Next Generation Biomarkers: From Omics to Precision Medicine offers a clear methodology for successfully discovering and validating biomarkers using next generation sequencing, along with a comprehensive overview of next generation biomarkers currently used in the clinic. With recent advances in genomics and -omics approaches, elaborative molecular profiling is increasingly employed to gain fundamental insights into disease etiology and progression. Through a case-study based approach, the book examines a variety of NGS genomic and omics approaches to biomarker discovery and validation, along with lessons learned from recent studies and clinical trials.
Chapters explore common challenges, regulations and strategies for more accurate and efficient development of next generation biomarkers, and NGS approaches, ranging from whole exome sequencing, to whole genome sequencing, epigenomic profiling, transcriptomics, peptidomics, proteomics, liquid biopsy, ethical considerations, and patient empowerment in biomarker development.
- Establishes a clear methodology for successfully discovering and validating biomarkers using next generation sequencing
- Provides a comprehensive overview of next generation biomarkers currently used
- Examines a variety of NGS approaches to biomarker identification, lessons learned from recent studies, common challenges, regulations, and strategies for more accurate and efficient identification of next generation biomarkers for use in precision medicine
- Covers NGS approaches, ranging from whole exome sequencing, to whole genome sequencing, epigenomic profiling, transcriptomics, peptidomics, proteomics, and liquid biopsy, as well as ethical considerations and patient empowerment in biomarker development
- Features contributions from leading international researchers working at the forefront of NGS biomarker discovery and validation
Table of Contents
Section 1: Introduction1. Scope
2. Biomarker is a biomarker is a biomarker
3. Omics
4. Precision medicine
Section 2: Biomarker Development Path
5. Overview clinical development path (analogy to Therapeutics) - Fit for purpose
6. Analytical Validation
7. Clinical Validation
8. Clinical Utility
Section 3: Statistical Considerations
9. Introduction
10. Discovery Informatics / Machine Learning
11. Statistical Issues for Biomarker Studies (confounding, statistical tests, multiplicity/overfitting, FDR)
12. Statistical versus clinical significance
13. Biomarker study design (RCT, Biomarker by Treatment Interaction Design, Adaptive Designs)
Section 4: Molecular Profiling
The Sample: Diagnostic Matrices
14. FFPE
15. Liquid Biopsies
16. Extracellular vesicles
The method: Technologies
17. PCR versus Sequencing: The Heisenberg Uncertainty
The test
18. From Central Reference Labs over IVD kits to Sample to Answers and Mobile Platforms
Section 5: Clinical Biomarkers
Genetic
19. Lessons learned 1
20. Lessons learned 2
21. Lessons learned 3
22. Whole genome-exome diagnostics
Epigenetic
23. Lessons learned 1
24. Lessons learned 2
25. Whole epigenome / Methylation atlas
Expression (RNA, miRNA, lncRNA)
26. Lessons learned 1
27. Lessons learned 2
28. Transcriptomics
Translation (Protein)
29. Lessons learned 1
30. Lessons learned 2
31. Proteomics
32. Peptidomics
Section 6: Clinico-Genomic
33. Best of both worlds
Section 7: The Economics of Molecular Diagnostics
34. HTA/Economic evaluation
35. Reimbursement
36. IP Intellectual Property
37. Commercialization Business Models Translating biomarkers successfully to the clinic
Section 8: Biomarkers and ELSI (Ethical, Legal and Social Implication)
38. Legal Regulations
39. Ethical and Social Implications
Section 9: Biomarkers and Patient Empowerment
40. Risk Management, A Review of Shared Decision-Making and/or Evidence-based advocacy
Section 10: Best Practices
41. Keys to success/lessons learned
