Tumor Profiling: Methods and Protocols

Description

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. Front Matter ....Pages i-xi 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 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 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 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 Biological Interpretation of Complex Genomic Data (Kathleen M. Fisch)....Pages 61-71 Clinical Validation of Targeted Solid Tumor Profiling (Guy Froyen, Brigitte Maes)....Pages 73-87 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 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 Overview of Fusion Detection Strategies Using Next-Generation Sequencing (Jan Schröder, Amit Kumar, Stephen Q. Wong)....Pages 125-138 Clinical Application of Fusion Gene Detection Using Next-Generation Sequencing and the NanoString Technology (Anna Karlsson, Johan Staaf)....Pages 139-152 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 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 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 Methylation Analysis Using Microarrays: Analysis and Interpretation (Teresia Kling, Helena Carén)....Pages 205-217 High-Throughput Targeted Repeat Element Bisulfite Sequencing (HT-TREBS) (Arundhati Bakshi, Muhammad B. Ekram, Joomyeong Kim)....Pages 219-228 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 Single-Cell Analysis of Circulating Tumor Cells (Jana- A. Thiele, Pavel Pitule, James Hicks, Peter Kuhn)....Pages 243-264 Back Matter ....Pages 265-268