentong, P., Hackl, H., Mlecnik, B., Bindea, G., Galon, J., Trajanoski, Z. (2012). Integrating Biomolecular and Clinical Data for Cancer Research: Concepts and Challenges. In: Trajanoski, Z. (eds) Computational Medicine. Springer, Vienna. https://doi.org/10.1007/978-3-7091-0947-2_9

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