Clinical Genomics
A Guide to Clinical Next Generation Sequencing
- 2nd Edition - October 20, 2025
- Editors: Shashikant Kulkarni, Somak Roy
- Language: English
- Paperback ISBN:9 7 8 - 0 - 3 2 3 - 9 0 0 2 4 - 9
- eBook ISBN:9 7 8 - 0 - 3 2 3 - 9 1 5 6 3 - 2
Clinical Genomics, Second Edition is a comprehensive, practical reference [AN1] designed specifically for laboratory directors, clinical medical directors, and genomic medici… Read more
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Clinical Genomics, Second Edition is a comprehensive, practical reference [AN1] designed specifically for laboratory directors, clinical medical directors, and genomic medicine professionals. Edited by renowned genomic pathology leaders Kulkarni and Roy, this updated edition offers clear guidance on the current technical, bioinformatic, clinical, regulatory, and reimbursement considerations involved in implementing next-generation sequencing technologies within clinical molecular diagnostic laboratories.
Structured for ease of reference, this book covers targeted gene sequencing methods, whole exome/genome approaches, emerging technologies such as long-read sequencing, and critical considerations for assay validation. Detailed sections address bioinformatics workflows, variant detection and interpretation methodologies, integration with clinical informatics systems, and essential IT infrastructure, including cloud-based solutions.
This book also thoroughly addresses practical topics essential to laboratory management, such as regulatory compliance, ethical frameworks, billing strategies, and reimbursement paradigms, helping directors navigate the evolving landscape of genomic diagnostics.
Structured for ease of reference, this book covers targeted gene sequencing methods, whole exome/genome approaches, emerging technologies such as long-read sequencing, and critical considerations for assay validation. Detailed sections address bioinformatics workflows, variant detection and interpretation methodologies, integration with clinical informatics systems, and essential IT infrastructure, including cloud-based solutions.
This book also thoroughly addresses practical topics essential to laboratory management, such as regulatory compliance, ethical frameworks, billing strategies, and reimbursement paradigms, helping directors navigate the evolving landscape of genomic diagnostics.
• Technical guidance: In-depth overview of sequencing platforms, chemistries, targeted capture methods, RNA sequencing, and methylome analysis for informed assay design and validation
• Bioinformatics workflows: Practical approaches for implementing pipelines to accurately detect and interpret genomic variants, structural changes, and complex genomic alterations
• Clinical implementation: Real-world applications for both constitutional and somatic disorders, including cancer diagnostics and precision medicine strategies
• Regulatory and ethical insights: Current regulatory requirements, ethical considerations, legal implications, and genomic reference standards pertinent to clinical practice.
• Operational and financial considerations: Guidance on billing, reimbursement, and operational integration of genomic medicine into clinical practice and electronic health records
• Bioinformatics workflows: Practical approaches for implementing pipelines to accurately detect and interpret genomic variants, structural changes, and complex genomic alterations
• Clinical implementation: Real-world applications for both constitutional and somatic disorders, including cancer diagnostics and precision medicine strategies
• Regulatory and ethical insights: Current regulatory requirements, ethical considerations, legal implications, and genomic reference standards pertinent to clinical practice.
• Operational and financial considerations: Guidance on billing, reimbursement, and operational integration of genomic medicine into clinical practice and electronic health records
Clinical Genomicists, Molecular Pathologists, Molecular Geneticists, Clinical Cytogeneticists, Clinical Geneticists, Primary Care Physicians (including Oncologists, Pediatricians, Neurologists, Cardiologists, and Neonatologists), and Genetic Counselors, Bioinformaticians, clinical informaticians, software developers involved with supporting clinical molecular laboratories, molecular laboratory technologists, and molecular pathology/molecular genetics trainees
Section I: Methods
1. Overview of Technical Aspects and Chemistries of Next-Generation Sequencing
2. Clinical Genome Sequencing
3. Targeted Hybrid Capture Methods
4. Amplification-Based Methods
5. Emerging DNA Sequencing Technologies
6. RNA-Sequencing and Methylome Analysis
Section II: Bioinformatics
7. Base Calling, Read Mapping, and Coverage Analysis
8. Single Nucleotide Variant Detection Using Next Generation Sequencing
9. Insertions and Deletions (Indels)
10. Translocation Detection Using Next-Generation Sequencing
11. Structural Variant Detection
12. The Human Reference Genome
Section III: Clinical Informatics and IT Infrastructure
13. Data Storage
14. Data Analytics – Platforms and Technologies
15. Genomic Data Security and Privacy
16. Cloud Computing
17. Clinical NGS IT infrastructure implementation and validation
Section IV: Interpretation
18. Reference Databases for Disease Associations
19. Reporting of Clinical Genomics Test Results
20. Reporting Software
21. Constitutional Diseases: Amplification-Based Next-Generation Sequencing
22. Targeted Hybrid Capture for Inherited Disease Panels
23. Constitutional Disorders: Whole Exome and Whole Genome Sequencing
24. Somatic Diseases (Cancer): Amplification-Based Next-Generation Sequencing
25. Targeted Hybrid-Capture for Somatic Mutation Detection in the Clinic
26. Somatic Diseases (Cancer): Whole Exome and Whole Genome Sequencing
Section V: Regulation, Reimbursement, and Legal Issues
27. Assay Validation
28. Regulatory Considerations Related to Clinical Next Generation Sequencing
29. Genomic Reference Materials for Clinical Applications
30. Ethical Challenges to Next-Generation Sequencing
31. Legal Issues
32. Billing and Reimbursement Index
1. Overview of Technical Aspects and Chemistries of Next-Generation Sequencing
2. Clinical Genome Sequencing
3. Targeted Hybrid Capture Methods
4. Amplification-Based Methods
5. Emerging DNA Sequencing Technologies
6. RNA-Sequencing and Methylome Analysis
Section II: Bioinformatics
7. Base Calling, Read Mapping, and Coverage Analysis
8. Single Nucleotide Variant Detection Using Next Generation Sequencing
9. Insertions and Deletions (Indels)
10. Translocation Detection Using Next-Generation Sequencing
11. Structural Variant Detection
12. The Human Reference Genome
Section III: Clinical Informatics and IT Infrastructure
13. Data Storage
14. Data Analytics – Platforms and Technologies
15. Genomic Data Security and Privacy
16. Cloud Computing
17. Clinical NGS IT infrastructure implementation and validation
Section IV: Interpretation
18. Reference Databases for Disease Associations
19. Reporting of Clinical Genomics Test Results
20. Reporting Software
21. Constitutional Diseases: Amplification-Based Next-Generation Sequencing
22. Targeted Hybrid Capture for Inherited Disease Panels
23. Constitutional Disorders: Whole Exome and Whole Genome Sequencing
24. Somatic Diseases (Cancer): Amplification-Based Next-Generation Sequencing
25. Targeted Hybrid-Capture for Somatic Mutation Detection in the Clinic
26. Somatic Diseases (Cancer): Whole Exome and Whole Genome Sequencing
Section V: Regulation, Reimbursement, and Legal Issues
27. Assay Validation
28. Regulatory Considerations Related to Clinical Next Generation Sequencing
29. Genomic Reference Materials for Clinical Applications
30. Ethical Challenges to Next-Generation Sequencing
31. Legal Issues
32. Billing and Reimbursement Index
- Edition: 2
- Published: October 20, 2025
- Language: English
SK
Shashikant Kulkarni
Dr. Shashikant Kulkarni is the Head of Clinical Genomics, Genomics and Pathology Services and also the Director of Cytogenomics and Molecular Pathology at Washington University School of Medicine. In addition, he is Associate Professor of Pathology and Immunology, Pediatrics, and Genetics. His lab's principle research interest is delineation of novel genomic structural and single nucleotide variants in cancer.
Affiliations and expertise
Head of Clinical Genomics, Genomics and Pathology Services; Director of Cytogenomics and Molecular Pathology, Washington University School of Medicine, USASR
Somak Roy
Dr. Somak Roy is an Assistant Professor, in the division of Molecular and Genomic Pathology, at the University of Pittsburgh Medical Center, in Pittsburgh, PA. He is also Director of Molecular Informatics and the Director of the MGP Fellowship Program, and Associate Laboratory Director of the Division of Molecular and Genomic Pathology. Dr. Roy's research is focused on understanding mechanisms of urothelial carcinogenesis and metastasis using next generation sequencing and microarray technologies. He also develops biomedical informatics solutions for optimizing clinical laboratory operations and quality management.
Affiliations and expertise
Assistant Professor, Division of Molecular and Genomic Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA; Director of Molecular Informatics and the Director of the MGP Fellowship Program, and Associate Laboratory Director of the Division of Molecular and Genomic Pathology