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Clinical Applications of Next-Generation Sequencing of Formalin-Fixed Paraffin-Embedded Tumors

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Book cover Next Generation Sequencing in Cancer Research, Volume 2

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Abstract

Significant progress has been made in next-generation sequencing (NGS) of tumors from formalin-fixed paraffin-embedded (FFPE) tumors. In this chapter, we review some of the recent developments in RNA and DNA sequencing from FFPE. We highlight some of the current challenges and considerations that must be in place before using NGS in a clinical setting. We begin with a discussion of the technical challenges in dealing with FFPE tumors, including nucleic acid degradation and the potential utility of adding in dissection methods to the tumors. We then discuss bioinformatical and statistical considerations that must be employed when analyzing data obtained from FFPE tissues. We end with a brief discussion of ethical implications and other issues that will need to be addressed before translating discoveries into the clinic.

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Author information

Authors and Affiliations

  1. Department of Family Medicine and Community Health, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA

    Cheryl L. Thompson Ph.D.

  2. Department of Epidemiology and Biostatistics, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA

    Cheryl L. Thompson Ph.D.

  3. Department of General Medical Sciences (Oncology), Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA

    Vinay Varadan Ph.D.

Authors
  1. Cheryl L. Thompson Ph.D.
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  2. Vinay Varadan Ph.D.
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Corresponding author

Correspondence to Cheryl L. Thompson Ph.D. .

Editor information

Editors and Affiliations

  1. Department of Pathology and Laboratory, Medicine, Southern Alberta Cancer Research Institute, University of Calgary, Calgary, Alberta, Canada

    Wei Wu

  2. Faculty of Science, Biochemistry Department, Center of Innovation in Personalized Medicine, King Fahd Center for Medical Research, King Abdulaziz University, Jeddah, Saudi Arabia

    Hani Choudhry

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© 2015 Springer International Publishing Switzerland

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Thompson, C.L., Varadan, V. (2015). Clinical Applications of Next-Generation Sequencing of Formalin-Fixed Paraffin-Embedded Tumors. In: Wu, W., Choudhry, H. (eds) Next Generation Sequencing in Cancer Research, Volume 2. Springer, Cham. https://doi.org/10.1007/978-3-319-15811-2_11

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