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Tumor Profiling

Methods and Protocols

  • Book
  • © 2019

Overview

Editors:
  1. Sarah S. Murray

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

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

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

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Table of contents (17 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

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

    • Eric Strengman, Francoise A. S. Barendrecht-Smouter, Carmen de Voijs, Paula de Vree, Isaac J. Nijman, Wendy W. J. de Leng
    Pages 1-17

  3. Library Preparation Using FFPE-Derived Tumor DNA for High-Throughput Hybridization-Based Targeted or Exome Sequencing

    • John A. Thorson, Sarah S. Murray
    Pages 19-36

  4. Bioinformatics Basics for High-Throughput Hybridization-Based Targeted DNA Sequencing from FFPE-Derived Tumor Specimens: From Reads to Variants

    • Shulei Sun, Sarah S. Murray
    Pages 37-48

  5. Annotation of Variant Data from High-Throughput DNA Sequencing from Tumor Specimens: Filtering Strategies to Identify Driver Mutations

    • Shulei Sun, John A. Thorson, Sarah S. Murray
    Pages 49-60

  6. Biological Interpretation of Complex Genomic Data

    • Kathleen M. Fisch
    Pages 61-71

  7. Clinical Validation of Targeted Solid Tumor Profiling

    • Guy Froyen, Brigitte Maes
    Pages 73-87

  8. Whole-Genome Single Nucleotide Polymorphism Microarray for Copy Number and Loss of Heterozygosity Analysis in Tumors

    • Ross Rowsey, Iya Znoyko, Daynna J. Wolff
    Pages 89-111

  9. Genome-Wide Copy Number Variation Detection Using NGS: Data Analysis and Interpretation

    • Wei Shen, Philippe Szankasi, Jacob Durtschi, Todd W. Kelley, Xinjie Xu
    Pages 113-124

  10. Overview of Fusion Detection Strategies Using Next-Generation Sequencing

    • Jan Schröder, Amit Kumar, Stephen Q. Wong
    Pages 125-138

  11. Clinical Application of Fusion Gene Detection Using Next-Generation Sequencing and the NanoString Technology

    • Anna Karlsson, Johan Staaf
    Pages 139-152

  12. Pipeline for Integrated Microarray Expression Normalization Tool Kit (PIMENTo) for Tumor Microarray Profiling Experiments

    • Thomas Nash, Matthew Huff, W. Bailey Glen Jr., Gary Hardiman
    Pages 153-168

  13. Molecular Profiling of RNA Tumors Using High-Throughput RNA Sequencing: Overview of Library Preparation Methods

    • Sean M. Courtney, Willian A. da Silveira, E. Starr Hazard, Gary Hardiman
    Pages 169-184

  14. Molecular Profiling of RNA Tumors Using High-Throughput RNA Sequencing: From Raw Data to Systems Level Analyses

    • Willian A. da Silveira, E. Starr Hazard, Dongjun Chung, Gary Hardiman
    Pages 185-204

  15. Methylation Analysis Using Microarrays: Analysis and Interpretation

    • Teresia Kling, Helena Carén
    Pages 205-217

  16. High-Throughput Targeted Repeat Element Bisulfite Sequencing (HT-TREBS)

    • Arundhati Bakshi, Muhammad B. Ekram, Joomyeong Kim
    Pages 219-228

  17. A Pipeline for ctDNA Detection Following Primary Tumor Profiling Using a Cancer-Related Gene Sequencing Panel

    • Satoshi S. Nishizuka, Kei A. Sato, Tsuyoshi Hachiya
    Pages 229-241

  18. Single-Cell Analysis of Circulating Tumor Cells

    • Jana- A. Thiele, Pavel Pitule, James Hicks, Peter Kuhn
    Pages 243-264

  19. Back Matter

    Pages 265-268
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Keywords

About this book

This book provides a practical guide to current methods for profiling and interpreting genomic alterations in tumors. Chapters detail methods to interrogate DNA variation, RNA expression, and epigenetic changes using both next-generation sequencing and microarray techniques, common bioinformatics and annotation tools to glean relevant driver genomic events, and different performance characteristics as well as quality metrics necessary for the robust validation of tumor profiling as a diagnostic test for medical laboratories. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Authoritative and cutting-edge, Tumor Profiling: Methods and Protocols aims to be a useful resource for learning about technical details, applications, and strengths and limitations of the latest technologies as applied to this increasingly important field.  



Editors and Affiliations

  • Department of Pathology, University of California San Diego, La Jolla, USA

    Sarah S. Murray

Bibliographic Information

  • Book Title: Tumor Profiling

  • Book Subtitle: Methods and Protocols

  • Editors: Sarah S. Murray

  • Series Title: Methods in Molecular Biology

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

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2019

  • Hardcover ISBN: 978-1-4939-9002-3Published: 17 January 2019

  • eBook ISBN: 978-1-4939-9004-7Published: 16 January 2019

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 268

  • Number of Illustrations: 15 b/w illustrations, 57 illustrations in colour

  • Topics: Molecular Medicine, Cancer Research

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