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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.
List of contents
Amplicon-based Targeted Next Generation Sequencing of Formalin Fixed Paraffin Embedded Tissue.- Library preparation using FFPE-derived Tumor DNA for High Throughput Hybridization-based Targeted or Exome Sequencing.- Bioinformatics Basics for High Throughput Hybridization-based Targeted DNA Sequencing From FFPE-Derived Tumor Specimens: From Reads to Variants.- Annotation of Variant Data from High Throughput DNA Sequencing from Tumor Specimens: Filtering Strategies to Identify Driver Mutations.- Biological Interpretation of Complex Genomic Data.- Clinical Validation of Targeted Solid Tumor Profiling.- Whole Genome Single Nucleotide Polymorphism Microarray for Copy Number and Loss of Heterozygosity Analysis in Tumors.- Genome-Wide Copy Number Variation Detection using NGS: Data Analysis and Interpretation.- Overview of Fusion Detection Strategies Using Next Generation Sequencing.- Clinical Application of Fusion Gene Detection Using Next-generation Sequencing and the NanoString Technology.- Pipeline for Integrated Microarray Expression Normalization Toolkit (PIMENTo) for Tumor Microarray Profiling Experiment.- Molecular Profiling of RNA Tumors using High Throughput RNA Sequencing: Overview of Library Preparation Methods.- Molecular Profiling of RNA Tumors using High Throughput RNA Sequencing: From Raw Data to Systems Level Analyses.- Methylation Analysis using Microarrays: Analysis and Interpretation.- High-Throughput Targeted Repeat Element Bisulfite Sequencing (HT-TREBS).- A Pipeline for ctDNA Detection Following Primary Tumor Profiling Using A Cancer-related Gene Sequencing Panel.- Single-cell Analysis of Circulating Tumor Cells.
Summary
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.
