Molecular surgical pathology

Molecular surgical pathology / Liang Cheng, George J. Netto, John N. Eble, editors.

Since the first edition of this book in 2012, the field of molecular pathology has expanded exponentially. The advent of complete cancer genome sequencing, new diagnostic molecular tests, and biomarkers for targeted therapy and immunotherapy have demonstrated the importance of molecular tools both i...

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Bibliographic Details
Other Authors: Cheng, Liang, Netto, George J., Eble, John N.
Format: eBook
Language:English
Published: Cham : Springer, 2023.
Edition:2nd ed.
Subjects:
Pathology, Molecular.
Pathology, Surgical.
Oncology.
Pathology.
Genetics.
pathology.
genetics.
Online Access:Click for online access
Table of Contents:
  • Intro
  • Preface
  • Contents
  • Contributors
  • 1: Molecular Techniques/Molecular Diagnostics for Surgical Pathologists: An Overview
  • Introduction
  • Roles for Molecular Surgical Pathology
  • Background Information for Molecular Genomics
  • Background on Genome Organization
  • DNA Sequence Variation
  • Background for RNA Analysis
  • Overview of Molecular Methods
  • Sample Preparation
  • Sample Types
  • Sample Adequacy
  • Fixatives
  • DNA/RNA Extraction Basic Steps
  • Preparation of DNA from Formalin Fixed Paraffin Embedded Tissue
  • DNA Methylation
  • RNA Extraction
  • Quality Assessment of DNA and RNA
  • Cytogenetics
  • Background Information for Cytogenetics
  • Classes of Pathogenic Cytogenetic Variation
  • Cytogenetic Methods
  • Karyotyping
  • Fluorescent In Situ Hybridization
  • Microarrays
  • Molecular Diagnostics Basic Methods
  • DNA/RNA Electrophoresis
  • The Art of Detection
  • Target Amplification Versus Signal Amplification
  • Methods: PCR
  • Principles of PCR
  • Real-Time PCR
  • PCR Contamination
  • Real-Time PCR Formats
  • SNV Detection by PCR
  • Methods: Digital Droplet PCR (ddPCR)
  • Methods: Rolling Circle Amplification (RCA)
  • Methods: Hybridization Chain Reaction (HCR)
  • Methods: Branched DNA (bDNA)
  • Methods: Whole-Genome Amplification (WGA)
  • Sequencing
  • General Remarks
  • Methods: Sequencing/Sanger Sequencing
  • Second-Generation Sequencing
  • Second Generation Sequencing Platforms
  • Outline of a Representative Illumina Protocol
  • Outline of a Representative Thermo-Fisher (Ion Torrent) Protocol
  • Third-Generation Sequencing
  • PacBio
  • Oxford Nanoporetech
  • Other Applications of NGS
  • Bioinformatics
  • Single-Cell 'Omics'
  • General Remarks
  • Single-Cell Protocols
  • Spatial 'Omics: Not Quite the Final Frontier
  • General Remarks
  • In Situ Hybridization (ISH)
  • Single Molecule FISH (smFISH)
  • Representative Method: SeqFISH+
  • Representative Method: MERFISH
  • In Situ Sequencing
  • In Situ Capture-Ex Situ Sequencing (Generic)
  • Representative Implementation: GeoMx Digital Space Profiler
  • Representative Implementation: Seq-Scope Illumina
  • Representative Implementation: HDST
  • Representative Implementation: Visium (10× Genomics)
  • In Situ Genomic (DNA) Sequencing Extended by Ex Situ Sequencing
  • Analysis
  • Achievements of Spatial Genomics
  • Future Directions/Predictions
  • Further Reading
  • 2: Bioinformatics, Digital Pathology, and Computational Pathology for Surgical Pathologists
  • Introduction
  • Bioinformatics, a Distinct Field in Pathology and Where Are We Now
  • Pathology Bioinformaticians and Their Role
  • Specialized Training in Bioinformatics
  • Definitions and Terminologies Related to Bioinformatics and Computational Pathology
  • Annotation
  • Artificial Intelligence (AI)
  • Black Box/Glass Box
  • Cloud Computing
  • Computational Pathology (CPATH)
  • Convolutional Neural Network (CNN)
  • Deep Learning
  • Data Augmentation

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