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