Clinical Applications for Next-Generation Sequencing - 1st Edition - ISBN: 9780128017395, 9780128018415

Clinical Applications for Next-Generation Sequencing

1st Edition

Editors: Urszula Demkow Rafal Ploski
eBook ISBN: 9780128018415
Paperback ISBN: 9780128017395
Imprint: Academic Press
Published Date: 29th September 2015
Page Count: 334
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Description

Clinical Applications for Next Generation Sequencing provides readers with an outstanding postgraduate resource to learn about the translational use of NGS in clinical environments.

Rooted in both medical genetics and clinical medicine, the book fills the gap between state-of-the-art technology and evidence-based practice, providing an educational opportunity for users to advance patient care by transferring NGS to the needs of real-world patients.

The book builds an interface between genetic laboratory staff and clinical health workers to not only improve communication, but also strengthen cooperation. Users will find valuable tactics they can use to build a systematic framework for understanding the role of NGS testing in both common and rare diseases and conditions, from prenatal care, like chromosomal abnormalities, up to advanced age problems like dementia.

Key Features

  • Fills the gap between state-of-the-art technology and evidence-based practice
  • Provides an educational opportunity which advances patient care through the transfer of NGS to real-world patient assessment
  • Promotes a practical tool that clinicians can apply directly to patient care
  • Includes a systematic framework for understanding the role of NGS testing in many common and rare diseases
  • Presents evidence regarding the important role of NGS in current diagnostic strategies

Readership

clinicians and trainees of different specialties, especially pediatricians, neonatologists, hematologists, oncologists, neurologists, psychiatrists, ophthalmologists, laryngologists, cardiologists, diabetologists and others with an interest in genetics and a desire to implement this new testing modality into their daily practice; genetic laboratory staff performing tests for clinicians; genetic counselors

Table of Contents

  • List of Contributors
  • Chapter 1. Next Generation Sequencing—General Information about the Technology, Possibilities, and Limitations
    • NGS Versus Traditional (Sanger Sequencing)
    • Coverage
    • NGS Library Preparation
    • Sequence Assembly: De Novo Sequencing vs Resequencing
    • Paired-End and Mate-Pair Libraries and Long Fragment Read Technology [8]
    • NGS Platforms
    • Targeted Resequencing/Enrichment Strategies
    • Whole Exome Sequencing and Whole Genome Sequencing
    • Limitations of NGS in Clinical Medicine
    • Conclusion
  • Chapter 2. Basic Bioinformatic Analyses of NGS Data
    • Software Tools
    • Input Sequence Preprocessing
    • Mapping
    • Processing and Interpreting Mapping
    • Variant Calling
    • Software and Hardware Issues
  • Chapter 3. Analysis of Structural Chromosome Variants by Next Generation Sequencing Methods
    • Introduction
    • Structural Variants in the Human Genome
    • Structural Variation and Human Disease
    • Analysis of Structural Variation by Legacy Technologies
    • Structural Variation and Next Generation Sequencing
    • Methods for Estimation of Copy Number Variation from NGS Data
    • Structural Variation, NGS, Cancer, and the Clinic
    • NGS-Based Structural Variation Detection Software
    • Future Directions
  • Chapter 4. Next Generation Sequencing in Oncology
    • NGS in Cancer Research
    • NGS in Clinical Settings
  • Chapter 5. Next Generation Sequencing in Hematological Disorders
    • Introduction
    • Childhood and Adult Acute Lymphoblastic Leukemias
    • T-Cell Acute Lymphoblastic Leukemia
    • BCR–ABL1-Like Acute Lymphoblastic Leukemia
    • Hypodiploid Acute Lymphoblastic Leukemia
    • Relapsed Acute Lymphoblastic Leukemia
    • Acute Myeloid Leukemia
    • Genetic Concept of Acute Myeloid Leukemia Pathogenesis
    • BRAF Mutation in Hairy Cell Leukemia
    • CSF3R Mutation in Chronic Neutrophilic Leukemia
    • NGS in Chronic Lymphocytic Lymphoma
    • Non-Hodgkin Lymphomas
    • Inherited Bone Marrow Failure Syndromes
    • Dyskeratosis Congenita
    • Thrombocytopenia Absent Radius Syndrome
    • Diamond–Blackfan Anemia
    • Commercial NGS-Based Assays for Clinical Use in Hematology Practice
    • Implementation of NGS-Based Techniques in Clinical Practice in Hematology
    • Conclusion
  • Chapter 6. Next Generation Sequencing in Neurology and Psychiatry
    • Introduction
    • Neuropsychiatric Disorders
  • Chapter 7. Next Generation Sequencing in Dysmorphology
    • Dysmorphology—Past and Present
    • Diagnostic Process in Dysmorphology
    • Genetic Testing in Dysmorphology
    • NGS Testing in Dysmorphology and Rare Multiple Congenital Defects Syndromes
    • Dilemmas
    • Reverse Dysmorphology
    • NGS and Screening of Rare Disorders in Newborns
    • Conclusions
    • List of Abbreviations
  • Chapter 8. Next Generation Sequencing in Vision and Hearing Impairment
    • Introduction
    • NGS Tests for Vision and Hearing Disorders
    • Compatibility of Standard Enrichment Panels with Genetic Vision and Hearing Disorders
    • Utility of NGS Testing for Diagnostic Purposes of Vision and Hearing Disorders
    • Cumulative Mutation Load
    • Digenic and Oligogenic Inheritance
    • De Novo Mutations
    • Copy Number Variations
    • Novel Genes and “Erroneous” Disease Genes
    • Conclusions
    • Abbreviations
  • Chapter 9. Next Generation Sequencing as a Tool for Noninvasive Prenatal Tests
    • Introduction
    • Conventional Prenatal Diagnostics and Methods
    • Use of Fetal Biological Material in the Maternal Circulation for Prenatal Diagnosis
    • Fetal DNA in Prenatal Diagnosis
    • Properties of Cell-Free Fetal DNA
    • Applications of Noninvasive Prenatal Tests
    • NGS in the Determination of Genomic Disorders by Using cffDNA in Maternal Plasma
    • Single-Nucleotide Polymorphism Sequencing of Cell-Free Fetal DNA
    • Limitations and Challenges of NGS-Based Noninvasive Prenatal Testing
    • Clinical Implementation of Noninvasive Prenatal Testing for Aneuploidies
    • Conclusion
  • Chapter 10. Clinical Applications for Next Generation Sequencing in Cardiology
    • Introduction
    • Cardiomyopathies
    • Arrhythmias
    • Thoracic Aortic Aneurysms and Dissections
    • Congenital Heart Disease
    • Familial Hypercholesterolemia
    • Conclusions
    • List of Acronyms and Abbreviations
  • Chapter 11. Next Generation Sequencing in Pharmacogenomics
    • Introduction
    • Cancer Therapy
    • Clinical Trials in Oncology
    • Ethical Issues in Oncopharmacogenomics
    • Multicenter Collaborations in Oncopharmacogenomics
    • NGS in Noncancer Pharmacogenomics
    • Cytochrome P450
    • Non-P450 Drug-Metabolizing Enzymes
    • Drug Transporters
    • Clinical Applications of Pharmacogenomics
    • Multigene Pharmacogenetic Tests Assessing Pharmacokinetics and Pharmacodynamics Response
    • Quality Requirements for NGS-Based Pharmacogenomic Tests
    • Guidelines for Clinical Application of Pharmacogenomics
    • NGS in Pharmacogenomics—Other Possible Applications
    • Limitations of NGS in Pharmacogenomics
    • Conclusions
  • Chapter 12. The Role of Next Generation Sequencing in Genetic Counseling
    • Introduction
    • Genetic Counseling
    • Genetic Counseling in the NGS Era
    • Future Perspectives
    • List of Acronyms and Abbreviations
  • Chapter 13. Next Generation Sequencing in Undiagnosed Diseases
    • Overview
    • The Overall Genetic Testing Strategy in Undiagnosed Diseases—Looking for the Needle in a Haystack
    • The Analysis of NGS Testing Results for Rare Diseases
    • Pathogenicity
    • Good Laboratory Practice in Genetic Testing for Undiagnosed Diseases
    • Test Validation
    • The Importance of Genetic Diagnosis in Rare Diseases
    • Conclusions
  • Chapter 14. Organizational and Financing Challenges
    • United States
    • Great Britain
    • Holland
    • Germany
    • Conclusions
  • Chapter 15. Future Directions
    • Sequencing Platforms
    • Future Directions of Clinical Genomics Data Processing
    • Electronic Health Records
    • Conclusion—Vision of Near-Future Medical Genomics Information Systems
  • Chapter 16. Ethical and Psychosocial Issues in Whole-Genome Sequencing for Newborns
    • Introduction
    • Differences between WGS and Genetic Testing in Other Contexts
    • The Specific Ethical Issues of Whole-Genome Sequencing for Clinical Diagnosis
    • Thinking about Harms and Benefits
    • Conclusions
  • Chapter 17. Next Generation Sequencing—Ethical and Social Issues
    • Unpredictable Consequences of the Next Generation Sequencing-Related Technological Revolution in Medical Genetics
    • Problem 1: The Right Not to Know
    • Problem 2: Incidental/Unsolicited Findings
    • Problem 3: Genetic Determinism and Discrimination
    • Problem 4: Genetically-Based Selection of Human Embryos and Assisted Reproductive Technology
    • Problem 5: NGS and Social Issues
    • Conclusions
  • Index

Details

No. of pages:
334
Language:
English
Copyright:
© Academic Press 2016
Published:
Imprint:
Academic Press
eBook ISBN:
9780128018415
Paperback ISBN:
9780128017395

About the Editor

Urszula Demkow

Urszula Demkow

Affiliations and Expertise

MD PhD, Head of the Department of Laboratory Diagnostics and Clinical Immunology, Children's Hospital of the Medical University of Warsaw

Rafal Ploski

Rafal Ploski

Affiliations and Expertise

MD PhD, Head of the Department of Medical Genetics, Medical University of Warsaw