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Proteogenomic Analysis of Single Amino Acid Polymorphisms in Cancer Research

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Proteogenomics

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 926))

Abstract

The integration of genomics and proteomics has led to the emergence of proteogenomics, a field of research successfully applied to the characterization of cancer samples. The diagnosis, prognosis and response to therapy of cancer patients will largely benefit from the identification of mutations present in their genome. The current state of the art of high throughput experiments for genome-wide detection of somatic mutations in cancer samples has allowed the development of projects such as the TCGA, in which hundreds of cancer genomes have been sequenced. This huge amount of data can be used to generate protein sequence databases in which each entry corresponds to a mutated peptide associated with certain cancer types. In this chapter, we describe a bioinformatics workflow for creating these databases and detecting mutated peptides in cancer samples from proteomic shotgun experiments. The performance of the proposed method has been evaluated using publicly available datasets from four cancer cell lines.

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Acknowledgments

All participating laboratories are members of ProteoRed-ISCIII. This work was supported by: Carlos III Health Institute of Spain (ISCIII, FIS PI11/02114 and FIS PI14/01538)-Fondos FEDER (EU); grants SAF2014-5478-R from Ministerio de Economía y Competitividad. The CIMA Proteomics Unit belongs to ProteoRed, PRB2-ISCIII, supported by grant PT13/0001 L We also thank the Proteomics, Genomics and Bioinformatics Core Facility of CIMA, especially to Elizabeth Guruceaga, María Mora and Leticia Odriozola for technical support.

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Authors and Affiliations

  1. Proteomics and Bioinformatics Unit, Center for Applied Medical Research, University of Navarra, Pamplona, Spain

    Alba Garin-Muga, Fernando J. Corrales & Victor Segura

  2. Division of Hepatology and Gene Therapy, Center for Applied Medical Research, University of Navarra, Pamplona, Spain

    Fernando J. Corrales

  3. IdiSNA, Navarra Institute for Health Research, Pamplona, Spain

    Fernando J. Corrales & Victor Segura

Authors
  1. Alba Garin-Muga
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  2. Fernando J. Corrales
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  3. Victor Segura
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Correspondence to Victor Segura .

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Editors and Affiliations

  1. Department of Pharmacology & Toxicology, University of Texas Medical Branch, Galveston, Texas, USA

    Ákos Végvári

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Garin-Muga, A., Corrales, F.J., Segura, V. (2016). Proteogenomic Analysis of Single Amino Acid Polymorphisms in Cancer Research. In: Végvári, Á. (eds) Proteogenomics. Advances in Experimental Medicine and Biology, vol 926. Springer, Cham. https://doi.org/10.1007/978-3-319-42316-6_7

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