Biomarker Validation Technological, Clinical and Commercial Aspects

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