Precision Cancer Medicine: Role of the Pathologist

Foreword
Preface
Contents
Part I: The Evolution of Pathology and Precision Medicine
	1: Introduction: From ‘Tissue Diagnosis’ to Biomarkers
		1.1	 A Brief History of Pathology: The Progression to Precision Cancer Medicine
			1.1.1	 Cure as a Generic Rationale for Cancer Treatment
		1.2	 The Microscope Invents Pathology and Pathologists
		1.3	 Seeking a Cure for Non-Symptomatic Early Stage Cancer; Cancer Screening
		1.4	 Development of Targeted Therapies
		References
	2: The Advent of Biomarker Testing
		2.1	 Biomarkers in Medicine and Cancer
			2.1.1	 Biomarkers in Cancer
		2.2	 Basis of Prediction of Response to Therapy
		2.3	 Role of Pathology and the Pathologist in the Advent of Precision Cancer Medicine
			2.3.1	 New Types of Tests: Companion and Complementary Diagnostics
			2.3.2	 Evolution to Revolution: The Changing Role for Pathology
		2.4	 The Development Pathway for Targeted Therapeutics and Precision Diagnostics
		References
	3: The Practical Challenges for Pathology: Multiple Rapidly Evolving Methods
		3.1	 Role in the Development Pathway for Targeted Therapeutics and Precision Diagnostics
			3.1.1	 Pre-Clinical Research
		3.2	 Conversion of IHC from a ‘Qualitative’ Stain; to a Quantitative Assay
		3.3	 ISH and Multiplex Immunofluorescence Methods for Multiple Biomarkers
		3.4	 FFPE Extraction Based Molecular Methods, PCR, NGS and Proteomics
		3.5	 Going Digital
		3.6	 Virtual Biomarkers—Molecular Morphology in the Digital Dimension
		3.7	 Total Integrative Pathology; the Big Data Problem
		3.8	 Part I as an entry to Parts II, III & IV
		References
Part II: Precision Medicine Demands Precision Pathology
	4: Evolution of the Total Test Approach to Tissue Based Pathological Analysis
		4.1	 Introduction: The Microscope ‘Invented’ the Pathologist
			4.1.1	 Re-Invention
			4.1.2	 Morphology Plus
		4.2	 IHC: A Stain ‘Repurposed’ as an Assay
		4.3	 In-Situ Hybridization
		4.4	 Molecular Extraction Based Methods; Abandoning Morphology?
		4.5	 Emerging Methods in Microscopy and Microimaging
		4.6	 The Total Test: Pre-Analytical, Analytical and Post-Analytical Phases (Table 4.3)
		References
	5: Pre-Analytic Phase: Test Selection; Specimen Acquisition and Handling
		5.1	 The Pre-Analytical Phase Defined
		5.2	 Test Selection—‘Fit for Purpose’
		5.3	 Digital Pre-Analytic Quality
		5.4	 Turn-Around Time (TAT); Cost; Reimbursement Issues
		References
	6: Pre-Analytic Phase: Specimen Type and Acquisition
		6.1	 The Specimen
		6.2	 Excision Biopsy and Surgical Resection
		6.3	 FNA, Core Needle Biopsy
		6.4	 Cytologic Preparations
		6.5	 Liquid Biopsy
		References
	7: Pre-Analytical Phase: Biopsy/Tissue Handling and Processing
		7.1	 Pre-Analytical Variables (Table 7.1)
		7.2	 Transport, Warm and Cold Ischemia
		7.3	 Fixation and Paraffin Embedding (FFPE)
			7.3.1	 Total Fixation Time
			7.3.2	 Nature of the Antigen
			7.3.3	 Fixation Time in Relation to Effectiveness of Different Antibodies
			7.3.4	 Antigen Retrieval (in Analytic Phase)
			7.3.5	 Fixation of Tissues Employed for Validation and Controls
		7.4	 Processing
		7.5	 Tissue Sectioning and Storage
			7.5.1	 Sectioning: Thickness
			7.5.2	 Glass Slides
			7.5.3	 Section Storage Time: Cut Slide Stability
		References
	8: Analytical Phase: Protocol and Antigen Retrieval
		8.1	 The Analytical Phase Defined
		8.2	 Deparaffinization and Optional Blocking Procedures
			8.2.1	 Blocking Steps
		8.3	 Antigen Retrieval (AR) or Heat Induced Epitope Retrieval (HIER)
		References
	9: Analytical Phase: Principles for Immunohistochemistry (IHC)
		9.1	 Reagents and Protocol for Biomarker Labelling; Selection and Validation
		9.2	 Lab Developed Tests (LDTs)—Manual and Automated
			9.2.1	 Manual IHC Stains
			9.2.2	 Automated IHC Stains
		9.3	 Ready to Use IHC Tests (RTUs)
		9.4	 Approved IHC Biomarker Assays (FDA, CE Marked)
		9.5	 Detection Systems and Amplification
		9.6	 Introduction to Fit for Purpose Controls: Required Characteristics
			9.6.1	 The Six Required Characteristics of Controls—Reference Standards
		9.7	 FDA Classification of IHC Tests: Classes I, II and III
		References
	10: Analytical Phase: Current Controls; Fit for Purpose Selection and Validation
		10.1	 Guides for Selection of Control Materials
		10.2	 Negative Controls
			10.2.1	 Negative Reagent Controls (See Table 10.2)
			10.2.2	 Negative Tissue Controls: External and Internal
		10.3	 Positive Controls: External and Internal
			10.3.1	 Positive External Tissue Controls
			10.3.2	 Positive Internal Tissue Controls
		10.4	 Tissue Micro-Arrays (TMAs): ‘Sausages’ and Tumor Tissue Banks
		References
	11: Analytical Phase: Alternative and New Control Systems
		11.1	 Alternative and New Control Systems
		11.2	 Cell Lines
		11.3	 Faux or Pseudo-Tissues
		11.4	 Protein Spots
		11.5	 Internal Controls and Internal Reference Standards
		11.6	 Quantifiable Internal Reference Standards (QIRS)
		11.7	 Quantitative In Situ Proteomics (QISP)
		References
	12: Post-Analytic Phase: Interpretation, Scoring and Reporting of Biopsy Results
		12.1	 Assessment of Controls
		12.2	 Sensitivity and Specificity
			12.2.1	 Positive and Negative Results in Relation to Controls
			12.2.2	 Sensitivity
			12.2.3	 Specificity
		12.3	 Verification and Validation IHC Biomarker Assays
			12.3.1	 Verification
			12.3.2	 Validation
		12.4	 Practical Issues in Validation
		12.5	 Validation of Pre-Analytical and Analytical Phases: LDTs, RTUs and Approved Biomarker Tests
		12.6	 Quality Management Systems (QMS): Quality Assurance (QA), Quality Control (QC)
			12.6.1	 External Quality Assessment and Proficiency Testing
		References
	13: Description and Interpretation of Results; The Pathology Report
		13.1	 Content and Organization of Report
			13.1.1	 Descriptive
			13.1.2	 Integrated and Standardized Reporting
		13.2	 Scoring; Including Validation of Scoring Method
		13.3	 Scoring Systems
		13.4	 Percentage Based Scores
			13.4.1	 Conversion to Positive and Negative Results
			13.4.2	 Percentage Combined with Intensity and/or Pattern
			13.4.3	 Concordance Training
			13.4.4	 Consensus or Ring Studies
		13.5	 Addition of Immune Cell Assessment
			13.5.1	 Immune Scoring; Immunoscore
			13.5.2	 Composite or Proportion Scores
			13.5.3	 Field of View (FOV) Selection Errors
		13.6	 Phenotypic Cell Identification and Scoring: Multiplex Methods
		13.7	 Digital Computerized Scoring Algorithms
		References
	14: Immunofluorescence, In Situ Hybridization and Alternative Forms of ‘Labeled’ Microscopy
		14.1	 Labeled Microscopy Methods
		14.2	 Immunofluorescence—IF
		14.3	 In Situ Hybridization—ISH
		14.4	 RNA Scope
		14.5	 Advanced Multiplex Microscopy and Other Emerging Methods
			14.5.1	 Brightfield (IHC) Versus Immunofluorescence (IF) Methods
			14.5.2	 Multiplex Digital IF
				14.5.2.1	 The Sequential Method
				14.5.2.2	 The Simultaneous Method
		14.6	 MIBI Microscopy (Multiplex Ion Beam Imaging)
		14.7	 Raman Microscopy (Vibrational) Spectroscopy (RMS)
		14.8	 Part II—Summary
		References
Part III: Role of the Pathologist in Predictive Biomarker Analysis
	15: Implementation of Precision Cancer Diagnostic Test
		15.1	 Introduction to Role of the Pathologist in Predictive Biomarker Analysis
		15.2	 Implementation of Predictive Biomarker Tests
		15.3	 Analytical Validation
			15.3.1	 Repeatability
			15.3.2	 Intermediate Precision
			15.3.3	 Role of the Pathologist in Repeatability and Intermediate Studies
			15.3.4	 Reproducibility
			15.3.5	 Total Test Reproducibility
			15.3.6	 Role of the Pathologist in Assay Reproducibility Studies
		15.4	 Clinical Validation
			15.4.1	 The Role of the Pathologist
		15.5	 Clinical Utility
			15.5.1	 The Role of the Pathologist
		15.6	 Summary & Future Needs & Trends
		References
	16: Role of Pathologist in Precision Cancer Diagnosis
		16.1	 Introduction
		16.2	 Regulatory Body and Expert Opinion Based Recommendations
		16.3	 Role of Pathologist in Assurance of Good Diagnostic Practice
		16.4	 Internal Quality Assurance of Pre-Analysis Phase
			16.4.1	 Potential Errors Due to Inadequate Tissue Preservation
				16.4.1.1	 Potential Causes of False Negative or Weak Results
			16.4.2	 Adequacy and Representativeness of Biopsy Material
		16.5	 Internal Quality Assurance of Analysis Phase
			16.5.1	 Pre-Analytic Phase Exclusion Factors
			16.5.2	 Analytic Phase Exclusion Factors
			16.5.3	 Evaluation of the Quality of Biopsy Material
			16.5.4	 Evaluation of Distribution and Quantity of Tumour Tissue
			16.5.5	 Assessment of Quality of Assay Performance
			16.5.6	 Selection and Use of Control
		16.6	 Quality Assurance of Post-Analytic Phase
			16.6.1	 Post Analysis Factors Influencing Quality of Biomarker Assessment
			16.6.2	 Indication Specific Interpretation, Scoring and Reporting
			16.6.3	 Assessment of Appropriateness and Completeness of Biomarker Analysis
			16.6.4	 Evaluation of Accuracy of the Results
		16.7	 Summary and Future Needs & Trends
		References
	17: Role of Pathologist in Precision Molecular and Digital Image Analyses
		17.1	 Introduction
		17.2	 Role of Pathologist in Morpho-Molecular Diagnosis of Cancer
		17.3	 Role of Pathologist in Molecular Analysis of Cancer
		17.4	 Role of Pathologist in Guidance of Cancer Molecular Profiling
		17.5	 Role of Pathologist in Analysis of Tumour Heterogeneity
		17.6	 Role of Pathologist in Analysis of Tumour Micro-Environment (TME)
		17.7	 Future Role of Pathologist in Emerging Morpho-Molecular Cancer Diagnostics
		References
Part IV: Digital and Computational Pathology and Their Role in Precision Oncology
	18: Introduction to Digital and Computational Pathology
		References
	19: AI in the Pre-Analytical Phase
		19.1	 The Workflow Design
		19.2	 Sample and Quality Management
		19.3	 Quality Control and Validation
		19.4	 CIS, LIS, DIS and PACS
		19.5	 Workflow Integration, Connectivity and Interoperability
		References
	20: AI in the Analytical Phase
		20.1	 Overcoming Variabilities
		20.2	 Telepathology
		20.3	 Standardization, Harmonization and Concordance
		20.4	 Scanning and Whole Slide Imaging
		20.5	 Image Analysis
		20.6	 Advanced Microscopy
		References
	21: AI in the Post-Analytical Phase
		21.1	 Dealing with Complexity
		21.2	 Artificial Intelligence, Machine Learning and Topology
		21.3	 Computational Pathology
		21.4	 The Science of Data or Data Science
		21.5	 Algebraic Pathology
		21.6	 Encoded Pathology
		21.7	 Disease Modelling and Simulation
		References
	22: AI in the Decision Phase
		22.1	 Examples of Clinical Utility
		22.2	 Prognosis of Cancer
		22.3	 Predicting Treatment Outcomes
		22.4	 Clinical Decision Support Through Applications
			22.4.1 Colorectal Cancer
			22.4.2 Lung Cancer
			22.4.3 Melanocytic Lesions
			22.4.4 Lymphoid Aggregates
			22.4.5 Bladder Cancer
			22.4.6 Renal Biopsies
			22.4.7 Breast Cancer
			22.4.8 Prostate Cancer
			22.4.9 Thyroid Cancer
			22.4.10 Cytology
			22.4.11 Biobanking
		22.5	 Opportunity for Discovery of Novel Biomarker
		References
Index