Oncology: Genomics, Precision Medicine and Therapeutic Targets

Preface
Acknowledgments
Contents
About the Editors
Abbreviations
Oncology: Way Forward from Clinical and Molecular Diagnosis to Treatment
	1 Introduction
	2 Cancer Diagnosis and Treatment Based on Molecular Pathology
		2.1 Retroviral Therapy
		2.2 Retroviral Vector Insertions
		2.3 RNA Interference
		2.4 Editing of Genome
		2.5 Epigenetics
			2.5.1 Epigenetics in Solid Tumors
				Breast Cancer
				Rhabdoid Tumor
		2.6 Clinician-Level Molecular Diagnostics
			2.6.1 Personalized Medicine Treatment
			2.6.2 Liquid Biopsy: A Multimodal Diagnostic Technique
			2.6.3 Artificial Intelligence in Clinical Oncology
	3 Conclusion
	References
Oncogenic Genomic Changes in Cancer
	1 Introduction
	2 Activation of Protooncogenes Mechanisms
		2.1 Insertion
		2.2 Chromosomal Translocation
			2.2.1 Cyclins and Cyclin-Dependent Kinases
			2.2.2 Cyclin D1 and Cyclin E Protooncogenes
			2.2.3 Telomeres and Telomerase Oncogene
		2.3 Gene Amplification
			2.3.1 Epidermal Growth Factor Receptor (ErbB)
			2.3.2 ErbB2 Gene (Her2/neu)
			2.3.3 Myc Gene
		2.4 Point Mutation
			2.4.1 Ras Gene
			2.4.2 Braf Gene
		2.5 Transduction Activation
	3 Activation of Oncogenes
		3.1 Physical and Chemical Factors
		3.2 Biological Factors
		3.3 Genetic Factors
	4 Oncogene Dependence on Tumours
	5 Tumour Suppressor Genes (TSGs)
		5.1 Gatekeeper Genes
		5.2 Caretaker Genes
	6 Tumour Suppressor Gene Inactivation
		6.1 Point Mutation in Tumour Suppressor Genes
		6.2 Loss of Heterozygosity (LOH)
		6.3 Methylation
		6.4 Microsatellite Instability (MSI)
	7 Nonprotein-Coding Protooncogenes and Tumour Suppressor Genes: Micro-RNAs (miRNAs)
	8 Conclusion
	References
MicroRNAs and Long Non-coding RNAs as Key Targets
	1 Introduction
	2 Exploring the Promising Potential of miRNAs for Diagnosis and Therapeutics of Cancer
	3 Integrated Analysis of miRNA-mRNA Interaction as a Potential Target for Cancer Therapy
	4 Functional Role and Emerging Therapeutic Target of Long Non-coding RNAs in Oncogenesis
	5 Conclusion
	References
Precision Medicine: Translation of Individualistic Treatment in Oncology
	1 Significance of Precision Medicine in Oncology
	2 Strategies of Precision Medicine in Oncology
	3 Liquid Biopsy
		3.1 Circulating Tumor Cells
		3.2 Cell-Free DNA
		3.3 Circulating RNAs
			3.3.1 Circulating miRNAs
			3.3.2 Circulating mRNAs
		3.4 Circulating Proteins
		3.5 Exosomes
	4 Targeted Therapies
		4.1 Breast Cancer
		4.2 Prostate Cancer
		4.3 Lung Cancer
		4.4 Colorectal Cancer
		4.5 Pancreatic Cancer
		4.6 Lymphoma
		4.7 Skin Cancer
		4.8 Ovarian Cancer
	5 Experiences from Clinical Trials
	6 Conclusion
	References
Pharmacogenetics and Pharmacogenomics in Precision Medicine
	1 Introduction
	2 Association of Pharmacogenomics with Pharmacodynamics
	3 Association of Pharmacogenomics with Pharmakokinetics
	4 Pharmacogenomics and Therapeutic Drug Monitoring
	5 Pharmacogenomics and Drug Interactions
	6 Pharmacogenomics of Fluoropyrimidine Drugs
	7 Pharmacogenomics of Abiraterone Acetate
	8 Pharmacogenomics of Bevasizumab
	9 Pharmacogenomics of Imatinib
	References
Pharmacogenetic Factors in Pharmacodynamic/Pharmacokinetic (PD/PK) Modulations of Medicines
	1 Clinical Pharmacokinetics
	2 Pharmacogenetic Factors in Relation to Pharmacokinetics
		2.1 Absorption
		2.2 Distribution
		2.3 Metabolism
		2.4 Excretion
	3 Pharmacogenetic Factors in Relation to Pharmacodynamics
		3.1 Efficacy
		3.2 Precision Immunotherapy in Cancer Progress
		3.3 Drug Resistance
		3.4 Pharmacogenomis Data in Clinical Decision Support
	4 Concluding Remarks
	References
Biomarkers in Precision Medicine with Special Reference to Oncology
	1 Introduction
	2 Types of Biomarkers
	3 Major Techniques to Identify Biomarkers
	4 Cancer Biomarkers
		4.1 Genomic Biomarkers
		4.2 Transcriptomic Biomarkers
		4.3 Epigenetic Biomarkers
		4.4 Proteomic Biomarkers
		4.5 Metabolomic Biomarkers
		4.6 Imaging Based Biomarkers
		4.7 Immune Checkpoint Inhibition Biomarkers
		4.8 B cell Maturation Antigen (BCMA) Biomarkers
	5 Biomarkers in Drug Development
	6 Challenges to Improve Biomarker Based Clinical Trials
	7 Conclusion and Future Perspectives
	References
Bioinformatics and Biostatistics in Precision Medicine
	1 Introduction
	2 Omics Technologies
	3 Genomics
	4 Epigenomics
	5 Transcriptomics
	6 Proteomics
	7 Metabolomics
	8 Pharmacogenomics
	9 Management and Processing Omics Data
	10 Predictive Modeling with Machine-Learning Algorithms
		10.1 Machine-Learning for Precision Medicine
	11 Discovery of Disease Subtypes
	12 Biomarker Discovery Analysis
	13 Prediction of Disease Outcomes
	14 Survival Analysis
	15 Drug Discovery Analysis
	16 Integration of Multi-Omics Data
	17 Studies with Data Integration
	18 Discussion
	19 Conclusion
	References
Omics in Precision Medicine
	1 Introduction
	2 Genomics Approaches in Precision Oncology
	3 Transcriptomic Approaches in Precision Oncology
	4 Proteomics and Phosphoproteomics Approaches in Precision Oncology
	5 Metabolomics Approaches in Precision Oncology
	6 The Other Omics Approaches in Precision Oncology
		6.1 Single-Cell Omics Approaches
		6.2 Epigenomics Approaches
	7 Conclusion
	References
Translational Therapeutic Targets: From Bench to Clinical Trials
	1 Role of Translational Research in Fighting Cancer
		1.1 Gaps in Current Therapy for Cancer
		1.2 Benefits of Translation Cancer Research
	2 How Translation Cancer Research Work
		2.1 Spectrum of Translational Research
		2.2 Translation of Cancer Research into Targeted Therapy
			2.2.1 Pharmacodynamics (PD) Biomarkers
			2.2.2 Predictive/Putative Predictive or Enrichment Biomarkers
	3 Currently Available Promising Targets from Bench to Clinical Trials
		3.1 NCCN
		3.2 TAPUR Study
		3.3 The NCI Community Oncology Research Program (NCORP)
		3.4 NCI Match and Paediatric Match Trial
	4 Importance of Precision Cancer Medicine and Therapeutics
	5 Newer Avenues and Role of Big Data in Translational Cancer Research
	6 Conclusion/Way Forward
	References