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El. knyga: Progress and Challenges in Precision Medicine

Edited by (Branch Chief, Methods and Technologies Branch, Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA), Edited by (Federal Univer)
  • Formatas: EPUB+DRM
  • Išleidimo metai: 22-Dec-2016
  • Leidėjas: Academic Press Inc
  • Kalba: eng
  • ISBN-13: 9780128095027
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Progress and Challenges in Precision MedicineDidesnis paveikslėlis
  • Formatas: EPUB+DRM
  • Išleidimo metai: 22-Dec-2016
  • Leidėjas: Academic Press Inc
  • Kalba: eng
  • ISBN-13: 9780128095027
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Progress and Challenges in Precision Medicine presents an insightful overview to the myriad factors of personalized and precision medicine. The availability of the human genome, large amounts of data on individual genetic variations, environmental interactions, influence of lifestyle, and cutting-edge tools and technologies for big-data analysis have led to the age of personalized and precision medicine.

Bringing together a global range of experts on precision medicine, this book collects previously scattered information into one concise volume which covers the most important developments so far in precision medicine and also suggests the most likely avenues for future development.

The book includes clinical information, informatics, public policy implications, and information on case studies. It is a useful reference and background work for students, researchers, and clinicians working in the biomedical and medical fields, as well as policymakers in the health sciences.

  • Provides an overview of the growing field of precision medicine
  • Contains chapters from geographically diverse experts in their field
  • Explores important aspects of precision medicine, including applications, ethics, and development

Daugiau informacijos

This book provides an exploration of the fundamentals and potential future of the customization of disease control and treatment in healthcare
List of Contributors
xv
Biography xvii
Dedication xix
Preface xxi
1 Introduction: Every Individual Is Different and Precision Medicine Offers Options for Disease Control and Treatment
C. Hizel
J. Tremblay
C. Bartlett
P. Hamet
1 What Is Precision Medicine? Personalized Medicine Versus Precision Medicine (C. Hizel, P. Hamet, and J. Tremblay)
1(16)
1.1 Precision Medicine in Complex Chronic Disease: A Focus on Diabetes
5(12)
2 Precision Medicine for Population Health (G. Bartlett)
17(2)
3 Conclusion
19(16)
References
20(15)
2 Clinical Next-Generation Sequencing: Enabling Precision Medicine
D. Dhawan
1 Introduction
35(1)
2 Technicalities and Chemistries of NGS
35(4)
2.1 Genome-Wide Methods
36(1)
2.2 Capture-Based Methods
37(1)
2.3 Amplification-Based Methods
38(1)
2.4 Latest Developments
38(1)
3 NGS Data Analysis
39(3)
3.1 Quality Assessment
39(1)
3.2 Alignment
40(1)
3.3 Variant Identification
40(1)
3.4 Variant Annotation
41(1)
3.5 Challenges in Data Analysis
41(1)
4 Reference Databases for Disease Associations and Drug Response
42(2)
5 Applications of NGS in Precision Medicine
44(3)
5.1 Expression Analysis
44(2)
5.2 Epigenetic Studies
46(1)
5.3 Genome Sequencing
46(1)
5.4 Noninvasive Prenatal Testing
46(1)
5.5 Disease Gene Identification
47(1)
6 Regulatory Concerns With NGS Clinical Genomics
47(1)
7 Conclusion
48(7)
References
48(7)
3 Phenotyping in Precision Medicine
R.Z. Paracha
A. Obaid
A. Ali
1 Introduction
55(2)
2 Deep Phenotyping
57(2)
3 Expressivity and Penetrance
59(1)
4 Expressivity
60(2)
5 Penetrance
62(1)
6 Phenotypic Variation in Expressivity and Penetrance
63(1)
7 Pleiotropy
64(1)
8 Diseases and Phenotypes
65(1)
9 Cancer
65(2)
10 Diabetes
67(1)
11 Respiratory Disorders
67(1)
12 Encephalopathy
68(1)
13 Data Mining and Phenotyping
69(1)
14 Approaches for Phenotyping
70(2)
15 Future Directions 72 References
72(7)
4 Cancer Genetic Screening and Ethical Considerations for Precision Medicine
R.C. Dumitrescu
1 Introduction
79(2)
2 Genetic Testing in Hereditary Cancers
81(3)
2.1 Genetic Testing for Hereditary Breast and Ovarian Cancers
81(1)
2.2 Genetic Testing for Hereditary Colorectal Cancers
82(1)
2.3 Genetic Testing for Lung Cancers
83(1)
3 Ethical Issues Related to Cancer Genetic Screening
84(12)
3.1 Competency of Genetic Screening Laboratories and Medical Personnel
84(2)
3.2 Direct-To-Consumers Genetic Testing
86(1)
3.3 Individual Rights Versus Community Rights
87(2)
3.4 Individual Informed Consent
89(1)
3.5 Return of the Results for Pediatric Patients
90(1)
3.6 Environmental and Distributive Justice
90(2)
3.7 Cancer Screening and Discrimination
92(1)
3.8 Cancer Screening and Stigma
93(1)
3.9 Implications of Genetic-Based Cancer Screening at the Population Level
94(2)
4 Summary and Conclusions
96(5)
References
96(5)
5 Precision Medicine in Primary Health Care
G. Bartlett
M. Dawes
Q. Nguyen
M.S. Phillips
1 The Case for Primary Health Care
101(1)
2 Precision Medicine in Primary Health Care: Warfarin and Pharmacogenomics
102(2)
3 Precision Medicine in Primary Health Care: Creating an Informatics System
104(1)
4 Precision Medicine: A Feasibility Study for Primary Health Care
104(2)
4.1 Outcomes
106(1)
4.2 Statistical Analysis
106(1)
4.3 Ethics
106(1)
5 Precision Medicine in Primary Health Care: Feasibility Results
106(2)
5.1 Informatics System Results
106(1)
5.2 PGx Testing Results
107(1)
6 Precision Medicine and Implications for Pharmacogenomics in Primary Health Care
108(7)
Abbreviations
110(1)
Acknowledgments
110(1)
References
110(5)
6 Population Approach to Precision Medicine
M. Verma
1 Background
115(1)
2 Examples of Different Tumor Types Where Precision Medicine Was Applied
116(3)
2.1 Breast Cancer
116(1)
2.2 Cervical Cancer
117(1)
2.3 Colorectal Cancer
117(1)
2.4 Head and Neck Cancer
117(1)
2.5 Hepatocellular Carcinoma (Liver Cancer)
118(1)
2.6 Melanoma
118(1)
2.7 Lung Cancer
118(1)
2.8 Prostate Cancer
119(1)
3 Different Approaches to Address Challenges in Precision Medicine
119(1)
4 Medical Applications in Health Care Settings
120(1)
5 Challenges and Potential Solutions
120(4)
5.1 Lengthy Time of Approval
120(1)
5.2 Validation of Genomic Association Studies
120(1)
5.3 Undruggable Targets
121(1)
5.4 Need for Longitudinal Studies
121(2)
5.5 Translating Molecular Information Into Clinics
123(1)
5.6 Side Effects and Overall Survival
123(1)
5.7 New Classification of Diseases
123(1)
5.8 Implication in Population Setup
123(1)
5.9 Too Many Details
123(1)
6 Looking Ahead
124(1)
7 Conclusion
124(5)
Acknowledgments
125(1)
References
125(4)
7 Regulation of Genomic Testing in the Era of Precision Medicine
A. Ali
A. Hassan
S. Rehman
S.T. Ashraf
K. Naz
A. Naz
1 Genomic Testing in the Era of Precision Medicine
129(1)
1.1 What Is Genomic Testing?
129(1)
2 Requisite for Regulation of Genomic Testing
130(2)
3 Perspective of "Beyond the Clinic"
132(1)
4 Assuring the Quality of Data
132(3)
4.1 Strategies Adapted for Ensuring the Quality of Genetic Data
133(1)
4.2 Ethics and Confidentiality Issues
134(1)
5 Significance of Feedback
135(1)
6 Requisite of Regulatory Body
136(5)
6.1 Role of Current Programs
137(1)
6.2 Establishing a Registry System
137(1)
References
138(3)
8 Image-Based Modeling and Precision Medicine
N.I. Soomro
S.M. Bakhtiar
1 Biomedical Visualization
141(5)
1.1 2D Image Generation and Display
144(1)
1.2 3D Image Generation and Display
144(1)
1.3 Multiplanar Reformatting
144(1)
1.4 Oblique Sectioning
145(1)
1.5 Curved Sectioning
145(1)
1.6 Surface Rendering Techniques
145(1)
1.7 Volume Rendering Techniques
146(1)
2 Diagnostic Imaging
146(5)
2.1 Imaging in Modern Oncology
148(1)
2.2 Major Anatomical Imaging Modalities
149(1)
2.3 Functional/Metabolic Imaging Modalities in Oncology
150(1)
3 Medical Simulation
151(1)
3.1 Human Factors in Medical Simulation
152(1)
4 Multiscale Engineering in Biology
152(2)
5 Visible Human Project
154(3)
5.1 Development of VHP at IT, CD-ROM, and Internet Level
155(2)
6 Image-Based Models
157(2)
6.1 The NIH/NIGMS Center for Integrative Biomedical Computing
159(1)
7 Functional Anatomy Simulation
159(4)
8 Cells and Subcellular Systems
163(1)
9 End User Applications
164(7)
9.1 Inflammatory Diseases and Precision Medicine
164(1)
9.2 Image-Based Computational Models of Cardiac Structure
164(1)
9.3 Diagnostic Imaging of Skeletal Malignancies
165(1)
9.4 Pulmonary Disease
165(1)
9.5 Image-Based Models
165(1)
References
166(5)
9 Sharing Outside the Sandbox? The Child's Right to an Open Data Sharing Future in Genomics and Personalized Medicine
V. Rahimzadeh
1 Introduction
171(1)
2 Children in Research
172(1)
3 A Changing Landscape for Pediatric Research Participation
173(2)
4 The Research Ethics Review Process and Implications for Data Sharing
175(1)
5 Sharing Outside the Sandbox
176(3)
5.1 Responsibility to the Data Source
177(1)
5.2 Responsibility to the Data Process
178(1)
5.3 Responsibility to the Data Impact
179(1)
6 Conclusion
179(8)
References
180(7)
10 Lessons Learned From Cohort Studies, and Hospital-Based Studies and Their Implications in Precision Medicine
A. Munshi
V. Sharma
S. Sharma
1 The Pyramid of Evidence: A Useful Construct
187(3)
2 An Overview of Study Designs
190(1)
3 Experimental Studies
190(2)
3.1 Randomized Controlled Trial
190(2)
4 Quasi-Experimental Studies
192(1)
5 Nonexperimental/Observational Study Designs
193(1)
6 Cohort Studies
193(2)
7 Case-Control Studies
195(2)
8 The STROBE Statement: The Strengthening the Reporting of Observational Studies in Epidemiology Statement
197(1)
9 Cross-Sectional Studies
197(1)
10 Case Series
198(1)
11 Other Study Designs
199(2)
11.1 Meta-Analyses
199(1)
11.2 Cost-Effectiveness Studies
199(1)
11.3 Qualitative Studies
200(1)
11.4 Cohort Studies in Health Sciences Librarianship
201(1)
12 Applications of Clinical Trials, Cohort Studies, and Hospital-Based Studies in Clinical Medicine
201(1)
13 Future Expectations
202(7)
References
202(7)
11 Clinical Trials in Precision Medicine
R. Simon
1 Introduction
209(1)
2 Phase II Basket Discovery Trials
210(1)
3 Targeted (Enrichment) Phase III Designs
211(1)
4 Adaptive Enrichment Designs
212(2)
4.1 Single Binary Biomarker
213(1)
4.2 More General Adaptive Enrichment
213(1)
5 Conclusion
214(3)
References
214(3)
12 Time to Educate Physicians and Hospital Staff in Electronic Medical Records for Precision Medicine
S. Sharma
A. Munshi
V. Sharma
1 Introduction
217(1)
2 Linking Clinical Information and Bench Science
217(1)
3 Electronic Medical Record and Clinical Decision Support System
218(1)
4 Electronic Medical Record as a Foundation for Clinical Decision Support System
219(1)
5 Precision Medicine and Supercomputers
220(4)
6 The Use of Bioinformatics and Integrated Knowledge Environments
224(1)
7 Data Integration Facilitating Medical Research
225(1)
8 Ethical Issues in Electronic Health Records
226(1)
9 System Implementation
227(1)
9.1 Data Inaccuracies
228(1)
10 eMERGE (Electronic Medical Records and Genomics) Consortium
228(1)
11 Conclusion
229(4)
References
230(3)
13 Computational Approaches in Precision Medicine
J. Espinal-Enriquez
R.A. Mejia-Pedroza
E. Hernandez-Lemus
1 Introduction
233(2)
2 Computational Tools in P4 Medicine I: Hardware and Infrastructure
235(2)
2.1 General Hardware Tools
235(2)
3 Computational Tools in P4 Medicine II: Software Resources
237(1)
3.1 An Overview for Software Tools in Precision Medicine
237(1)
3.2 Systems Biology Software
238(1)
4 Computational Tools in P4 Medicine III: Biological Databases, Standards, and Ontologies
238(5)
4.1 Systems Biology Markup Language (SBML): An Approach for Unifying Biomedical Information
239(1)
4.2 BioNetGen Language (BNGL)
239(1)
4.3 BioModels Database
239(1)
4.4 COPASI
240(1)
4.5 Computational Tools for Metabolomics
240(1)
4.6 Computational Tools for Epigenetics
241(1)
4.7 Computational Tools for Imaging
242(1)
4.8 Computational Tools in P4 Medicine IV: Data Mining and Natural Language Processing
242(1)
5 Some Relevant Works on Computational Tools in Precision Medicine
243(1)
6 Final Considerations
244(7)
Acknowledgments
245(1)
References
246(5)
14 Handling Big Data in Precision Medicine
E. Hernandez-Lemus
J. Espinal-Enriquez
R. Garcia-Herrera
1 Introduction
251(1)
2 From Evidence-Based Medicine to Information-Based Precision Medicine
252(3)
2.1 The Promise of Big Data Analytics
254(1)
3 Computational Challenges for Big Data in Precision Medicine
255(5)
3.1 Cloud-Based Computations and Precision Medicine
256(1)
3.2 Software Resources for High-Throughput Data
257(1)
3.3 Data Integration in Precision Medicine
258(1)
3.4 The Dark Sea of Metadata
259(1)
4 Ethical and Legal Challenges for Big Data in Precision Medicine
260(2)
5 Conclusions and Perspectives
262(7)
Acknowledgments
262(1)
References
263(6)
15 Trends in Precision Medicine
Jaspreet Kaur
B. Rahat
S. Thakur
Jyotdeep Kaur
1 Introduction
269(3)
2 Phenotyping in Precision Medicine
272(5)
2.1 Limitations of Earlier Phenotyping
272(1)
2.2 Deep Phenotyping
273(1)
2.3 Precise Matching of Deep Genomic and Phenotypic Models
274(1)
2.4 New Approach for Capturing Phenotypes
274(1)
2.5 Utility of Electronic Health Records for Precision Medicine
275(1)
2.6 Modeling with Nonhuman Species
275(1)
2.7 Human Phenome Project
276(1)
2.8 Transcriptome Data Sets
277(1)
3 Precision Diagnosis
277(1)
3.1 NGS in Precision Diagnosis
277(1)
4 Biomarkers in Precision Medicine
278(1)
5 Precision Medicine in Diseases
279(3)
5.1 Precision Medicine in Cancer Care
279(2)
5.2 Precision Medicine in Diabetes
281(1)
6 Role of Nanomedicine in Precision Medicine
282(2)
6.1 Role of siRNA in Precision Nanomedicine
282(2)
6.2 CRISPR-CAS Technology for Gene Editing and Precision Medicine
284(1)
7 Computational Approaches and Handling of Big Data in Precision Medicine
284(5)
7.1 The Big Data
284(2)
7.2 Variant Databases
286(1)
7.3 Extracting Variant Data From Literature
286(2)
7.4 Determining the Deleterious Variants
288(1)
8 Commercial and Market Access Considerations in Precision Medicine
289(1)
9 Policies and Ethical Issues in Precision Medicine
289(2)
10 Precision Medicine for Population Health
291(1)
11 Conclusion
291(10)
References
292(9)
16 Personalized Medicine: Interdisciplinary Perspective, World Tidal Wave, and Potential Growth for the Emerging Countries
V. Lemay
P. Hamet
C. Hizel
E. Lemarie
Y. Tremblay
1 A Social and Epistemologic Reflection That Goes Beyond Medicine Frontier
301(2)
2 Exportable Virtues of Precision Medicine
303(7)
2.1 Place of Pharmacogenetics in Precision Medicine
304(5)
2.2 Conclusion
309(1)
3 Conclusion
310(5)
References
310(5)
Index 315
Dr. Mukesh Verma is a Program Director and Chief in the Methods and Technologies Branch (MTB), Epidemiology and Genetics Research Program (EGRP) of the Division of Cancer Control and Population Sciences (DCCPS) at the National Cancer Institute (NCI), National Institutes of Health (NIH). Before coming to the DCCPS, he was a Program Director in the Division of Cancer Prevention (DCP), NCI, providing direction in the areas of biomarkers, early detection, risk assessment and prevention of cancer, epigenetics, epidemiology, and cancers associated with infectious agents. Since joining the NCI, he has sought to champion the visibility of and investment in cancer epigenetics research both within the Institute and across other federal and non-governmental agencies, and to raise public awareness about controlling cancer. He represents NIH in Common Fund Programs on Epigenomics, Metabolomics, and Molecular Transducers of Physical Activity. Dr. Mukesh Verma holds a M.Sc. from Pantnagar University and a Ph.D. from Banaras Hindu University. He did postdoctoral research at George Washington University and was a faculty member at Georgetown University Medical Center. He has published 161 research articles and reviews and edited five books in cancer biomarkers, epigenetics and epidemiology field. Dr. Debmalya Barh is currently a Visiting Full Professor (Titular, Grade-E) in Bioinformatics and Precision Health at the Department of Genetics, Ecology, and Evolution, ICB, Federal University of Minas Gerais, Brazil and honorary scientist of the Institute of Integrative Omics and Applied Biotechnology (IIOAB), India. With over 20 years of experience, he has led academic, healthcare, molecular diagnostic, and bioinformatics industry endeavors. He works with more than 400 scientists from 100+ top ranked organizations across 40+ countries and has 220+ publications and a branded editor for 10+ cutting-edge omics related reference books. He is an expert in in precision/personalized health and integrative omics-based biomarker and target discovery in infectious and complex lifestyle diseases.
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