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Tumor Profiling pp 1–17Cite as

Amplicon-Based Targeted Next-Generation Sequencing of Formalin-Fixed, Paraffin-Embedded Tissue

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1908))

Abstract

Next-generation sequencing (NGS) is rapidly becoming the method of choice for mutation analysis in both research and diagnostics. The benefit of targeted NGS compared to whole-genome and whole-exome sequencing is that smaller amounts of input material can be used as well as qualitatively suboptimal tissue samples, like formalin-fixed, paraffin-embedded archival tissue.

Here, we describe the protocol for targeted next-generation sequencing using the Ion Torrent PGM platform in combination with Ion Ampliseq NGS gene panels for formalin-fixed, paraffin-embedded tissues. Both the manual and the automated workflow are described as well as the bioinformatics for data analysis.

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Author notes

  1. Isaac J. Nijman and Wendy W. J. de Leng contributed equally to this work.

Authors and Affiliations

  1. Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands

    Eric Strengman, Carmen de Voijs, Paula de Vree & Wendy W. J. de Leng

  2. Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands

    Francoise A. S. Barendrecht-Smouter & Isaac J. Nijman

Authors
  1. Eric Strengman
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  2. Francoise A. S. Barendrecht-Smouter
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  3. Carmen de Voijs
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  4. Paula de Vree
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  5. Isaac J. Nijman
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  6. Wendy W. J. de Leng
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Corresponding author

Correspondence to Wendy W. J. de Leng .

Editor information

Editors and Affiliations

  1. Department of Pathology, University of California San Diego, La Jolla, CA, USA

    Sarah S. Murray

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Strengman, E., Barendrecht-Smouter, F.A.S., de Voijs, C., de Vree, P., Nijman, I.J., de Leng, W.W.J. (2019). Amplicon-Based Targeted Next-Generation Sequencing of Formalin-Fixed, Paraffin-Embedded Tissue. In: Murray, S. (eds) Tumor Profiling. Methods in Molecular Biology, vol 1908. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9004-7_1

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  • DOI: https://doi.org/10.1007/978-1-4939-9004-7_1

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-9002-3

  • Online ISBN: 978-1-4939-9004-7

  • eBook Packages: Springer Protocols

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