From the Contents:
Biomarkers Past and Future
Quantitative Proteomics Techniques in Biomarker Discovery
Biomarker Qualification: A Company Point of View
Biomarker Discovery and Medical Diagnostic Imaging
Breath: An Often Overlooked Medium in Biomarker Discovery
HTA in Personalized Medicine Technologies
Bone Remodeling Biomarkers: New Actors on the Old Cardiovascular Stage
Identification and Validation of Breast Cancer Biomarkers
Evaluation of Proteomic Data: From Profiling to Network Analysis by Way of Biomarker Discovery
Biomarkers: From Discovery to Commercialization
Clinical Validation
Genomics and Proteomics for Biomarker Validation
For Biochemists, Clinical Chemists, Oncologists, Laboratory Medics, and Analytical Research Institutes.
Table of Contents
List of Contributors XI
Preface XV
1 Biomarkers Past and Future 1
Siegfried Neumann
1.1 Introduction 1
1.2 Definitions of Biomarkers 2
1.3 Biomarkers in the Past 3
1.4 Novel Molecules and Structural Classes of Biomarkers by New Technologies 7
1.5 Biomarkers in Drug Research 9
1.6 Current Development and Future Trends for Biomarkers in Laboratory Diagnostics 12
1.6.1 Biomarker Test Validation 12
1.6.2 Companion Diagnostics in Clinical Pharmacology 14
1.6.3 Biomarker Multivariate Index Assays 16
1.6.4 Regulatory Policies on Biomarker Tests 17
1.7 Summary and Outlook 19
References 20
2 Quantitative Proteomics Techniques in Biomarker Discovery 23
Thilo Bracht, Dominik AndreMegger,Wael Naboulsi, Corinna Henkel, and Barbara Sitek
2.1 Introduction 23
2.1.1 General Considerations 24
2.2 2D–Difference Gel Electrophoresis 27
2.3 Mass Spectrometry–Based Proteomics 29
2.3.1 Principles and Instrumentation 29
2.3.1.1 Ionization Methods 29
2.3.1.2 Mass Analyzers 30
2.3.2 Label–Free Protein Quantification 30
2.3.2.1 Area Under Curve (AUC) or Signal Intensity Measurement 30
2.3.2.2 Spectral Counting 31
2.3.3 Label–Based Proteome Analysis 31
2.4 MALDI Mass Spectrometry Imaging 33
2.5 Conclusion 36
References 36
3 Biomarker Qualification: A Company Point of View 39
Maximilian Breitner, Kaïdre Bendjama, and Hüseyin Firat
3.1 Introduction 39
3.2 Biomarker Uses 40
3.3 Biomarker Types 41
3.4 Validation vs. Qualification 43
3.5 Strategic Choices in Business Models 43
3.6 Validation of Analytical Methods 44
3.6.1 Currently Applicable Guidelines for the Validation of Analytical Methods 45
3.6.2 Laboratory Proficiency 46
3.6.3 Establishment of Reference Ranges for Candidate Biomarkers 46
3.7 Clinical Qualification of Candidate Biomarkers 47
3.7.1 Methodological Approaches 47
3.7.2 Study Size for Biomarker Performance Characterization 48
3.7.3 Sample Quality and Biobanking 50
3.7.3.1 Sample Collection 50
3.7.3.2 Storage of Sample 51
3.7.3.3 Clinical Data (Sample Annotation) 52
3.7.3.4 Ethical Considerations 53
3.8 Biomarker Qualification in the omics Era 53
3.9 An Example of a Biomarker Provider 54
3.10 Conclusion 55
References 55
4 Biomarker Discovery and Medical Diagnostic Imaging 59
Andreas P. Sakka and James R.Whiteside
4.1 Introduction 59
4.1.1 Imaging Modalities 59
4.1.1.1 Positron Emission Tomography (PET) 59
4.1.1.2 Single Photon Emission Computed Tomography (SPECT) 60
4.1.1.3 Computed Tomography (CT) 60
4.1.1.4 Magnetic Resonance Imaging (MRI) 60
4.1.1.5 Ultrasound (US) 61
4.2 Factors to Consider in Biomarker Selection for Imaging 61
4.3 Defining the Insertion Point of the Assay and Its Business Case 62
4.4 Practical In Vitro Methods Used to Identify Biomarkers 63
4.5 Preclinical Models 64
4.5.1 Model Species 64
4.5.2 Inducing Human Disease and Relevant Biomarker Expression 64
4.5.3 Genetic Manipulation 65
4.5.4 Pharmacological/Chemical Induction 65
4.5.5 Xenografts: Grafting Foreign Cells or Tissues 66
4.5.6 Physical Induction 66
4.6 Preclinical Analysis Techniques 67
4.7 Translational Considerations and Restrictions 67
4.8 Other Uses of Preclinical Models 68
4.9 Nuclear Imaging Infrastructure 69
4.10 Image Processing 70
4.11 Concluding Remarks 70
References 71
5 Breath: An Often Overlooked Medium in Biomarker Discovery 75
Jonathan D Beauchamp and Joachim D Pleil
5.1 Introduction 75
5.1.1 Breath Analysis: Past and Present 76
5.2 Breath Analysis Studies: Targets, Techniques, and Approaches 77
5.2.1 Exhaled Breath Gas, Condensate, and Aerosols 79
5.2.2 Sampling Techniques and Analytical Tools 80
5.2.3 Discovery Versus Targeted Study Approaches 81
5.3 Biomarker Confounders 83
5.3.1 Sampling Impact 83
5.3.1.1 Online Breath Sampling and Direct Analysis 84
5.3.1.2 Breath Sampling for Offline Analysis 84
5.3.2 Contributions from the Exposome 85
5.4 Biomarkers in Breath 86
5.4.1 Inorganic Breath Biomarkers 86
5.4.2 Organic Biomarkers in Breath 87
5.5 Outlook for Breath Analysis 88
Acknowledgments 90
References 90
6 HTA in Personalized Medicine Technologies 95
Franz Hessel
6.1 Introduction 95
6.2 Health Technology Assessment (HTA) 96
6.3 Validation and Evaluation of Biomarker Tests 99
6.4 Health Technology Assessment of Personalized Medicine Technologies 100
6.5 Concluding Remarks 104
References 105
7 Bone Remodeling Biomarkers: New Actors on the Old Cardiovascular Stage 107
Cristina Vassalle, SilviaMaffei, and Giorgio Iervasi
7.1 Introduction 107
7.2 Cardiovascular Disease and Osteoporosis: Common Risk Factors and Common Pathophysiological Mechanisms 108
7.3 Biomarkers of Bone Health in CVD 112
7.3.1 Cathepsin K 112
7.3.2 Tartrate–Resistant Acid Phosphatase 115
7.3.3 Sclerostin 115
7.3.4 Fibroblast Growth Factor 23 116
7.3.5 Osteopontin 116
7.3.6 Osteocalcin 117
7.3.7 Osteoprotegerin 118
7.3.8 Vitamin D 120
7.3.9 Other Factors 121
7.3.10 Genetic Factors 123
7.4 Conclusion 125
References 128
8 Identification and Validation of Breast Cancer Biomarkers 147
Kori Jackson and Edward Sauter
8.1 Introduction 147
8.2 Current Detection and Treatment Modalities 148
8.2.1 Detection: In Clinical Use 148
8.2.1.1 Physical Examination 148
8.2.1.2 Breast Imaging 148
8.2.2 Detection: Being Evaluated 149
8.2.2.1 Bodily Fluid Analyses 150
8.2.3 Treatment: In Clinical Use 150
8.2.3.1 Surgery and Radiation 150
8.2.3.2 SystemicTherapy 151
8.2.4 Treatment: Being Evaluated/Newly Available 153
8.2.4.1 Biomarkers in Tissue: Single Markers 153
8.2.4.2 Biomarkers in Tissue: Gene Panels 154
8.3 Current Biomarker Limitations 154
8.3.1 Tumor Heterogeneity 154
8.3.2 Treatment Effect 155
8.3.3 Primary Versus Recurrent Tumor 155
8.4 Future Biomarker Discovery Targets 156
8.4.1 Autoantibodies 156
8.4.2 Inflammatory Markers 156
8.4.3 DNA Methylation 157
8.4.4 Benign Breast Disease 157
8.4.5 Pregnancy–Associated Breast Cancer 157
8.4.6 Challenges with New Biomarker Development and Validation 157
8.4.7 Sample Type Selection for Validation Studies of Diagnostic Biomarkers 158
8.4.7.1 Why Ductal Lavage for DNA Analysis? 158
8.4.7.2 Why Nipple Aspirate Fluid for Protein Analysis? 158
8.4.7.3 Why Circulating Samples for Protein Analysis? 158
8.4.7.4 DNA Candidates 159
8.4.7.5 RNA Candidates 159
8.4.7.6 Protein Candidates 159
8.5 Summary 160
References 161
9 Evaluation of Proteomic Data: From Profiling to Network Analysis by Way of Biomarker Discovery 163
Dario Di Silvestre, Francesca Brambilla, Sara Motta, and Pierluigi Mauri
9.1 Introduction 163
9.2 Proteomic Methodologies 164
9.3 Shotgun Proteomics 165
9.3.1 Targeted Proteomics 168
9.3.2 Data–Independent Acquisition (DIA) MS 169
9.4 Biomarker Discovery 170
9.4.1 MudPIT Data Processing 172
9.5 Protein Protein Interaction Network Analysis 174
9.6 Conclusion 176
References 177
10 Biomarkers: From Discovery to Commercialization 183
Sebastian Hoppe and Henry Memczak
10.1 Comparison of Different Platforms 184
10.2 Mass Spectrometry 185
10.3 Enzyme–Linked Immunosorbent Assay 187
10.4 SPR Imaging 188
10.5 Reverse Phase Protein Microarrays 189
10.6 Next–Generation Sequencing (NGS) 190
10.7 Still a Struggle: Achieving Clinical Trial Status 193
10.8 Commercial Biomarker Assays 195
10.9 Quo Vadis, Biomarker Assays? 197
References 199
11 Clinical Validation 207
Mads Almose Røpke
11.1 Introduction 207
11.2 Classification of Biomarkers 208
11.3 Translational Use of Biomarkers 209
11.4 Biomarkers in Clinical Studies 210
11.4.1 Healthy Volunteer Studies 210
11.4.2 Early Patient Studies 211
11.4.3 Confirmatory Clinical Studies 214
11.4.4 Enrichment Design 215
11.4.5 Biomarker–Stratified Design 216
11.5 Safety Markers in Clinical Development 216
11.6 Statistical Considerations 218
11.7 Validation 218
11.8 Regulatory Considerations for Implementation of Biomarkers in Clinical Studies 221
11.9 Biorepositories and Ethics 222
11.10 Conclusion 224
References 225
12 Genomics and Proteomics for Biomarker Validation 231
Paula Díez, RosaMa Dégano, Nieves Ibarrola, Juan Casado, and Manuel Fuentes
12.1 Introduction 231
12.1.1 Biomarker Discovery 233
12.2 Challenges in Biomarker Discovery/Verification Phases 234
12.3 Verification of Biomarkers 235
12.3.1 Protein Binding Assays 235
12.3.2 Targeted Proteomics 237
12.3.3 Correlation Between MRM and ELISA 237
12.3.4 MRM and Biomarker Pipeline 238
12.4 Role of Biobanking in Biomarkers Validation 238
12.4.1 Biobanking Challenges Associated with Biomarker Discovery and Validation 239
12.4.1.1 Preanalytical Variations and Lack of SOPs 239
12.4.1.2 Biological Diversities 239
12.4.1.3 Disease Heterogeneity 239
12.4.1.4 Technical Limitations 240
12.4.1.5 Validation and Clinical Trials 240
12.4.1.6 Lack of Stable Biorepository 240
12.5 Conclusions 240
References 241
Index 243
