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Genomic and Personalized Medicine
 
 

Genomic and Personalized Medicine, 2nd Edition

V1-2

 
Genomic and Personalized Medicine, 2nd Edition,Geoffrey Ginsburg,Huntington Willard,ISBN9780123822284
 
 
 

Ginsburg  &   Willard   

Academic Press

9780123822284

1352

Winner of a Highly Commended BMA Medical Book Award for Medicine

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Key Features

  • Highly Commended 2013 BMA Medical Book Award for Medicine
  • More than 100 chapters, from leading researchers, review the many impacts of genomic discoveries in clinical action, including 63 chapters new to this edition
  • Discusses state-of-the-art genome technologies, including population screening, novel diagnostics, and gene-based therapeutics
  • Wide and inclusive discussion encompasses the formidable ethical, legal, regulatory and social challenges related to the evolving practice of genomic medicine
  • Clearly and beautifully illustrated with 280 color figures, and many thousands of references for further reading and deeper analysis

Description

Genomic and Personalized Medicine, Second Editionwinner of a 2013 Highly Commended BMA Medical Book Award for Medicine — is a major discussion of the structure, history, and applications of the field, as it emerges from the campus and lab into clinical action. As with the first edition, leading experts review the development of the new science, the current opportunities for genome-based analysis in healthcare, and the potential of genomic medicine in future healthcare. The inclusion of the latest information on diagnostic testing, population screening, disease susceptability, and pharmacogenomics makes this work an ideal companion for the many stakeholders of genomic and personalized medicine.

With advancing knowledge of the genome across and outside protein-coding regions of DNA, new comprehension of genomic variation and frequencies across populations, the elucidation of advanced strategic approaches to genomic study, and above all in the elaboration of next-generation sequencing, genomic medicine has begun to achieve the much-vaunted transformative health outcomes of the Human Genome Project, almost a decade after its official completion in April 2003.

Readership

Specialists across medical disciplines, research professionals in human genetics/genomics, oncology, neuroscience, gene therapy, molecular medicine, and related areas. It will be indispensable to medical students and graduate students in genetics and biomedical sciences.

Geoffrey Ginsburg

Dr. Ginsburg is the founding Director of the Center for Applied Genomics & Precision Medicine in the Duke Institute for Genome Sciences & Policy. He is also Professor of Medicine and of Pathology at Duke University Medical Center, Professor of Biomedical Engineering at Duke Pratt School of Engineering, and Co-Director of the Duke Translational Medicine Institute.

Affiliations and Expertise

Institute for Genome Sciences & Policy, Duke University, Durham, NC, USA

View additional works by Geoffrey S. Ginsburg

Huntington Willard

PhD

Huntington Willard is President and Director of the Marine Biological Laboratory and Professor of Human Genetics at the University of Chicago. Prior to his appointment at the MBL, Willard was on the faculty at Duke University, where he was founding director of the university-wide Duke Institute for Genome Sciences & Policy from 2003 to 2014, the Nanaline H. Duke Professor of Genome Sciences, and the Arts & Sciences Professor of Biology & Genome Sciences.

Affiliations and Expertise

President and Director, The Marine Biological Laboratory, Woods Hole, Massachusetts, and Professor of Human Genetics, University of Chicago, Chicago, IL, USA

View additional works by Huntington F Willard

Genomic and Personalized Medicine, 2nd Edition

Foreword

Preface

Acknowledgments

Abbreviations

Contributors

Volume 1

Chapter 1. The Human Genome: A Window on Human Genetics, Biology, and Medicine

Introduction

The Human Genome

Variation in the Human Genome

Expression of the Human genome

Genes, Genomes, and Disease

From Genomes to Personalized Medicine

Conclusion

References

Chapter 2. Mapping the Functional Genome: The ENCODE and Roadmap Epigenomics Projects

Introduction

General Organization and Directives for ENCODE and Roadmap

Scientific Parameters and Elements of the Projects

Challenges and the Future

References

Recommended Resources

Chapter 3. Population Perspectives on Genome Variation and Complex Disease

Introduction

Why Study Complex Disease in Populations?

What can be Studied? Phenotypes in Population Genomic Studies of Complex Disease

Human Population History and the Reservoir of Human Genome Sequence Variation

Human Genomes Contain Footprints of Human Evolution and the Human Past

Conclusions

References

Chapter 4. Gene–Environment Interactions: Eco-Genetics and Toxicogenomics

Introduction

Eco-Genetics

Methods to Study G × E Interactions

Nutrigenomics

Pathogens and Host Susceptibility or Resistance Gene Variants

Inhaled Chemical Air Pollutants and Allergens and Sensitizing Agents

Examples of Risk Factors

Epigenomics and the Environment

Effects on Protein Folding

Toxicogenomics and Predictive Toxicology

Will Personalized Genomic Risk Profiles Motivate PEOPLE to Adopt More Healthful Behaviors?

Future Prospects: Balancing the Gxe Equation

References

Recommended Resources

Chapter 5. Systems Biology and Systems Medicine

Introduction

Systems Science in Biology and Medicine

Multi-Parameter Blood-Borne Biomarkers

Emerging in Vivo and in Vitro Technologies

Computational and Mathematical Challenges in Systems Medicine

Conclusions and Perspectives

References

Chapter 6. Personal Genomics

Introduction

Domains of Personal Genomics

Key Ethical, Legal, and Social Questions

Personal Genomics and Research Participation

Summary

References

Recommended Resources

Chapter 7. Whole-Genome Sequencing: New Technologies, Approaches, and Applications

Introduction

Fundamentals of Next-Generation Sequencing Instruments

Considerations of Next-Generation Sequence Read Data

Fundamentals of Whole-Genome Sequencing

Bioinformatics-Based Discovery with Whole-Genome Sequencing Data

Validation of Identified Variants by Orthogonal Data

Future Prospects and Challenges for Whole-Genome Sequencing

Clinical Applications of Whole-Genome Sequencing to Cancer

References

Recommended Resources

Chapter 8. Human Genome Variation Discovery via Exome and Whole-Genome Sequencing

Introduction

Population-Based Variation Discovery

Sequencing Approaches to Variation Discovery

Informatic Approaches to Variation Discovery

Exome and Whole-Genome Sequencing in Rare Early-Onset Disease

References

Chapter 9. Clinical Genome Sequencing

Introduction

Challenges of Genome Sequencing in the Clinical Laboratory

Challenges of Using Genome Sequencing in Medical Practice

Conclusions

Acknowledgments

References

Chapter 10. Structural Genomic Variation in the Human Genome

Introduction

Basic Principles of Copy Number Variation

Detecting CNVs in a Genome-Wide Manner

Association of CNVs to Disease and Disease Susceptibility

Implications of CNVs

References

Recommended Resources

Chapter 11. Clinical Applications of Whole-Genome Chromosomal Microarray Analysis

Introduction

Whole-Genome Copy Number Variant Arrays Designed for Clinical Diagnostic Use

Interpretation of CMA in a Clinical Setting

Incomplete Penetrance and Variable Expressivity

CMA in Postnatal Populations

Potential for CMA in other Clinical Settings

Whole-Genome CMA as a Model for the Clinical Introduction of Whole-Genome Sequencing

Summary and Conclusions

References

Recommended Resources

Chapter 12. Transcriptomics in the Age of Ultra High-Throughput Sequencing

Introduction

A Paradigm Shift in Gene Expression Analysis

Quantitative Analysis of Novel and Alternative Expression

Nucleotide-Level Sequence Differences in Transcriptomes

Utility of SNVs for Analyzing Tumor Transcriptomes

Correspondence of SNVs with Gene Expression in Healthy Individuals

MicroRNAs as Biomarkers

Perspectives

References

Chapter 13. Quantitative Proteomics in Genomic Medicine

Introduction

Clinical Proteomics

Enabling Technologies of Proteomics

Exemplar Clinical Proteomics Study

Summary

References

Recommended Resources

Chapter 14. The Human Microbiome and Personalized Medicine

Introduction

The Relationship Between Human Microbes and Disease

Advanced Technologies for the Study of the Human Microbiome

International Metagenome Projects

Personalized Medicine Targeting our “Other” Genome

References

Recommended Resources

Chapter 15. Glycomics, Glycobiology, and Glyco-Medicine

Introduction

Glycomics

Biosynthetic Pathways and Glycan Functions

Congenital Disorders of Glycosylation

Examples of Multisystemic Disorders

Disorders with More Restricted Phenotypes

Other Disorders Affecting N-Glycans

Excessive N-Glycosylation?

Disorders in Golgi Homeostasis

Defects of O-Linked Glycosylation

Defects in O-Xylose Glycosaminoglycans

Defects in O-Galnac Glycans

Defects in O-Fucose Glycans

Defects in Glycolipid Synthesis

Conclusions and Perspectives

Acknowledgments

References

Chapter 16. Genome-Wide RNA Interference Screening

Introduction

Brief History of RNAi

General Mechanisms of RNAi

RNAi Screening

Validation and Analysis

Future of RNAi Technology and Therapeutics

References

Chapter 17. Application of Human Genome Information to Clinical Practice

Introduction

Genome-Wide Variation and Medicine

Whole-Genome Sequencing for the Clinic

Family History

Assessment of Chronic Disease Risk

Diagnosis and Disease Classification Using Molecular Profiles

Single and Multimarker Predictors of Prognosis

Drug Response

A Roadmap for Translation

Challenges to clinical Application

Privacy

New Models needed for translational Genomics

Summary

References

Chapter 18. Genomic, Personalized Medicine and Public Health

Introduction

Public Health Assessment

Preventive and Preemptive Medicine

Assessing Validity and Utility

Conclusion

References

Recommended Resources

Chapter 19. Biospecimen Banking in the Post-Genome Era

Introduction

Garbage In, Garbage Out

Preanalytical Variations

Importance of Standardization

Researchers’ Biobank Wish List

Biobanks Must Evolve

Need for Guidelines

Need for Biospecimen Research

Need for Investment

Conclusions

Acknowledgments

References

Recommended Resources

Chapter 20. Designing Genomics-Based Clinical Studies

Introduction

Stages of Development and Validation of Prognostic and Predictive Classifiers

Validation of Prognostic Biomarkers

Prospective Validation of Predictive Biomarker Classifiers

Predictive Analysis of Clinical Trials

Conclusion

References

Recommended Resource

Chapter 21. Genomic Biomarkers in Human Population Studies

Genomic Biomarkers

Genetic Biomarkers for Intermediate Phenotypes

The Use of Genomic Biomarkers in Risk Prediction

Pharmacogenetics

Future Directions

References

Chapter 22. Validation of Candidate Protein Biomarkers

Introduction

From Discovery to Validation

Validation of Protein Biomarkers

Preferred Methods of Validating Protein Biomarkers

Emerging Technologies for Validating Protein Biomarkers

Conclusion

References

Chapter 23. Translational Bioinformatics for Genomic Medicine

Introduction

Diagnosis

Therapeutics

Histopathology

Nosology

Analytic Methods

Where Data for Studies may be Found

Bioinformatics Vocabularies and Ontologies

Freely Available Bioinformatics Tools

Conclusion: High-Bandwidth Approaches for Genomic Medicine

Acknowledgments

References

Recommended Resources

Chapter 24. Electronic Health Records in Genomic Medicine

Introduction

EHRs and Genomic Information

Federal Influence on EHR Development

Opportunities for Integration of Genomic Information with EHRs

EHR End-User Case Study: the Geisinger Health System

Conclusion

References

Chapter 25. Clinical Implementation of Genomic Medicine in Primary Care

Introduction

Role in Primary Care

Barriers

Summary

A Case Study: Genomic Markers for Type 2 Diabetes Mellitus Risk

References

Chapter 26. Family History and Health Risk Assessment

The Rationale for Familial Risk Assessment

The Rationale for Family History Tools

Family History Tools: Development, Structure, and Applications

Test Performance of Family History Tools

Family History, Risk Perception and Motivation of Healthy Behaviors

Clinical Decision Support

References

Recommended Resources

Chapter 27. Clinical Decision Support

Introduction

Brief History of CDS and Prototypical Systems

Application of CDS to Support Genomic and Personalized Medicine

Challenges and Potential Solutions

Conclusion

Acknowledgments

Disclosures

References

Recommended Resources

Ongoing Research

Chapter 28. Knowledge Management to Support Personalized Healthcare

Introduction to Knowledge Management

Policy Implications

Infrastructure to Support Knowledge Management

Case Study

The Business Case for Knowledge Management

Summary

References

Chapter 29. Delivery of Personalized Medicine in an Integrated Healthcare System

Introduction

The Clinical Problem – Identification of Patients with Lynch Syndrome

Building on Success

Conclusion

References

Recommended Resources

Chapter 30. Pharmacogenomics in Drug Discovery and Development

Introduction

Identifying New Molecular Targets for Drug Discovery

Pharmacogenomics of Drug Absorption, Distribution, Metabolism, and Elimination

Pharmacogenomics in Drug Development

Conclusions

References

Recommended Resources

Chapter 31. Pharmacogenetics and Pharmacogenomics

Introduction

Molecular Diagnostics for Optimizing Drug Therapy

Drug Metabolism

Genetic Polymorphisms of Drug Targets

Global Health Applications

Application in Drug Development

Challenges Going Forward

References

Recommended Resources

Chapter 32. Point-of-Care Devices

Introduction

Point-of-Care Devices: Design Considerations, Progress of Development

Novel Sensor Implementation for Point of Care Devices

Current Challenges and Outlook for Point of Care Devices

References

Chapter 33. Patient-Specific Pluripotent Stem Cells

Introduction

Reprogramming: An Evolving Technology

Generating Disease-Relevant Cell Types from Human Stem Cells

Working toward the Ultimate Goal: Transplantation and Tissue Engineering

Additional Roles for Patient-specific iPS Cells

Summary

References

Chapter 34. Overview of Policy, Ethical and Social Considerations in Genomic and Personalized Medicine

Introduction

Ethical Issues in Large-Scale Genetics and Genomics Research and Individual Whole-Genome Analysis

Integrating Genomic Medicine Applications in Healthcare

Conclusion

References

Chapter 35. Informed Consent

Introduction

When is Informed Consent Required?

Informed Consent Disclosures and Comprehension

Special Considerations

Conclusions

References

Recommended Resources

Chapter 36. Educational Issues and Strategies for Genomic Medicine

Introduction

Gaps in Current Understanding

Educational Opportunities to Close the GAPS

The Future

Concluding Thoughts

References

Recommended Resources

Chapter 37. Regulatory Issues for Genomic Technologies

Introduction

Regulation of Genomic Tests: an Overview

Pharmacogenomics in Drug Development and Clinical Medicine: the Role of Regulation

Federal Regulation of Genetic Therapeutics

FDA Efforts to Advance Genomic Product Development

Conclusions

References

Recommended Resources

Chapter 38. Challenges and Regulation of Direct to Consumer Testing

Introduction

The Meaning of “DTC”

Risks and Benefits

Consumer Impact

Federal Oversight of DTC Testing

Conclusion

References

Recommended Resources

Chapter 39. Economic Issues and Genomic Medicine

Introduction

Economic Evaluation and Cost-Effectiveness Analysis

Evaluating Genomic Technologies

Economic Incentives and the Future of Genomic Medicine

Summary

References

Chapter 40. Strategic Issues in the Adoption of Genome-Based Diagnostics

Introduction

Clinical Validation

Modulators of Test Adoption

Regulatory Requirements

Physician Practice Factors Associated with Test Adoption

Companion Diagnostics

Maturity/Plateau Phase

Conclusions

References

Chapter 41. Reimbursement

Introduction

Coding, Coverage, and Payment

Conclusions and Outlook

References

Recommended Resources

Chapter 42. Genomics and Patents: A Practical Guide for Genome Scientists and Clinical Researchers

Introduction

Some Famous Cases

Some Questions About Patenting and Licensing Genomic Inventions

Conclusions

References

Recommended Resources

Chapter 43. Public–Private Partnerships in Biomarker Research

Introduction

The Challenge of Biomarker Research and Development

The Growth of Public–Private Partnerships in Biomarker Research

Public–Private Partnerships in Biomarker Research

Common Challenges and Approaches

Critical Success Factors

The Future of Biomarker PubLic–Private Partnerships

References

Recommended Resources

Volume 2

Chapter 44. Hypertension

Introduction

Finding Blood Pressure Genes

New Insights into Blood Pressure Biology

Developing New Therapies for Cardiovascular Disease

Utility of a Genetic Risk Score

Conclusion

Acknowledgments

References

Chapter 45. Lipoprotein Disorders

Introduction

Overview of Lipoprotein Metabolism

Inherited Basis of Plasma Lipid Traits

Mendelian Disorders of Lipoprotein Metabolism

Association of Common Variants with Plasma Lipid Traits and Relationship to Cardiovascular Disease

Future Directions

References

Chapter 46. Coronary Artery Disease and Myocardial Infarction

Introduction

Scanning for Susceptibility SNPs

Mendelian Randomization

Lipid Traits

Coronary Artery Disease and Myocardial Infarction

Pharmacogenomics

Non-DNA Approaches to CAD and MI

Future Directions

References

Chapter 47. Atherosclerosis, Vulnerable Plaques, and Acute Coronary Syndromes

Plaque Rupture and Erosion

Plaque Vulnerability

Challenges for Prevention

Personalized Risk Prediction

Challenges for Treatment of Advanced Atherosclerosis

References

Chapter 48. Heart Failure

Definitions

Predisposition – Genetic and Non-Genetic

Screening

Pathophysiology

Diagnosis

Prognosis

Monitoring

Novel Therapeutics and Future Directions

Disease Modeling for Personalized Healthcare

Conclusions and Recommendations

Acknowledgments

References

Chapter 49. Cardiac Transplant Rejection

Introduction

Types of Cardiac Allograft Rejection

Immunosuppression Strategies to Prevent Rejection

Strategies for Monitoring Transplant Recipients

Development of a Gene Expression Signature for Acute Cellular Rejection in Cardiac Transplant Recipients

Pathways Monitored by the AlloMap® Test

Regulatory Approvals of the AlloMap® Test

Clinical Use of the AlloMap® Test

Future Directions of Gene Expression Profile Testing

References

Chapter 50. Hypertrophic Cardiomyopathies

Definitions, Clinical Presentation and Diagnosis

Molecular Genetics of Hypertrophic Cardiomyopathy

Screening and Treatment for HCM

Conclusions

References

Chapter 51. Arrhythmias

Introduction

Inherited Arrhythmia Syndromes and Arrhythmia Mechanisms

Gene- and Mutation-Specific Features in Inherited Arrhythmia Syndromes

Genetic and Genomic Modifiers in Inherited Arrhythmia Syndromes

Bradyarrhythmias and Mechanisms of Heart Rate Control

Genetic and Genomic Modifiers of Heart Rate

Atrial Fibrillation/Flutter and Arrhythmia Mechanisms

Genetic and Genomic Modifiers in Atrial Fibrillation

Ventricular Tachyarrhythmias and Mechanisms of Sudden Cardiac Death

Genetic and Genomic Modifiers of Sudden Cardiac Death

Genetic and Genomic Modifiers of Arrhythmia Therapies

Clinical Applications of Genetic Testing

Conclusion

References

Chapter 52. Hemostasis and Thrombosis

Hemostasis and Blood Coagulation

Evolutionary Genomics and Coagulation

Heritability of Coagulation

Genetics of Platelet Function

Genetic–Environmental Interface

Race, Culture, and Ethnicity

Patient and Population Screening

Treatment Considerations in Thrombosis and Pharmacogenetics

Pharmacogenetics

Future Directions in Genetics and Genomics

References

Chapter 53. Peripheral Arterial Disease

Introduction

Epidemiology and Risk Factors for Peripheral Arterial Disease

Clinical Manifestations of Peripheral Arterial Disease

Therapeutic Strategies for Peripheral Arterial Disease

Intermittent Claudication and Critical limb Ischemia are Distinct Clinical Outcomes of Peripheral Arterial Disease

Genetic Susceptibility to Peripheral Arterial Disease

Biomarkers of Peripheral Arterial Disease

Future Potential use of Genomic Methodologies in Peripheral Arterial Disease

References

Chapter 54. Congenital Heart Disease

Introduction

What is Congenital Heart Disease?

Origins of Congenital Heart Disease

Congenital Heart Disease and Single Gene Disorders

Origins of Pleiotropic Heart Defects in Single Gene Disorders

What are Complex Traits?

Issues to Consider in Future Studies

Summary

References

Recommended Resources

Chapter 55. Perioperative Genomics

Scientific Rationale for Perioperative Genomic Medicine

Perioperative Cardiac Adverse Events

Perioperative Atrial Fibrillation

Postoperative Event-Free Survival

Postoperative Stroke and Neurocognitive Dysfunction

Perioperative Acute Kidney Injury

Dynamic Genomic Markers of Perioperative Outcomes

Conclusions

Acknowledgments

References

Chapter 56. Stroke

Introduction

Dissecting the Stroke Phenotype

Heritability of Stroke

Monogenic Forms of Stroke

Genomics of Common Complex Stroke

Pharmacogenetics

Overcoming Heterogeneity in the Stroke Phenotype

Future Directions

Clinical Implications of Genomic Discoveries in Stroke

Conclusion

Acknowledgments

References

Chapter 57. Lymphomas

Introduction

Clinical Presentation and Staging

The Role of Key Genes in Lymphoma

MicroRNA

Gene Expression Signatures

Genomics by Lymphoma Type

Summary

References

Chapter 58. Leukemias

Introduction

Leukemia Cytogenetics and Molecular Genetics

A Decade of Transcriptomics in Leukemia

Genomics has Opened New Avenues in Leukemia Research

Leukemia Epigenomics

Proteomics and Functional Genomics – The Future has Begun

Future Challenges of Genomics in Leukemia

Acknowledgments

References

Recommended Resources

Chapter 59. Lung Cancer

Introduction

Early Diagnosis/Screening of Lung Cancer

Classification and Prognosis

Pathogenesis and Treatment of Lung Cancer

Conclusion

References

Chapter 60. Breast Cancer

Introduction

Risk Factors

Prognostic Factors

Predicting Therapeutic Response

Discovery of New Biomarkers

Individualizing Treatment

References

Chapter 61. Ovarian Cancer

Origins of Epithelial Ovarian Cancer

Inherited Syndromes of Ovarian Cancers

Genome-Wide Association Studies

Transcriptional Profiling of Ovarian Cancer Histologic Subtypes

Metastasis of Ovarian Cancers

Integrated Genomic Analyses of Ovarian Carcinoma

Angiogenesis

Epigenetics

Pharmacogenomics and Ovarian Cancer

Summary

References

Chapter 62. Colorectal Cancer

Introduction

Genetics of Colorectal Cancer

Epigenetics of Colorectal Cancer

Genetics of Colorectal Cancer-Associated Syndromes

Missing Heritability in Colorectal Cancer

“Epimutations” and Hereditary Colorectal Cancer

Gene Silencing from Transcriptional Read-Through

Novel Colorectal Cancer Predisposing Genes

Functional Grouping of Variants in Pathways

Moderate Risks and Modifier Genes

Perspectives

Acknowledgments

References

Chapter 63. Prostate Cancer

Introduction

Germline Genetics of Prostate Cancer

Somatic Genetics of Prostate Cancer

Epigenetics of Prostate Cancer

Conclusions

References

Chapter 64. Head and Neck Cancer

Head and Neck Squamous Cell Carcinoma

Conclusion

References

Chapter 65. Brain Tumors and Gliomas

Introduction

Predisposition

Screening

Diagnosis and Prognosis

Pharmacogenomics

Monitoring

Novel and Emerging Therapeutics

Conclusions

References

Chapter 66. Melanoma

Introduction

Melanoma Progression

Genetics of Melanoma

Genomic Strategies to Characterize Melanoma

Clinical Applications of Genomics in Melanoma

Conclusion

References

Recommended Resources

Chapter 67. Metastatic Cancer

Introduction

The Genetics of Metastasis

The Genomics of Metastasis

New Treatment Possibilities for Metastatic Cancer

Clinical Diagnostics

Conclusions

References

Recommended Resources

Chapter 68. Bioinformatics in Personalized Cancer Care

Introduction

Biomedical Informatics Capabilities Driven by the Study of Cancer

Translatable Informatics

Toward an IT-Enabled Ecosystem

References

Recommended Resources

Chapter 69. Diagnostic-Therapeutic Combinations

Introduction

Targeted Therapies for Cancer

The Ideal Target

The First Diagnostic-Therapeutic Combination

Diagnostic-Therapeutic Combinations for Leukemia and Lymphoma

Selected Targeted Anticancer Therapies Using Small Molecules

Pharmacogenomics

Pharmacogenetics

Whole Genome Analysis by Next-Generation DNA Sequencing

Developing Diagnostic-Therapeutic Combinations

Conclusion

References

Chapter 70. Autoimmune Disorders

Introduction

HLA and Autoimmunity

Gene Discovery in Autoimmunity: The Example of Multiple Sclerosis

Systematic Assessment of Commonalities and Differences Among Autoimmune Diseases

The Next Steps in Complex Genetics Research

Systems Biology

Conclusions

References

Chapter 71. Rheumatoid Arthritis

Introduction

Clinical Features

Predisposition

Screening

Diagnosis, Prognosis, and Monitoring

Pharmacogenomics

Conclusions

References

Chapter 72. Multiple Sclerosis

Introduction

Genomics

Transcriptomics

Immunomics

Proteomics

Platforms for the Identification of New Therapeutic Targets

Conclusion

References

Chapter 73. Inflammatory Bowel Disease

Introduction

Epidemiology

Disease Phenotypes

Pathogenesis and Risk Factors

What Was Known Before Genome-Wide Association Studies

Genome-Wide Association Study Findings

Implications of Disease-Associated Loci to Pathogenesis

Risk Prediction

Pharmacogenomics

Conclusion

References

Ongoing Research

Recommended Resources

Chapter 74. Asthma

Introduction

Candidate Gene Studies

Positionally Cloned Genes

Whole-Genome Association Studies

Vitamin D and Asthma

Lessons Learned

References

Chapter 75. Chronic Obstructive Pulmonary Disease

Summary

Introduction

Predisposition

Pathophysiology

Cellular and Molecular Mechanisms

Diagnosis and Screening

Prognosis

Management

New Treatments

Conclusions

References

Chapter 76. Interstitial Lung Disease

Introduction

Genetic Determinants of Diffuse Parenchymal Lung Disease in Mouse Strains

Genetic Determinants of Sarcoidosis

Genomic Medicine and Sarcoidosis

Proteomics in Sarcoidosis

Surfactant Proteins and Diffuse Parenchymal Lung Disease

Genetic Determinants of Pulmonary Fibrosis Identified in Rare Inherited Disorders

Genetic Determinants of Familial Interstitial Pneumonia

Conclusion

References

Recommended Resources

Chapter 77. Peptic Ulcer Disease

Introduction

The Helicobacter Genome and Virulence Markers

Host Polymorphisms

Pharmacogenomics

Proteomics and Genomics of Ulcer Detection

Genomics and Treatment of Peptic Ulcers

Conclusions

Acknowledgments

References

Ongoing Research

Chapter 78. Cirrhosis

Introduction

Liver Structure

Fibrosis and Cirrhosis

Diagnosis of Cirrhosis

Treatment of Cirrhosis

Genetics of Cirrhosis

The Liver Transcriptome

The Liver Proteome

Development of Liver Fibrosis

Transcriptome Analysis of Liver Disease

Proteomic Studies of Liver Disease

Genetic Markers and Pharmacogenomics of Liver Fibrosis

Future Impact of Genomics

Conclusions

References

Chapter 79. Systemic Sclerosis

Definition

Subsets of SSC

Epidemiology

Etiology and Pathogenesis

Genetic Markers

Clinical Presentation

Development of the Classification Criteria for SSC

Prognostic Markers and Systemic Sclerosis Activity Score

Treatment

Prognosis

References

Chapter 80. Systemic Lupus Erythematosus

Classification and Clinical Features

Epidemiology and Etiology

Mendelian SLE – The Role of Rare Variants

SLE and the MHC

Genome Wide Association Studies

SLE and Copy Number Variation

Epigenetics

The Current Genetic Model and its Uncertainties

Genomics and the Prediction of Disease

Genomics and the Prediction of Clinical Manifestations

Genomics and Individualized Prescribing

References

Recommended Resources

Chapter 81. Osteoarthritis

Personalized Medicine – Choice Versus Cost

Osteoarthritis – The Magnitude of the Problem

Paradigms for Studying Early Osteoarthritis Events

Identifying the Molecular Stage of Osteoarthritis

Joint Injury as a Paradigm for Early OA Identification and Treatment

Advantages of Early Arthritis Identification Illustrated by Rheumatoid Arthritis

Outlook for the Future

References

Chapter 82. Diabetes

Introduction

Epidemiology and Genetics

The Search for Genetic Determinants of Type 2 Diabetes

Insights Gained from Genetic Studies in Type 2 Diabetes

Conclusions and Future Directions

Acknowledgments

References

Chapter 83. The Metabolic Syndrome

Introduction

Heritability of Metabolic Syndrome

Lessons from Monogenic Models of Metabolic Syndrome

Genetics of Common Metabolic Syndrome

The Thrifty Gene Hypothesis

Finding the Missing Heritability

Clinical Implications to Genetic Findings in Metabolic Syndrome

Conclusion

Acknowledgments

References

Chapter 84. Neuroscience and the Genomic Revolution: An Overview

Introduction

Challenges for Genetics in Neuroscience

The Genetic Architecture of Neuropsychiatric Disorders

Environmental and Epigenetic Interactions in Neurogenetics

The Outlook for Personalized and Genomic Medicine in Neuroscience

Conclusion

References

Recommended Resources

Chapter 85. Alzheimer’s Disease

Introduction

Early-Onset Familial AD with Mendelian Transmission

Late-Onset AD without Mendelian Transmission

AD Genetics Beyond GWAS

Conclusion

References

Recommended Resources

Chapter 86. Parkinson’s Disease

Introduction

The Need for Reliable Parkinson’s Disease Biomarkers

Technology for Protein Identification and Validation

Unbiased Profiling Using Cerebrospinal Fluid

Unbiased Profiling Using Brain Tissue

Targeted Validation of Candidate Biomarkers

From Discovery to Validation

Concluding Remarks

Acknowledgments

References

Chapter 87. Epilepsy

Introduction

Why Genomic and Personalized Medicine in Epilepsy?

Genomics in Epilepsy: What Do We Know?

The Future: Challenges and Potential

References

Chapter 88. Schizophrenia and Bipolar Disorder

Introduction

GWAS for Schizophrenia and Bipolar Disorder

Studies of Copy Number Variation

Role of CNVs in Schizophrenia and Bipolar Disorder

Conclusions and Future Directions

References

Chapter 89. Depression

Introduction

Diagnosis, Prevalence, and Course of Depression

Molecular Neurobiology of Depression

Genetic Basis of Major Depression

Conclusions and Future Aspects of Depression Genomics

References

Chapter 90. Autism Spectrum Disorders

Introduction

Defining Autism in the Clinic and in the Laboratory

“Syndromic” Associations with ASD

Chromosomal Disorders and Copy Number Variants

“Nonsyndromic” Genes for ASD

Recessive Mutations in ASD

What are the Roles of Common Variants in ASD?

Early Results of Whole-Exome and Whole-Genome Sequencing in ASD

Mechanistic Insights into Autism from Genetic Studies

Acknowledgments

References

Ongoing Research

Chapter 91. Eye Diseases

Introduction

Genome-Wide Association Studies

Functional Genomics

Pharmacogenomics

Whole-Exome and Whole-Genome Sequencing

Gene-Based Therapies for Ocular Disease

Epigenetics

Ocular Genetic and Genomic Resources

Outlook for the Future

References

Chapter 92. Glaucoma

Introduction

Primary Open-Angle Glaucoma

Exfoliation Glaucoma

Primary Congenital Glaucoma

Developmental Glaucoma

Glaucoma Genetics and Personalized Medicine

References

Recommended Resources

Chapter 93. Diagnosis and Classification of Pathogens

Introduction

Hypothesis and In Vitro Studies

In Vitro Studies

Initial Human Studies: Proof of Concept

New Areas for Improving Diagnosis

References

Chapter 94. Host–Pathogen Interactions

Introduction

Host Response to Bacterial Pathogens

Bacterial Response to the Host

Future Perspective

References

Chapter 95. Microbial Vaccine Development

Introduction

The Ideal Vaccine and Measurement of Response

The Biology of Immune Response to Vaccines

Small Animal Models

Studies in Non-Human Primates and Humans

Practical Considerations

Conclusions

Acknowledgments

References

Chapter 96. Bacterial Infections

Introduction

In Vitro Studies: Host Cell Responses

In Vivo Studies: Genomic Technologies

Future Directions

Conclusion

Acknowledgments

References

Chapter 97. Emerging Viral Infections

Introduction

Viral Genomics

Host Genomics

Future Challenges

Acknowledgments

References

Chapter 98. Sepsis

Introduction

Definitions, Incidence, and Temporal Dynamics

Genetic Variations Associated with Sepsis

Pathogen Recognition/Signaling

Cytokine Polymorphisms

Coagulation

Metabolism

Neurohormonal System

Future Investigations

Integrative Genomics, Molecular Signatures, and Sepsis

Therapeutics

Conclusions

References

Chapter 99. Viral Hepatitis

Introduction

Virology of Hepatitis Viruses

Acquisition and Predisposition to Viral Hepatitis

Screening and Diagnosis of Viral Hepatitis

Viral Hepatitis Prognosis and Natural History

Therapeutics and Pharmacogenomics

Future Impact of GenomicS

ConclusionS

References

Chapter 100. Malaria

Introduction

Malaria and its Causal Agent

Pathogenesis in the Human Host and Immunity

Genomics for the Development of New Antimalarial Strategies

Personalized Medicine and Malaria: How, Where, and When

Acknowledgment

References

Chapter 101. HIV Pharmacogenetics and Pharmacogenomics

Introduction

Pharmacogenetics of Combined Antiretroviral Therapy Toxicity

Established Pharmacogenetic Predictors in HIV Treatment

The Future of HIV Pharmacogenetics and Pharmacogenomics

Conclusions

References

Recommended Resources

Glossary

Index

Quotes and reviews

"I found this book fascinating. The review of the variation in the human genome is outstanding, and the coverage of epigenetics is unique and extremely useful for an understanding of the influence of the environmental factors on gene behavior…The book includes carefully selected illustrations of excellent quality. This is a well-designed publication that readers will find inviting." Rating: 4 Stars--Doody.com, March 21, 2014
"The first volume covers the principles of human genomics and of genome-based approaches to medicine, as well as the enabling and integration of genomic strategies, clinical research, and informatics (including policy challenges). The 58 chapters in the second volume are devoted to the specifics of approaches to particular diseases— cardiovascular, cancer, inflammatory and metabolic, neuropsychiatric, and infectious."--Reference & Research Book News, October 2013
"Publication of this second edition of Genomic and Personalized Medicine 2nd edition occurs roughly nine and half years  after the official completion of the Human Genome Project in April 2003. That monumental, international, and historic Project catapulted forward the fields of genetics and genomics at a pace that only the most optimistic scientific leaders realistically envisioned at that time. Indeed, it is truly stunning to consider what has been accomplished in the past nine-plus years, especially with respect to accomplishments relevant to genomic and personalized medicine. These ~100 chapters elegantly showcase the depth and breadth of this rapidly growing area of biomedicine. Once again, Ginsburg and Willard have recruited an impressive cast of geneticists and genomicists to contribute chapters spanning a wide spectrum of topics - from fundamentals in genomics research to key clinical areas that represent some of the ‘lowest hanging fruit’ in terms of opportunities to have genomics change medical practice. Together, these chapters provide unequivocal evidence about the current state of genomic and personalized medicine - that the opportunities are breathtaking, that the challenges are immense, and that the potential to improve health is nearly unlimited."--Eric Green MD, PhD, Director, NHGRI
"This is the definitive textbook providing the content for a new era of medicine. An era where disease is defined at the molecular level rather than the anatomic level; where therapies are individualized and targeted rather than uniformly applied across a population. We have an opportunity with this text to improve patient outcomes using new tools and strategies, which is certainly an exciting prospect for each of us. This text should be mandatory reading for every physician, or physician in training."--Dietrich Stephan, President and CEO of Silicon Valley Biosystems, Co-Founder of Navigenics, Board of Directors of Personalized Medicine Coalition
[on the first edition] "With genetic discoveries being published weekly, and increasing efforts to translate genomics to the clinic, there is a pressing need to educate medical students, physicians ad policy-makers on the emerging discipline of genomic medicine. This valuable book is first of its kind, offering a comprehensive overview of the field's foundations, applications to each area of medicine, and translation into clinical medicine and policy."--David Altshuler MD, PhD, Professor of Genetics and Medicine, Harvard Medical School, Massachusetts General Hospital

 
 
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