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E-grāmata: Clinical Genomics

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Edited by (Assistant Professor, Division of Molecular and Genomic Pathology, University), Edited by (Head of Clinical Genomics, Genomics and Pathology Services; Director of Cytogenomics and Molecular Pathology, Washington University School of Medicine, USA)
  • Formāts: EPUB+DRM
  • Izdošanas datums: 10-Nov-2014
  • Izdevniecība: Academic Press Inc
  • Valoda: eng
  • ISBN-13: 9780124051737
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Clinical GenomicsPalielināt
  • Formāts: EPUB+DRM
  • Izdošanas datums: 10-Nov-2014
  • Izdevniecība: Academic Press Inc
  • Valoda: eng
  • ISBN-13: 9780124051737
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Clinical Genomics provides an overview of the various next-generation sequencing (NGS) technologies that are currently used in clinical diagnostic laboratories. It presents key bioinformatic challenges and the 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.

This book is also focused on the challenges of diagnostic interpretation of NGS results in a clinical setting. Its final sections are devoted to the emerging regulatory issues that will govern clinical use of NGS, and reimbursement paradigms that will affect the way in which laboratory professionals get paid for the testing.

  • Simplifies complexities of NGS technologies for rapid education of clinical genomicists and genomic pathologists towards genomic medicine paradigm
  • Tried and tested practice-based analysis for precision diagnosis and treatment plans
  • Specific pipelines and meta-analysis for full range of clinically important variants

Recenzijas

"...presents key bioinformatic challenges and the 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." --Anticancer Research, February 2015

Papildus informācija

Reviews high throughput translational genomic sequencing for diagnosis, prognosis and precision management of inherited and somatic disorders
List of Contributors
xi
Foreword xiii
Preface xv
Acknowledgments xvii
I Methods
1 Overview of Technical Aspects and Chemistries of Next-Generation Sequencing
Ian S. Hagemann
Clinical Molecular Testing: Finer and Finer Resolution
3(1)
Sanger Sequencing
4(3)
Cyclic Array Sequencing
7(1)
Illumina Sequencing
8(3)
SOLiD Sequencing
11(3)
Ion Torrent Sequencing
14(2)
Roche 454 Genome Sequencers
16(2)
Third-Generation Sequencing Platforms
18(1)
References
18(3)
2 Clinical Genome Sequencing
Tina M. Hambuch
John Mayfield
Shankar Ajay
Michelle Hogue
Carri-Lyn Mead
Erica Ramos
Introduction
21(3)
Applications and Test Information
24(2)
Laboratory Process, Data Generation, and Quality Control
26(8)
Conclusion
34(1)
References
34(4)
3 Targeted Hybrid Capture Methods
Elizabeth C. Chastain
Introduction
38(1)
Basic Principles of Hybrid Capture-Based NGS
38(5)
Hybrid Capture-Based Target Enrichment Strategies
43(5)
Clinical Applications of Target Capture Enrichment
48(3)
Variant Detection
51(1)
Practical and Operational Considerations
52(1)
Conclusions
53(1)
References
53(4)
4 Amplification-Based Methods
Marina N. Nikiforova
William A. Laframboise
Yuri E. Nikiforov
Introduction
57(1)
Principles of Amplification-Based Targeted NGS
58(1)
Nucleic Acids Preparation
59(1)
Primer Design for Multiplex PCR
60(1)
Library Preparation and Amplification
61(1)
Other Amplification-Based Target Enrichment Approaches
62(1)
Comparison of Amplification- and Capture-Based Methods
62(2)
Clinical Applications
64(2)
Conclusion
66(1)
References
66(4)
5 Emerging DNA Sequencing Technologies
Shashikant Kulkarni
John Pfeifer
Introduction
70(1)
Third-Generation Sequencing Approaches
71(2)
Fourth-Generation Sequencing
73(1)
Selected Novel Technologies
74(1)
Summary
75(1)
References
75(3)
6 RNA-Sequencing and Methylome Analysis
Shamika Ketkar
Shashikant Kulkarni
Introduction
78(1)
Approaches to Analysis of RNA
78(1)
Workflow
79(5)
Utility of RNA-Seq to Characterize Alternative Splicing Events
84(1)
Utility of RNA-Seq for Genomic Structural Variant Detection
84(1)
RNA-Seq: Challenges, Pitfalls, and Opportunities in Clinical Applications
85(1)
Methylome Sequencing
85(1)
Conclusions
86(1)
References
86(2)
List of Acronyms and Abbreviations
88(4)
II Bioinformatics
7 Base Calling, Read Mapping, and Coverage Analysis
Paul Cliften
Introduction
92(2)
Platform-Specific Base Calling Methods
94(6)
Read Mapping
100(3)
Coverage Analysis: Metrics for Assessing Genotype Quality
103(3)
Summary
106(1)
References
107(3)
8 Single Nucleotide Variant Detection Using Next Generation Sequencing
David H. Spencer
Bin Zhang
John Pfeifer
Introduction
110(1)
Sources of SNVs
111(2)
Consequences of SNVs
113(1)
Technical Issues
114(3)
Bioinformatic Approaches for SNV Calling
117(5)
Interpretation of SNVs
122(1)
Reporting
123(1)
Summary
123(1)
References
124(6)
9 Insertions and Deletions (Indels)
Jennifer K. Sehn
Overview of Insertion/Deletion Events (Indels)
130(3)
Sources, Frequency, and Consequences of Indels
133(6)
Technical Issues That Impact Indel Detection by NGS
139(2)
Specimen Issues That Impact Indel Detection by NGS
141(1)
Bioinformatics Approaches to NGS Indel Detection
142(6)
Summary
148(1)
References
148(4)
10 Translocation Detection Using Next-Generation Sequencing
Haley Abel
John Pfeifer
Eric Duncavage
Introduction to Translocations
152(1)
Translocations in Human Disease
153(3)
Translocation Detection
156(2)
Informatic Approaches to Translocation Detection
158(2)
Translocation Detection in Clinical Practice
160(3)
Summary and Conclusion
163(1)
References
163(3)
11 Copy Number Variant Detection Using Next-Generation Sequencing
Alex Nord
Stephen J. Salipante
Colin Pritchard
Overview of Copy Number Variation and Detection via Clinical Next-Generation Sequencing
166(1)
Sources, Frequency, and Functional Consequences of Copy Number Variation in Humans
167(3)
CNV Detection in Clinical NGS Applications
170(3)
Conceptual Approaches to NGS CNV Detection
173(7)
Detection in the Clinic: Linking Application, Technical Approach, and Detection Methods
180(2)
Reference Standards
182(2)
Orthogonal CNV Validation
184(1)
Summary and Conclusion
184(1)
References
184(2)
Glossary
186(1)
List of Acronyms and Abbreviations
187(5)
III Interpretation
12 Reference Databases for Disease Associations
Wendy S. Rubinstein
Deanna M. Church
Donna R. Maglott
Introduction
192(1)
Identification and Validation of Human Variation
193(2)
Identification of Common Variation
195(4)
Interpretation of Common Variation
199(1)
Defining Diseases and Phenotypes
199(2)
Representation of Variation Data in Public Databases
201(4)
Data Access and Interpretation
205(5)
Determination of Variant Pathogenicity
210(2)
Global Data Sharing
212(1)
Conclusion
213(1)
References
213(2)
List of Acronyms and Abbreviations
215(4)
13 Reporting of Clinical Genomics Test Results
Kristina A. Roberts
Rong Mao
Brendan D. O'Fallon
Elaine Lyon
Introduction
219(1)
Components of the Written NGS Report
219(8)
Beyond the Written Report: Other NGS Reporting Issues to Consider
227(1)
Conclusion
228(1)
References
228(1)
List of Acronyms and Abbreviations
229(3)
14 Reporting Software
Rakesh Nagarajan
Introduction
232(1)
Clinical Genomic Test Order Entry
232(1)
Laboratory Information Management Systems (LIMS) Tracking
233(1)
Analytics: From Reads to Variant Calls
233(2)
Analytics: Variant Annotation and Classification
235(1)
Variant Interpretation
236(1)
Final Report Transmission to the EMR
236(1)
Leveraging Standards in Clinical Genomics Software Systems
237(1)
Regulatory Compliance
237(1)
Support Personnel
237(1)
Conclusion
238(1)
References
238(1)
List of Acronyms and Abbreviations
239(2)
15 Constitutional Diseases: Amplification-Based Next-Generation Sequencing
Vanessa L. Horner
Madhuri R. Hegde
Introduction
241(2)
Multigene Panel Validation
243(2)
Clinical Workflow
245(2)
Conclusion
247(1)
References
248(1)
List of Acronyms and Abbreviations
249(3)
16 Targeted Hybrid Capture for Inherited Disease Panels
Sami S. Amr
Birgit Funke
Introduction
252(3)
Target Selection Using Hybridization-Based Capture
255(2)
Design and Implementation of Targeted Hybridization-Based Capture Panels
257(5)
Targeted Hybrid Capture: Selecting a Panel for Constitutional Diseases
262(4)
Applications in Clinical Practice: Lessons Learned
266(2)
References
268(5)
17 Constitutional Disorders: Whole Exome and Whole Genome Sequencing
Benjamin D. Solomon
Introduction
273(3)
Genomic Sequencing
276(3)
Analyzing Individual and Multiple Data Sets for Causal Mutation Discovery
279(12)
Conclusion and Future Directions
291(1)
Acknowledgment
292(1)
References
292(4)
Glossary
296(2)
18 Somatic Diseases (Cancer): Amplification-Based Next-Generation Sequencing
Fengqi Chang
Geoffrey L. Liu
Cindy J. Liu
Marilyn M. Li
Introduction
298(1)
NGS Technologies
298(4)
Amplification-Based NGS Technologies
302(5)
Advantages and Disadvantages of Amplification-Based NGS
307(1)
Clinical Application of Amplification-Based NGS in Cancer
308(6)
Data Analysis
314(1)
Interpretation and Reporting
315(1)
Challenges and Perspectives
316(1)
References
317(5)
19 Targeted Hybrid Capture for Somatic Mutation Detection in the Clinic
Catherine E. Cottrell
Andrew J. Bredemeyer
Hussam Al-Kateb
Introduction
322(1)
Clinical Utility of Somatic Mutation Detection in Cancer
322(1)
Description of Hybridization-Based Methodology
323(3)
Utility of Targeted Hybrid Capture
326(7)
NGS in a Clinical Laboratory Setting
333(5)
Conclusion
338(1)
References
338(6)
20 Somatic Diseases (Cancer): Whole Exome and Whole Genome Sequencing
Jennifer K. Sehn
Introduction to Exome and Genome Sequencing in Cancer
344(1)
Interpretative Considerations in Exome and Genome Cancer Sequencing
344(8)
Analytic Considerations for Exome and Genome Sequencing in Cancer
352(4)
Summary
356(1)
References
357(7)
IV Regulation, Reimbursement, And Legal Issues
21 Assay Validation
Amy S. Gargis
Lisa Kalman
Ira M. Lubin
Introduction
364(1)
NGS Workflow
364(3)
The Regulatory and Professional Framework for Assuring Quality
367(1)
Assay Validation
367(2)
Accuracy
369(1)
Precision
370(1)
Analytical Sensitivity and Analytical Specificity
371(1)
Reportable and Reference Ranges
372(1)
Quality Control
372(1)
Reference Materials
373(1)
Conclusion
373(1)
Acknowledgment
374(1)
References
374(2)
List of Acronyms and Abbreviations
376(2)
22 Regulatory Considerations Related to Clinical Next Generation Sequencing
Shashikant Kulkarni
John Pfeifer
Introduction
378(1)
Regulatory Standards
378(1)
FDA Oversight of Clinical NGS
379(2)
Total Quality Management: QC
381(5)
Total Quality Management: QA
386(2)
Conclusion
388(1)
References
389(4)
23 Genomic Reference Materials for Clinical Applications
Justin Zook
Marc Salit
Introduction
393(1)
Genome in a Bottle Consortium
394(5)
Reference Data
399(1)
Other Reference Materials for Genome-Scale Measurements
400(1)
Conclusion
401(1)
References
401(3)
24 Ethical Challenges to Next-Generation Sequencing
Stephanie Solomon
Introduction
404(4)
Challenging Existing Frameworks
408(3)
Notifying of Results
411(10)
Privacy and Confidentiality
421(4)
Informed Consent
425(5)
Conclusion
430(1)
References
430(3)
Glossary
433(1)
List of Acronyms and Abbreviations
434(1)
25 Legal Issues
Roger D. Klein
Introduction
435(1)
Patent Overview
436(1)
History of Gene Patents
436(2)
Arguments for and Against Gene Patents
438(1)
Important Legal Cases
438(5)
Implication of Recent Court Decisions for Genetic Testing
443(1)
Genetic Information Nondiscrimination Act
443(2)
References
445(3)
26 Billing and Reimbursement
Kris Rickhoff
Andrew Drury
John Pfeifer
Introduction
448(1)
Insurance Payers
448(1)
Reimbursement Processes
448(4)
Test Design Factors That Impact Reimbursement
452(2)
Patient Protection and Affordable Care Act
454(2)
Cost Structure
456(1)
Summary
456(1)
References
457(1)
Glossary 457(1)
List of Acronyms and Abbreviations 458(1)
Index 459
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. 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.
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