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E-grāmata: Clinical Applications for Next-Generation Sequencing

Edited by (MD PhD, Head of the Department of Laboratory Diagnostics and Clinical Immunology, Children's Hospital of the Medical University of Warsaw), Edited by (MD PhD, Head of the Department of Medical Genetics, Medical University of Warsaw)
  • Formāts: EPUB+DRM
  • Izdošanas datums: 10-Sep-2015
  • Izdevniecība: Academic Press Inc
  • Valoda: eng
  • ISBN-13: 9780128018415
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  • Formāts: EPUB+DRM
  • Izdošanas datums: 10-Sep-2015
  • Izdevniecība: Academic Press Inc
  • Valoda: eng
  • ISBN-13: 9780128018415

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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.Fills the gap between state-of-the-art technology and evidence-based practiceProvides an educational opportunity which advances patient care through the transfer of NGS to real-world patient assessmentPromotes a practical tool that clinicians can apply directly to patient careIncludes a systematic framework for understanding the role of NGS testing in many common and rare diseasesPresents evidence regarding the important role of NGS in current diagnostic strategies

Papildus informācija

A thorough examination of the translational use of NGS in clinical environments to help clinicians address the needs of real-world patients
List of Contributors xiii
Chapter 1 Next Generation Sequencing—General Information about the Technology, Possibilities, and Limitations 1(18)
Ratal Ploski
NGS Versus Traditional (Sanger Sequencing)
2(1)
Coverage
3(1)
NGS Library Preparation
3(1)
Sequence Assembly: De Novo Sequencing vs Resequencing
4(1)
Paired-End and Mate-Pair Libraries and Long Fragment Read Technology
5(1)
NGS Platforms
6(6)
Illumina
6(2)
Semiconductor-based platforms
8(1)
Sequencing by the Oligo Ligation Detection (SOLiD) Platform
9(1)
Pyrosequencing on Roche/454 platforms
10(1)
Complete genomics analysis (CGATM) platform
10(1)
Single-Molecule Sequencing
11(1)
Targeted Resequencing/Enrichment Strategies
12(2)
Whole Exome Sequencing and Whole Genome Sequencing
14(1)
Limitations of NGS in Clinical Medicine
15(1)
Conclusion
16(1)
References
17(2)
Chapter 2 Basic Bioinformatic Analyses of NGS Data 19(20)
Piotr Stawinski
Ravi Sachidanandam
Izabela Chojnicka
Rafal Ploski
Software Tools
20(1)
Input Sequence Preprocessing
21(2)
Mapping
23(3)
Processing and Interpreting Mapping
26(1)
Insertions and Deletions Realignment
26(1)
Base Quality Recalibration
27(1)
Variant Calling
27(5)
Major Approaches to the Variant Calling
28(1)
Variant Calling Format
28(2)
Variant Annotation
30(2)
Software and Hardware Issues
32(3)
Computational Architecture
32(2)
Storage Architecture
34(1)
References
35(4)
Chapter 3 Analysis of Structural Chromosome Variants by Next Generation Sequencing Methods 39(24)
Dariusz Plewczynski
Slawomir Gruca
Przemyslaw Szalaj
Krystian Gulik
Silviene Fabiana de Oliveira
Ankit Malhotra
Introduction
39(1)
Structural Variants in the Human Genome
40(1)
Structural Variation and Human Disease
40(1)
Analysis of Structural Variation by Legacy Technologies
41(1)
Structural Variation and Next Generation Sequencing
42(1)
Methods for Estimation of Copy Number Variation from NGS Data
42(2)
Structural Variation, NGS, Cancer, and the Clinic
44(2)
NGS-Based Structural Variation Detection Software
46(5)
Future Directions
51(6)
Acknowledgments
57(1)
References
57(6)
Chapter 4 Next Generation Sequencing in Oncology 63(12)
Eliza Glodkowska-Mrowka
Tomasz Stoklosa
NGS in Cancer Research
64(1)
NGS in Clinical Settings
65(7)
Familial Genetic Testing
66(1)
Molecular Disease Classification
66(1)
Pharmacogenomics
67(1)
Testing in "Last-Resort" Patients
67(1)
Circulating Cell-Free Tumor DNA and Circulating Tumor Cells
67(2)
Treatment Monitoring
69(1)
Biomarkers in Clinical Decision-Making
70(1)
Current Obstacles Preventing NGS from Wide Application in Clinical Settings
70(1)
Targeted versus Genome-Wide Approach
71(1)
Future of Oncogenomics
72(1)
Pros and Cons of Traditional versus NGS Sequencing Approach
72(1)
Challenges in Clinical Oncogenomics
72(1)
References
72(3)
Chapter 5 Next Generation Sequencing in Hematological Disorders 75(22)
Iwona Malinowska
Eliza Glodkowska-Mrowka
Introduction
75(1)
Childhood and Adult Acute Lymphoblastic Leukemias
76(2)
T-Cell Acute Lymphoblastic Leukemia
78(1)
BCR—ABL1-like Acute Lymphoblastic Leukemia
79(1)
Hypodiploid Acute Lymphoblastic Leukemia
79(1)
Relapsed Acute Lymphoblastic Leukemia
80(1)
Acute Myeloid Leukemia
80(2)
Genetic Concept of Acute Myeloid Leukemia Pathogenesis
82(2)
BRAF Mutation in Hairy Cell Leukemia
84(1)
CSF3R Mutation in Chronic Neutrophilic Leukemia
84(1)
NGS in Chronic Lymphocytic Lymphoma
84(1)
Non-Hodgkin Lymphomas
85(2)
Inherited Bone Marrow Failure Syndromes
87(1)
Fanconi Anemia
87(1)
Dyskeratosis Congenita
88(1)
Thrombocytopenia Absent Radius Syndrome
89(1)
Diamond—Blackfan Anemia
89(1)
Commercial NGS-Based Assays for Clinical Use in Hematology Practice
90(1)
Implementation of NGS-Based Techniques in Clinical Practice in Hematology
91(1)
Conclusion
92(1)
References
92(5)
Chapter 6 Next Generation Sequencing in Neurology and Psychiatry 97(40)
Krystyna Szymatiska
Krzysztof Szczaluba
Anna Kostera-Pruszczyk
Tomasz Wolanczyk
Introduction
98(16)
Genetic Testing in Neurology and Psychiatry
98(3)
Epilepsy
101(4)
Ataxia
105(2)
Hereditary Spastic Paraplegias
107(1)
Movement Disorders
108(2)
Neuromuscular Disorders
110(2)
Neurodegenerative Diseases with Dementia
112(2)
Neuropsychiatric Disorders
114(14)
Intellectual Disability
114(2)
Autism
116(4)
Intellectual Disability and Autism—A Practical Approach
120(1)
Genetic Testing in Autism and ID—A Proposal
120(2)
Autism Databases
122(2)
Major Psychiatric Disorders
124(4)
References
128(9)
Chapter 7 Next Generation Sequencing in Dysmorphology 137(16)
Robert Smigiel
Urszula Demkow
Dysmorphology—Past and Present
137(1)
Diagnostic Process in Dysmorphology
138(1)
Genetic Testing in Dysmorphology
139(2)
NGS Testing in Dysmorphology and Rare Multiple Congenital Defects Syndromes
141(4)
Dilemmas
145(1)
Reverse Dysmorphology
146(1)
NGS and Screening of Rare Disorders in Newborns
146(1)
Conclusions
147(1)
List of Abbreviations
147(1)
References
148(5)
Chapter 8 Next Generation Sequencing in Vision and Hearing Impairment 153(18)
Monika Oldak
Introduction
153(2)
NGS Tests for Vision and Hearing Disorders
155(5)
Compatibility of Standard Enrichment Panels with Genetic Vision and Hearing Disorders
160(1)
Utility of NGS Testing for Diagnostic Purposes of Vision and Hearing Disorders
161(1)
Cumulative Mutation Load
162(1)
Digenic and Oligogenic Inheritance
162(1)
De Novo Mutations
163(1)
Copy Number Variations
163(1)
Novel Genes and "Erroneous" Disease Genes
164(1)
Conclusions
165(1)
Abbreviations
166(1)
Acknowledgments
166(1)
References
166(5)
Chapter 9 Next Generation Sequencing as a Tool for Noninvasive Prenatal Tests 171(18)
Ozgur Cogulu
Introduction
171(2)
Conventional Prenatal Diagnostics and Methods
173(1)
Use of Fetal Biological Material in the Maternal Circulation for Prenatal Diagnosis
173(1)
Fetal DNA in Prenatal Diagnosis
174(1)
Properties of Cell-Free Fetal DNA
174(2)
Applications of Noninvasive Prenatal Tests
176(3)
NGS in the Determination of Genomic Disorders by Using cffDNA in Maternal Plasma
179(1)
Single-Nucleotide Polymorphism Sequencing of Cell-Free Fetal DNA
180(2)
Limitations and Challenges of NGS-Based Noninvasive Prenatal Testing
182(1)
Clinical Implementation of Noninvasive Prenatal Testing for Aneuploidies
183(1)
Conclusion
184(1)
References
184(5)
Chapter 10 Clinical Applications for Next Generation Sequencing in Cardiology 189(28)
Joanna Poninska
Rafal Ploski
Zofia T. Bilinska
Introduction
189(3)
General Information on Multigene Panels
191(1)
Cardiomyopathies
192(7)
Hypertrophic Cardiomyopathy
195(1)
Dilated Cardiomyopathy
196(1)
Arrhythmogenic Right Ventricular Cardiomyopathy
197(1)
Restrictive Cardiomyopathy
198(1)
Left-Ventricular Noncompaction
198(1)
Arrhythmias
199(3)
Long QT Syndrome
199(1)
Brugada Syndrome
200(1)
Catecholaminergic Polymorphic Ventricular Tachycardia
200(1)
Cardiac Conduction Disease
201(1)
Short QT Syndrome
201(1)
Atrial Fibrillation
202(1)
Thoracic Aortic Aneurysms and Dissections
202(2)
Congenital Heart Disease
204(1)
Familial Hypercholesterolemia
205(1)
Conclusions
206(1)
List of Acronyms and Abbreviations
206(1)
Acknowledgments
207(1)
References
207(10)
Chapter 11 Next Generation Sequencing in Pharmacogenomics 217(24)
Urszula Demkow
Introduction
217(1)
Cancer Therapy
218(3)
Clinical Trials in Oncology
221(1)
Ethical Issues in Oncopharmacogenomics
222(1)
Multicenter Collaborations in Oncopharmacogenomics
222(2)
NGS in Noncancer Pharmacogenomics
224(1)
Cytochrome P450
224(3)
Non-P450 Drug-Metabolizing Enzymes
227(1)
Drug Transporters
227(1)
Clinical Applications of Pharmacogenomics
228(2)
Anticoagulants
228(1)
Psychiatry
229(1)
Analgesics
229(1)
Transplantology
229(1)
Anti-Human Immunodeficiency Virus Drugs
229(1)
Multigene Pharmacogenetic Tests Assessing Pharmacokinetics and Pharmacodynamics Response
230(1)
Quality Requirements for NGS-Based Pharmacogenomic Tests
231(2)
Guidelines for Clinical Application of Pharmacogenomics
233(1)
NGS in Pharmacogenomics—Other Possible Applications
234(1)
Limitations of NGS in Pharmacogenomics
234(1)
Conclusions
235(1)
References
236(5)
Chapter 12 The Role of Next Generation Sequencing in Genetic Counseling 241(18)
Asude Durmaz
Burak Durmaz
Introduction
241(1)
Genetic Counseling
242(2)
Genetic Counseling in the NGS Era
244(11)
Pretest Genetic Counseling
244(2)
Informed Consent Form
246(2)
Return of Results
248(7)
Future Perspectives
255(1)
List of Acronyms and Abbreviations
256(1)
References
256(3)
Chapter 13 Next Generation Sequencing in Undiagnosed Diseases 259(12)
Urszula Demkow
Overview
259(1)
The Overall Genetic Testing Strategy in Undiagnosed Diseases—Looking for the Needle in a Haystack
260(2)
The Analysis of NGS Testing Results for Rare Diseases
262(1)
Pathogenicity
263(2)
Good Laboratory Practice in Genetic Testing for Undiagnosed Diseases
265(1)
Test Validation
265(1)
The Importance of Genetic Diagnosis in Rare Diseases
266(1)
Conclusions
267(1)
References
267(4)
Chapter 14 Organizational and Financing Challenges 271(10)
Jacub Owoc
United States
275(1)
Great Britain
275(1)
Holland
276(1)
Germany
276(1)
Conclusions
277(1)
References
278(3)
Chapter 15 Future Directions 281(14)
Michal Okoniewski
Rafal Ploski
Marek Wiewiorka
Urszula Demkow
Sequencing Platforms
281(3)
Nanopore Sequencing
282(1)
Emerging Commercial Solutions
283(1)
Future Directions of Clinical Genomics Data Processing
284(6)
Data Size Estimates and Current Processing Limitations
284(1)
Data Processing Models
285(1)
Hadoop Ecosystem Tools That Can Be Used in Genomic Medicine
286(2)
Data Security and Biobanking
288(1)
Currently Developing Scenarios and Cases
288(1)
Expected Challenges and Limitations of Future Data Processing Tools and Models
289(1)
Education of Physicians and Medical Researchers in the Understanding and Use of Genomic Data Processing
289(1)
Electronic Health Records
290(1)
Conclusion—Vision of Near-Future Medical Genomics Information Systems
291(1)
References
291(4)
Chapter 16 Ethical and Psychosocial Issues in Whole-Genome Sequencing for Newborns 295(6)
John D. Lantos
Introduction
295(2)
Differences between WGS and Genetic Testing in Other Contexts
297(2)
Newborn Metabolic Screening
297(1)
Carrier Testing in Carefully Selected High-Risk Populations
298(1)
Genetic Testing of Stored Samples in Biorepositories
298(1)
The Specific Ethical Issues of Whole-Genome Sequencing for Clinical Diagnosis
299(1)
Thinking about Harms and Benefits
299(1)
Conclusions
300(1)
Chapter 17 Next Generation Sequencing—Ethical and Social Issues 301(8)
Andrzej Kochanski
Urszula Demkow
Unpredictable Consequences of the Next Generation
Sequencing-Related Technological Revolution in Medical Genetics
301(1)
Problem 1: The Right Not to Know
302(1)
Problem 2: Incidental/Unsolicited Findings
303(1)
Problem 3: Genetic Determinism and Discrimination
304(1)
Problem 4: Genetically-Based Selection of Human Embryos and Assisted Reproductive Technology
304(1)
Problem 5: NGS and Social Issues
305(1)
Conclusions
306(1)
References
306(3)
Index 309