Clinical Genomics

Clinical Genomics: A Guide to Clinical Next Generation Sequencing, 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.

Section I: Methods1. Overview of Technical Aspects and Chemistries of Next-Generation Sequencing2. Clinical Genome Sequencing3. Targeted Hybrid Capture Methods4. Amplification-Based Methods5. Emerging DNA Sequencing Technologies6. RNA-Sequencing and Methylome AnalysisSection II: Bioinformatics7. Base Calling, Read Mapping, and Coverage Analysis8. Single Nucleotide Variant Detection Using Next Generation Sequencing9. Insertions and Deletions (Indels)10. Translocation Detection Using Next-Generation Sequencing11. Structural Variant Detection12. The Human Reference GenomeSection III: Clinical Informatics and IT Infrastructure13. Data Storage14. Data Analytics - Platforms and Technologies15. Genomic Data Security and Privacy16. Cloud Computing17. Clinical NGS IT infrastructure implementation and validationSection IV: Interpretation18. Reference Databases for Disease Associations19. Reporting of Clinical Genomics Test Results20. Reporting Software21. Constitutional Diseases: Amplification-Based Next-Generation Sequencing22. Targeted Hybrid Capture for Inherited Disease Panels23. Constitutional Disorders: Whole Exome and Whole Genome Sequencing24. Somatic Diseases (Cancer): Amplification-Based Next-Generation Sequencing25. Targeted Hybrid-Capture for Somatic Mutation Detection in the Clinic26. Somatic Diseases (Cancer): Whole Exome and Whole Genome SequencingSection V: Regulation, Reimbursement, and Legal Issues27. Assay Validation28. Regulatory Considerations Related to Clinical Next Generation Sequencing29. Genomic Reference Materials for Clinical Applications30. Ethical Challenges to Next-Generation Sequencing31. Legal Issues32. Billing and Reimbursement Index