Molecular Diagnostics

3rd Edition - October 27, 2016
Editors: George P. Patrinos, Wilhelm Ansorge, Phillip B. Danielson
Language: English
Hardback ISBN:
9 7 8 - 0 - 1 2 - 8 0 2 9 7 1 - 8
eBook ISBN:
9 7 8 - 0 - 1 2 - 8 0 2 9 8 8 - 6

Molecular Diagnostics, Third Edition, focuses on the technologies and applications that professionals need to work in, develop, and manage a clinical diagnostic laborator… Read more

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Molecular Diagnostics, Third Edition, focuses on the technologies and applications that professionals need to work in, develop, and manage a clinical diagnostic laboratory. Each chapter contains an expert introduction to each subject that is next to technical details and many applications for molecular genetic testing that can be found in comprehensive reference lists at the end of each chapter.

Contents are divided into three parts, technologies, application of those technologies, and related issues. The first part is dedicated to the battery of the most widely used molecular pathology techniques. New chapters have been added, including the various new technologies involved in next-generation sequencing (mutation detection, gene expression, etc.), mass spectrometry, and protein-specific methodologies.

All revised chapters have been completely updated, to include not only technology innovations, but also novel diagnostic applications. As with previous editions, each of the chapters in this section includes a brief description of the technique followed by examples from the area of expertise from the selected contributor.

The second part of the book attempts to integrate previously analyzed technologies into the different aspects of molecular diagnostics, such as identification of genetically modified organisms, stem cells, pharmacogenomics, modern forensic science, molecular microbiology, and genetic diagnosis. Part three focuses on various everyday issues in a diagnostic laboratory, from genetic counseling and related ethical and psychological issues, to safety and quality management.

List of Contributors
Preface, Third Edition
Chapter 1. Molecular Diagnostics: Past, Present, and Future
- 1.1. Introduction
- 1.2. History of Molecular Diagnostics: Inventing the Wheel
- 1.3. The Post-Polymerase Chain Reaction Revolution
- 1.4. Molecular Diagnostics in the Post-Genomic Era
- 1.5. Future Perspectives: What Lies Beyond
- 1.6. Conclusions
Chapter 2. Describing DNA Variants (Mutation Nomenclature)
- 2.1. Introduction
- 2.2. History
- 2.3. Authorization
- 2.4. Definitions
- 2.5. Variant Descriptions
- 2.6. Mutalyzer
- 2.7. Concluding Remarks
Chapter 3. Low- and Medium-Throughput Variant Detection Methods: A Historical Perspective
- 3.1. Introduction
- 3.2. Genetic Screening Methods
- 3.3. Genetic Scanning Methods
- 3.4. Conclusions
Chapter 4. Quantitative Polymerase Chain Reaction
- 4.1. History of the Polymerase Chain Reaction
- 4.2. Principle of Real-Time Polymerase Chain Reaction
- 4.3. Real-Time Thermal Cyclers
- 4.4. How Data Are Obtained
- 4.5. How Data Are Quantified
- 4.6. Multiplex Quantitative Polymerase Chain Reaction
- 4.7. Applications of Quantitative Polymerase Chain Reaction and Reverse Transcriptase-Quantitative Polymerase Chain Reaction
- 4.8. Criteria for Optimizing Quantitative Polymerase Chain Reaction Assays
- 4.9. Conclusions
Chapter 5. Integrated Polymerase Chain Reaction Technologies (Sample-to-Answer Technologies)
- 5.1. Introduction
- 5.2. Commercial Sample-to-Answer Assay Systems
- 5.3. Clinical Applications: Performance for Infectious Pathogen Diagnostics
- 5.4. Forensic Applications: Performance for Human Identity Testing
- 5.5. Continuing Evolution of Sample-to-Answer Technologies
Chapter 6. High-Resolution Melting Curve Analysis for Molecular Diagnostics
- 6.1. Introduction to Melting Analysis
- 6.2. Genotyping of Known Variants by High-Resolution Melting
- 6.3. Variant Scanning by High-Resolution Melting
- 6.4. Specific Examples of High-Resolution Melting in Clinical Diagnostics
- 6.5. Other Applications of High-Resolution Melting in Molecular Diagnostics
- 6.6. Melting Curve Prediction and Assay Design Tools
- 6.7. Conclusions
Chapter 7. Molecular Techniques for DNA Methylation Studies
- 7.1. Introduction
- 7.2. Clinical Applications of DNA Methylation Analysis
- 7.3. Methods for DNA Methylation Analysis
- 7.4. Single-Cell DNA Methylation Analysis
- 7.5. Conclusions
Chapter 8. Perspectives for Future DNA Sequencing Techniques and Applications
- 8.1. Introduction
- 8.2. Commercially Available Analysis Platforms
- 8.3. Techniques/Systems in Development
- 8.4. Potential Future Techniques/Systems/Analysis Platforms
- 8.5. Perspectives for Future Applications and Diagnostics Techniques
- 8.6. Conclusions
Chapter 9. Advanced Personal Genome Sequencing as the Ultimate Diagnostic Test
- 9.1. Introduction
- 9.2. Advanced Whole-Genome Sequencing
- 9.3. What Is Needed to Implement This Vision of Genomic Precision Health Care Fully?
- 9.4. Conclusion
Chapter 10. Application of Padlock and Selector Probes in Molecular Medicine
- 10.1. Introduction
- 10.2. Padlock and Selector Probes
- 10.3. Application of Padlock and Molecular Inversion Probes for Genotyping
- 10.4. Biosensor Approaches Based on Rolling Circle–Amplified Padlock Probes
- 10.5. Application of Padlock Probes for Infectious Disease Diagnostics
- 10.6. Targeted Multiplex Copy Number Variation Analysis Using Selector Probes
- 10.7. High-Throughput Targeted Sequencing Using Selectors and Gap-Fill Padlock Probes
- 10.8. In Situ Nucleic Acid Detection Using Padlock Probes
- 10.9. Automation and Miniaturization of Padlock Probe/Rolling Circle Amplification Assays
- 10.10. Conclusions
Chapter 11. Advances in Microfluidics and Lab-on-a-Chip Technologies
- 11.1. Overview
- 11.2. Microfluidics for DNA Amplification and Analysis
- 11.3. Microfluidics for High-Resolution Melting Analysis
- 11.4. Microfluidics in Cytogenetics
- 11.5. Microfluidics for Protein Detection and Analysis
- 11.6. Microfluidic Sample Preparation
- 11.7. Microfluidics in Cell Sorting
- 11.8. Future of Microfluidics for Medical Diagnostics
Chapter 12. Protein Diagnostics by Proximity Ligation: Combining Multiple Recognition and DNA Amplification for Improved Protein Analyses
- 12.1. Introduction
- 12.2. Binding the Proteome
- 12.3. Current Affinity-Based Protein Detection Assays
- 12.4. Proximity-Dependent Nucleic Acid–Based Assays
- 12.5. Conclusion and Future Perspectives
Chapter 13. Application of Proteomics to Medical Diagnostics
- 13.1. Introduction
- 13.2. Clinical Impact and “Proteomics” Potential
- 13.3. Strategies for Mass Spectrometry–Based Proteomics: Discovery and Verification
- 13.4. Bioinformatics
- 13.5. Examples of Discovery and Verification Proteomics
- 13.6. Examples of Protein-Based Diagnostics Assays
- 13.7. Challenges in Clinical Proteomics
- 13.8. Future Advances and Concluding Remarks
Chapter 14. Molecular Cytogenetics in Molecular Diagnostics
- 14.1. Introduction
- 14.2. From Conventional to Molecular Cytogenetics
- 14.3. Fluorescence In Situ Hybridization
- 14.4. Basic Technical Elements and Materials
- 14.5. Types of Fluorescence In Situ Hybridization Probes and Fluorescence In Situ Hybridization Approaches for Metaphase and Interphase Fluorescence In situ Hybridization
- 14.6. Multicolor Fluorescence In Situ Hybridization Screening Assays
- 14.7. Multicolor Whole-Metaphase Scanning Techniques
- 14.8. Multicolor Chromosome Banding Techniques
- 14.9. Whole-Genome Scanning and Comparative Genomic Hybridization
- 14.10. Array-Based Techniques (Microarray)
- 14.11. Conclusions and Future Perspectives
- Glossary
Chapter 15. Cytogenomics of Solid Tumors by Next-Generation Sequencing: A Clinical Perspective
- 15.1. A Tumor Presents
- 15.2. From Microscopic Examination to Molecular Cytogenomics
- 15.3. The Promise of Liquid Biopsy for Cancer Diagnostics
- 15.4. Cytogenomic Applications
- 15.5. Implementation of Cytogenomics in the Clinic
- 15.6. Bioinformatics and Data Analysis
- 15.7. Concluding Remarks
Chapter 16. Pharmacogenomics in Clinical Care and Drug Discovery
- 16.1. Introduction
- 16.2. Pharmacogenetics Versus Pharmacogenomics
- 16.3. History of Pharmacogenomics
- 16.4. Analytical Methods in Pharmacogenomics
- 16.5. Pharmacogenomics in Clinical Settings
- 16.6. Population Differences in Pharmacogenomics
- 16.7. Complex Phenotypes
- 16.8. Pharmacogenomics and Regulatory Agencies
- 16.9. Pharmacogenomics in Drug Development
- 16.10. Useful Resources in Pharmacogenomics
- 16.11. New Trends in Pharmacogenomics
- 16.12. Ethical Implications
- 16.13. Public Health Pharmacogenomics
- 16.14. Conclusions and Future Perspectives
Chapter 17. Nutrigenomics: Integrating Genomic Approaches Into Nutrition Research
- 17.1. Introduction
- 17.2. Nature of Genetic Variation
- 17.3. Nutritional Epidemiology
- 17.4. Experimental Models
- 17.5. Defining the Phenotype
- 17.6. Integrating Complex Data Sets: Data Management, Bioinformatics, and Statistics
- 17.7. Conclusions
Chapter 18. DNA Microarrays and Genetic Testing
- 18.1. Introduction
- 18.2. DNA Microarrays
- 18.3. New Developments in DNA Microarrays and Genetic Testing
Chapter 19. Bioinformatics Tools for Data Analysis
- 19.1. Introduction
- 19.2. Next-Generation Sequencing Pipelines
- 19.3. Molecular Pathway Analysis: Why and What?
- 19.4. Conclusions
Chapter 20. Genomic Databases: Emerging Tools for Molecular Diagnostics
- 20.1. Introduction
- 20.2. Historical Overview of Genetic Databases
- 20.3. Models for Database Management
- 20.4. Mutation Database Types
- 20.5. Locus-Specific Databases in Molecular Genetic Testing
- 20.6. National/Ethnic Mutation Databases: Archiving the Genomic Basis of Human Disorders on a Population Basis
- 20.7. Database Management Systems for Locus-Specific Databases and National/Ethnic Mutation Databases
- 20.8. Incentivizing Data Sharing: The Microattribution Approach
- 20.9. Future Challenges
- 20.10. Conclusions
Chapter 21. Molecular Diagnostic Applications in Forensic Science
- 21.1. Introduction
- 21.2. Genetic Markers Commonly Used for Forensic Analysis
- 21.3. DNA Extraction Methodologies
- 21.4. DNA Quantitation
- 21.5. Capillary Electrophoresis and Data Interpretation
- 21.6. Statistical Calculations
- 21.7. Next Generation of Forensic DNA Technologies
- 21.8. Conclusions
Chapter 22. New Perspectives in Mass Disaster Victim Identification Assisted by DNA Typing and Forensic Genomics
- 22.1. Introduction
- 22.2. Classification of Mass Fatalities and Diverse Scenarios for Human Remains Retrieval
- 22.3. Conventional Identification Criteria Routinely Used for Human Identification
- 22.4. Criteria for the Preservation of Remains
- 22.5. DNA Polymorphisms Used for Tracing Kinship Between Fragmentary Human Remains and the Relatives Claiming Them
- 22.6. Challenges Concerning DNA Degradation and Contamination
- 22.7. Criteria Evolution and Technical Approaches Applied to DNA-Based Victim Identification in Mass Disasters From the Early 1990s to Date
- 22.8. Description of Analyzed Cases
- 22.9. From Forensic Genetics to Forensic Genomics: The Change of a Paradigm Driven by Technology
- 22.10. Future Perspectives
Chapter 23. Preimplantation Genetic Diagnosis
- 23.1. Introduction
- 23.2. Assisted Reproductive Technology and Biopsy
- 23.3. Preimplantation Genetic Diagnosis for Monogenic Disorders
- 23.4. Preimplantation Genetic Diagnosis for Chromosomal Aberrations
- 23.5. Emerging Technologies
- 23.6. Clinical Outcome of Preimplantation Genetic Diagnosis
- 23.7. Accuracy and Quality Control
- 23.8. Conclusions and Future Perspectives
- Web Resources
Chapter 24. Noninvasive Cell-Free DNA Prenatal Testing for Fetal Aneuploidy in Maternal Blood
- 24.1. Introduction
- 24.2. Established Prenatal Screening and Diagnosis Practices
- 24.3. Historical Background of Noninvasive Prenatal Testing
- 24.4. Origin of Cell-Free Fetal DNA
- 24.5. Noninvasive Prenatal Testing Methodologies
- 24.6. Biological and Technical Factors That Affect Noninvasive Prenatal Testing Results
- 24.7. Noninvasive Prenatal Testing in Clinical Trials
- 24.8. Noninvasive Prenatal Testing in the Clinical Setting
- 24.9. Counseling and Ethical Issues
- 24.10. Future Applications of Noninvasive Prenatal Testing
- 24.11. Conclusions
Chapter 25. Genetic Testing and Psychology
- 25.1. Introduction
- 25.2. Getting to the Test: Awareness, Access, and Advertising
- 25.3. Individual Factors Influencing the Utilization of Genetic Testing
- 25.4. Getting the Genetic Test Results: Personal Impact and Professional Communication
- 25.5. Family Communication
- 25.6. Future Challenges: Complexity and Diversity
Chapter 26. Genomic Medicine in Developing Countries and Resource-Limited Environments
- 26.1. Introduction
- 26.2. Conclusions and Future Perspectives
Chapter 27. Public Understanding of Genetic Testing and Obstacles to Genetics Literacy
- 27.1. Genetics Literacy and the Public Understanding of Genetic Testing
- 27.2. Obstacles to Genetics Literacy and How These Might Be Overcome
- 27.3. Conclusions and Suggestions
Chapter 28. Safety and the Biorepository
- 28.1. Introduction
- 28.2. Understanding Regulatory and Other Safety Issues Relevant to Biorepositories
- 28.3. Individuals Involved in Oversight of a Biorepository
- 28.4. Safety Training/Employee Education in a Biorepository
- 28.5. Biorepository Safety Areas
- 28.6. Conclusions
Chapter 29. Quality Assurance in Genetic Laboratories
- 29.1. Introduction
- 29.2. International Standards
- 29.3. Accreditation and Certification
- 29.4. Elements of a Quality Management System
- 29.5. Quality Control
- 29.6. Quality Assessment
- 29.7. Diagnostic Validation
- 29.8. Quality Improvement
- 29.9. Conclusions
Index

George P. Patrinos

George P. Patrinos is a Professor of Pharmacogenomics and Pharmaceutical Biotechnology in the University of Patras (Greece), Department of Pharmacy, and Head of Division of Pharmacology and Biosciences of the same department and holds adjunct Full Professorships at Erasmus MC, Faculty of Medicine, and Health Sciences, Rotterdam (the Netherlands), and the United Arab Emirates University, College of Medicine, Department of Genetics and Genomics, Al-Ain (UAE). Also, from 2018 until the end of 2024, he was Chair of the Global Genomic Medicine Collaborative (G2MC). He served 12.5 years as a full member and Greece’s National representative in the CHMP Pharmacogenomics Working Party of the European Medicines Agency (EMA). George has more than 340 publications in peer-reviewed scientific journals, some of them in leading scientific journals, such as The Lancet, Nature Genetics, Nature Reviews Genetic, Nucleic Acids Research, Genes & Development. He has also coauthored and coedited more than 15 textbooks, among which the renowned textbook Molecular Diagnostics, published by Academic Press, now in its 3rd edition, while he is the editor of Translational and Applied Genomics book series, published by Elsevier. Furthermore, he serves as the Editor-In-Chief of the prestigious Pharmacogenomics Journal (TPJ), published by Nature Publishing Group, Associate Editor, and member of the editorial board of several scientific journals, and advisory and evaluation committees. Apart from that, George is the main coorganizer of the Golden Helix Conferences, an international meeting series on Pharmacogenomics and Genomic Medicine with more than 50 conferences organized in more than 25 countries worldwide.

Affiliations and expertise

Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece; Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates; Zayed Center of Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates

Wilhelm Ansorge

Prof. Dr. Wilhelm Ansorge is a Senior Research Scientist and coordinator of the Biochemical Instrumentation Programme at the European Molecular Biology Laboratory in Heidelberg, Germany. His research interests include the development of the first complete Human Genome microarray, with numerous applications in gene expression studies and high-throughput Molecular Diagnostics.

Affiliations and expertise

Visiting Professor, Ecole Polytechnique Federale Lausanne, Switzerland

Phillip B. Danielson

Phillip B. Danielson is Professor of Molecular Biology at the University of Denver and is the Science Advisor for the National Law Enforcement and Corrections Technology Center - Rocky Mountain Region. He received research training at the University of Tokyo’s Department of Biochemistry and Biophysics, the University of Colorado at Boulder’s Department of Molecular, Cellular and Developmental Biology and the University of Denver’s Department of Biological Sciences. He currently oversees a forensic research and development program, serves as a forensic DNA consultant and also teaches courses in Forensic Science, Infectious Human Disease, Immunology and Molecular Biology. Danielson’s primary research focus is in the field of forensic genetics emphasizing the analysis and resolution of mitochondrial DNA mixtures and the use of comparative proteomics to facilitate the identification of biological stains. Together with the Colorado District Attorneys Council, the Office of the Alternate Defense Counsel and State Crime Laboratories, he has also developed training programs on the identification, collection and use of DNA evidence in criminal investigations. His work is funded by the National Institute of Justice and has been featured in academic and professional journals as well as the popular press including the Proceedings of the National Academy of Sciences, The Scientist magazine, USA Today and Law Enforcement Technology magazine. Danielson also has 12+ years of experience in the development of instructional workshops to familiarize precollege instructors and students with many aspects of modern biology including the use of inquiry-driven student laboratory exercises. He has been involved in a diversity of science education outreach activities through the University of Denver’s Life Sciences Curriculum Center, the BSCS Keys to Science Program, the Leaders in Learning: Goals 2000 Program, the High School Human Genome Project and the NSF’s Math Science Partnership Program.

Affiliations and expertise

Professor, Department of Biological Sciences, Division of Natural Sciences & Mathematics, University of Denver, CO, USA

Life Sciences

Physical Sciences & Engineering

Social Sciences & Humanities

Health

Molecular Diagnostics

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George P. Patrinos

Wilhelm Ansorge

Phillip B. Danielson