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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.  

Tumor Profiling: Methods and Protocols

1. 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, and Wendy W. J. de Leng

2. Library preparation using FFPE-derived Tumor DNA for High Throughput Hybridization-based Targeted or Exome Sequencing

John A. Thorson and Sarah S. Murray

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

Shulei Sun and Sarah S. Murray

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

Shulei Sun, John A. Thorson, and Sarah S. Murray

5. Biological Interpretation of Complex Genomic Data
Kathleen M. Fisch

6. Clinical Validation of Targeted Solid Tumor Profiling

Guy Froyen and Brigitte Maes

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

Ross Rowsey, Iya Znoyko,  and Daynna J. Wolff

8. Genome-Wide Copy Number Variation Detection using NGS: Data Analysis and Interpretation

Wei Shen, Philippe Szankasi, Jacob Durtschi, Todd W. Kelley,and Xinjie Xu

9. Overview of Fusion Detection Strategies Using Next Generation Sequencing

Jan Schröder, Amit Kumar,and Stephen Q. Wong

10. Clinical Application of Fusion Gene Detection Using Next-generation Sequencing and the NanoString Technology

Anna Karlsson and Johan Staaf

11. Pipeline for Integrated Microarray Expression Normalization Toolkit (PIMENTo) for Tumor Microarray Profiling Experiments

Thomas Nash, Matthew Huff, William B. Glen^, and Gary Hardiman

12. 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, and Gary Hardiman

13. 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, and Gary Hardiman

14. Methylation Analysis using Microarrays: Analysis and Interpretation

Teresia Kling and Helena Carén

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

Arundhati Bakshi, Muhammad B. Ekram, and Joomyeong Kim

16. A Pipeline for ctDNA Detection Following Primary Tumor Profiling Using A Cancer-related Gene Sequencing Panel

17. Single-cell Analysis of Circulating Tumor Cells

Jana- A. Thiele, Pavel Pitule, James Hicks, and Peter Kuhn