Clinical Genomics

Clinical Genomics

A Guide to Clinical Next Generation Sequencing

2nd Edition - October 1, 2023

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  • Editors: Shashikant Kulkarni, Somak Roy
  • Paperback ISBN: 9780323900249

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Clinical Genomics, Second Edition provides a full overview of next-generation sequencing (NGS) technologies that are currently used in clinical diagnostic laboratories. The book presents key bioinformatic challenges and solutions that must be addressed by clinical genomicists and genomic pathologists, such as specific pipelines for identification of the full range of variants that are clinically important. It focuses on the challenges of diagnostic interpretation of NGS results in a clinical setting, with later sections devoted to emerging regulatory issues governing the clinical use of NGS and reimbursement paradigms that will affect the way in which laboratory professionals get compensated for testing.Following the wide use of the current edition by clinicians and researchers alike, this fully revised, new edition addresses the evolving landscape of genomics medicine, along with recent advances in our understanding of molecular mechanisms of human diseases and developmental biology. In addition, the book updates on sequencing chemistry and platforms, bioinformatics algorithms, clinical informatics, IT infrastructure and emerging applications of artificial intelligence in genomics.

Key Features

  • Simplifies the complexities of NGS technologies for rapid education of clinical genomicists and genomic pathologists
  • Instructs in tested practice-based analysis for precision diagnosis and treatment plans, as well as pipelines and meta-analysis for a full range of clinically important variants
  • Provides technical consideration for the validation and implementation of bioinformatics pipelines and related resources in the clinical molecular laboratory
  • Addresses novel sequencing technologies, including long-read sequencing for detecting structural variants and haplotypes
  • Covers cloud computing and Modern IT infrastructure (data storage, security, analytics) for scalable and secure genomics medicine


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

Table of Contents

  • 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

Product details

  • No. of pages: 562
  • Language: English
  • Copyright: © Academic Press 2023
  • Published: October 1, 2023
  • Imprint: Academic Press
  • Paperback ISBN: 9780323900249

About the Editors

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, USA

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

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