Personalized Medicine - Scientific & Commercial Aspects

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Personalized Medicine - scientific & commercial aspects

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Summary

The aim of personalized medicine or individualized treatment is to match the right drug to the right patient and, in some cases, even to design the appropriate treatment for a patient according to his/her genotype. This report describes the latest concepts of development of personalized medicine based on pharmacogenomics, pharmacogenetics,pharmacoproteomics, and metabolomics. Basic technologies of molecular diagnostics play an important role, particularly those for single nucleotide polymorphism (SNP) genotyping. Diagnosis is integrated with therapy for selection of the treatment as well for monitoring the results. Biochip/microarray technologies are also important and finally bioinformatics is needed to analyze the immense amount of data generated by various technologies.

Pharmacogenetics, the study of influence of genetic factors on drug action and metabolism, is used for predicting adverse reactions of drugs. Several enzymes are involved in drug metabolism of which the most important ones are those belonging to the family of cytochrome P450. The knowledge of the effects of polymorphisms of genes for the enzymes is applied in drug discovery and development as well as in clinical use of drugs. Cost-effective methods for genotyping are being developed and it would be desirable to include this information in the patient's record for the guidance of the physician to individualize the treatment. Pharmacogenomics, a term that overlaps with pharmacogenetics but is distinct, deals with the application of genomics to drug discovery and development. It involves the mechanism of action of drugs on cells as revealed by gene expression patterns. Pharmacoproteomics is an important contribution to personalized medicine as it is a more functional representation of patient-to-patient variation than that provided by genotyping.A 'pharmacometabonomic' approach to personalizing drug treatment is also described.

Biological therapies such as those which use patient's own cells are considered to be personalized medicines. Vaccines are prepared from individual patient's tumor cells. Individualized therapeutic strategies using monoclonal bodies can be directed at specific genetic and immunologic targets. Ex vivo gene therapy involves the genetic modification of the patient's cells in vitro, prior to reimplantation of these cells in the patient's body.

Various technologies are integrated to develop personalized therapies for specific therapeutic areas described in the report. Examples of this are genotyping for drug resistance in HIV infection, personalized therapy of cancer, antipsychotics for schizophrenia, antidepressant therapy, antihypertensive therapy and personalized approach to neurological disorders. Although genotyping is not yet a part of clinically accepted routine, it is expected to have this status by the year 2014.

Several players are involved in the development of personalized therapy. Pharmaceutical and biotechnology companies have taken a leading role in this venture in keeping with their future role as healthcare enterprises rather than mere developers of technologies and manufacturers of medicines.

Ethical issues are involved in the development of personalized medicine mainly in the area of genetic testing. These along with social issues and consideration of race in the development of personalized medicine are discussed. Regulatory issues are discussed mainly with reference to the FDA guidelines on pharmacogenomics.

Increase in efficacy and safety of treatment by individualizing it has benefits in financial terms. Information is presented to show that personalized medicine will be cost-effective in healthcare systems. For the pharmaceutical companies, segmentation of the market may not leave room for conventional blockbusters but smaller and exclusive markets for personalized medicines would be profitable. Marketing opportunities for such a system are described with market estimates from 2010-2020.

Profiles of 245 companies involved in developing technologies for personalized medicines, along with 459 collaborations are included in the part II of the report. Finally the bibliography contains over 600 selected publications cited in the report.The report is supplemented by 63 tables and 17 figures.

TABLE OF CONTENTS

0. Executive Summary 19

1. Basic Aspects 21

Definition of personalized medicine 21

History of medical concepts relevant to personalized medicine 22

Molecular biological basis of personalized medicine 24

The human genome 24

Chromosomes 25

Genes 25

The genetic code 25

Gene expression 25

DNA sequences and structure 26

Genetic variations in the human genome 26

Single nucleotide polymorphisms 27

Copy number variations in the human genome 27

Insertions and deletions in the human genome 29

Large scale variation in human genome 29

Structural variations in the human genome 30

Mapping and sequencing of structural variation from human genomes 30

1000 Genomes Project 31

Role of DNA sequencing in the development of personalized medicine 32

Human Variome Project 33

Interconnected genetic and genomic patterns in human diseases 33

Basics technologies for developing personalized medicine 34

Definitions of technologies relevant to personalized medicine 34

Problems with the ICH definitions of pharmacogenomcis and pharmacogenetics 34

Relationship of various technologies to personalized medicine 35

Conventional medicine versus personalized medicine 35

Role of genetics in future approaches to healthcare 36

Genetic medicine 36

Human disease and genes 36

Genetic and environmental interactions in etiology of human diseases 37

Role of genetics in development of personalized medicines 37

Genetic databases 37

Genetic epidemiology 38

Limitations of medical genetics and future prospects 38

Genetics vs. epigenetics 39

Role of systems biology in personalized medicine 39

Systems pharmacology 40

Systems medicine 41

Synthetic biology and development of personalized medicines 41

A personalized approach to environmental factors in disease 42

Reclassification of diseases 43

2. Molecular Diagnostics in Personalized Medicine 45

Introduction 45

Molecular diagnostic technologies 45

PCR-based methods 46

DirectLinear™ Analysis 46

Denaturing high-performance liquid chromatography 47

Multiplex Allele-Specific Diagnostic Assay 47

Representational oligonucleotide microarray analysis 47

Restriction fragment length polymorphism (RFLP) 47

Real-time PCR for detection of CNVs 47

Non-PCR methods 48

Arrayed primer extension (APEX) 48

Enzymatic Mutation Detection (EMD) 48

DNA sequencing 48

Sanger-sequencing technology 49

ABI PRISM® 310 Genetic Analyzer 50

High-throughput paired end transcriptome sequencing 50

Emerging sequencing technologies 50

4300 DNA analyzer 51

Apollo 100 51

"Color blind" approach to DNA sequencing 52

Cyclic array sequencing 52

CEQ™ 8000 52

DeepCAGE sequencing 52

Electron microscope-based DNA sequencing 53

Genometrica? sequencer 53

GS-FLEX system (Roche/454) 54

IBS sequencing technology 55

Illumina Genome Analyzer System 55

MegaBACE 500 56

Microdroplet-based PCR for large-scale targeted sequencing. 56

Multiplex amplification of human DNA sequences 57

Nanoscale sequencing 57

Polonator sequencer 57

RainStorm™ microdroplet technology 58

Sequential DEXAS 58

SOLiD technology 59

Sequencing by hybridization 60

Whole genome sequencing 60

Bioinformatic tools for analysis of genomic sequencing data 60

Detection of single molecules in real time 61

Direct observation of nucleotide incorporation 61

Molecular Combing 61

Nanopore sequencing 61

DNA sequence by use of nanoparticles 62

Zero-mode waveguide nanostructure arrays 62

Future prospects of sequencing 62

Role of sequencing in development of personalized medicine 63

Biochips and microarrays 63

Application of biochip technology in developing personalized medicine 63

Standardizing the microarrays 65

Biochip technologies 65

GeneChip 65

AmpliChip CYP450 65

Microfluidics 67

Lab-on-a-chip 67

Micronics' microfluidic technology 68

LabCD 68

Microfluidic automated DNA analysis using PCR 68

Integrated microfluidic bioassay chip 68

Electronic detection of nucleic acids on microarrays 69

Strand displacement amplification on a biochip 69

Rolling circle amplification on DNA microarrays 70

Universal DNA microarray combining PCR and ligase detection reaction 70

Protein biochips 70

ProteinChip 71

LabChip for protein analysis 72

TRINECTIN proteome chip 72

Protein expression microarrays 72

Microfluidic devices for proteomics-based diagnostics 73

New developments in protein biochips/microarrays 73

Protein biochips/microarrays for personalized medicine 74

SNP genotyping 74

Genotyping and haplotyping 75

Haplotype Specific Extraction 76

Computation of haplotypes 76

HapMap project 76

Haplotyping for whole genome sequencing 78

Predictingdrug response with HapMap 78

Companies developing haplotyping technology 78

Technologies for SNP analysis 79

Biochip and microarray-based detection of SNPs 80

SNP genotyping by MassARRAY 80

Biochip combining BeadArray and ZipCode technologies 80

SNP-IT primer-extension technology 80

Affymetrix Variation Detection Arrays 81

Use of NanoChip for detection of SNPs 81

Electrochemical DNA probes 81

Single base extension-tag array 82

Laboratory Multiple Analyte Profile 82

PCR-CTPP (confronting two-pair primers) 83

SNP genotyping on a genome-wide amplified DOP-PCR template 83

TaqMan real-time PCR 83

Non-Enzymatic Amplification Technology 83

SNP genotyping with gold nanoparticle probes 84

Locked nucleic acid 84

Molecular inversion probe based assays 84

Pyrosequencing 85

Reversed enzyme activity DNA interrogation test 85

Smart amplification process version 2 86

Zinc finger proteins 86

UCAN method (Takara Biomedical) 86

Mitochondrial SNPs 87

Limitations of SNP in genetic testing 87

Concluding remarks on SNP genotyping 87

Companies involved in developing technologies/products for SNP analysis 88

Impact of SNPs on personalized medicine 89

Detection of copy number variations 90

Study of rare variants in pinpointing disease-causing genes 90

Optical Mapping 91

Role of nanobiotechnology in molecular diagnostics 91

Cantilevers for personalized medical diagnostics 92

Nanopore-based technology for single molecule identification 92

Role of biomarkers in personalized medicine 93

Biomarkers for diagnostics 93

Biomarkers for drug development 94

Application of proteomics in molecular diagnosis 94

Proteomic strategies for biomarker identification 94

Proteomic technologies for detection of biomarkers in body fluids 94

Protein patterns 95

Layered Gene Scanning 95

Comparison of proteomic and genomic approaches in personalized medicine 96

Gene expression profiling 96

DNA microarrays 97

Analysis of single-cell gene expression 97

Gene expression profiling based on alternative RNA splicing 98

Whole genome expression array 99

Tangerine™ expression profiling 99

Gene expression analysis on biopsy samples 100

Profiling gene expression patterns of white blood cells 100

Serial analysis of gene expression (SAGE) 101

Multiplexed Molecular Profiling 101

Gene expression analysis using competitive PCR and MALDI TOF MS 102

Monitoring in vivo gene expression by magnetic resonance imaging 102

Companies involved in gene expression analysis 102

Monitoring in vivo gene expression by molecular imaging 103

Molecular imaging and personalized medicine 104

Glycomics-based diagnostics 104

Combination of diagnostics and therapeutics 104

Use of molecular diagnostics for stratification in clinical trials 105

Companion diagnostics 105

Companies involved in companion diagnostics 105

Point-of-care diagnosis 107

Companies developing point-of-care diagnostic technologies 108

Point-of-care diagnosis of infections 110

Advantages versus disadvantages of point-of-care diagnosis 111

Future prospects of point-of-care diagnosis 111

Genetic testing for disease predisposition 112

Preventive genetics by early diagnosis of mitochondrial diseases 112

Direct-to-consumer genetic services 112

Role of diagnostics in integrated healthcare 114

Concept of integrated healthcare 114

Components of integrated healthcare 115

Screening 115

Disease prediction 115

Early diagnosis 115

Prevention 115

Therapy based on molecular diagnosis 115

Monitoring of therapy 115

Advantages and limitations of integrated healthcare 116

Commercially available systems for integrated healthcare 116

Future of molecular diagnostics in personalized medicine 117

3. Pharmacogenetics 119

Basics of pharmacogenetics 119

Role of molecular diagnostics in pharmacogenetics 120

Role of pharmacogenetics in pharmaceutical industry 121

Study of the drug metabolism and pharmacological effects 121

Causes of variations in drug metabolism 121

Enzymes relevant to drug metabolism 122

Pharmacogenetics of phase I metabolism 122

CYP450 122

P450 CYP 2D6 inhibition by selective serotonin reuptake inhibitors 124

Cytochrome P450 polymorphisms and response to clopidogrel 125

Lansoprazole and cytochrome P450 125

Glucose-6-phosphate dehydrogenase 125

Pharmacogenetics of phase II metabolism 126

N-Acetyltransferase 126

Uridine diphosphate-glucuronosyltransferase 127

Measurement of CYP isoforms 127

Polymorphism of drug transporters 128

Genetic variation in drug targets 128

Polymorphisms of kinase genes 129

Effect of genetic polymorphisms on disease response to drugs 129

Ethnic differences in drug metabolism 130

Gender differences in pharmacogenetics 130

Role of pharmacogenetics in drug safety 131

Adverse drug reactions 131

Adverse drug reactions in children 132

Adverse drug reactions related to toxicity of chemotherapy 132

Genetically determined adverse drug reactions 132

Malignant hyperthermia 134

Pharmacogenetics of clozapine-induced agranulocytosis 134

Role of pharmacogenetics in antiplatelet therapy with clopidrogrel 134

Role of pharmacogenetics in warfarin therapy 135

Role of pharmacogenetics in antiplatelet therapy 136

Role of pharmacogenetics in carbamazepine therapy 137

Role of pharmacogenetics in statin therapy 137

FDA consortium linking genetic biomarkers to serious adverse events 137

Therapeutic drug monitoring, phenotyping, and genotyping 138

Therapeutic drug monitoring 138

Phenotyping 139

Genotyping 140

Genotyping vs phenotyping 140

Phenomics 141

Limitations of genotype-phenotype association studies 141

Molecular toxicology in relation to personalized medicines 142

Toxicogenomics 142

Biomarkers of drug toxicity 142

Drug-induced mitochondrial toxicity 143

Companies involved in molecular toxicology 143

Gene expression studies 144

Pharmacogenetics in clinical trials 144

Postmarketing pharmacogenetics 145

Clinical implications of pharmacogenetics 145

Application of CYP450 genotyping in clinical practice 145

Pharmacogenomic biomarker information in drug labels 145

Genotype-based drug dose adjustment 145

Examples of use of pharmacogenetics in clinical pharmacology 146

Genotyping for identifying responders to sulfasalazine 146

HLA alleles associated with lumiracoxib-related liver injury 146

Pharmacogenetic basis of thiopurine toxicity 147

Tranilast-induced hyperbilirubinemia due to gene polymorphism 147

Linking pharmacogenetics with pharmacovigilance 147

Genetic susceptibility to ADRs 147

Linking genetic testing to postmarketing ADR surveillance 147

Recommendations for the clinical use of pharmacogenetics 148

Limitations of pharmacogenetics 148

Pharmacoepigenomics vs pharmacogenetics in drug safety 149

Future role of pharmacogenetics in personalized medicine 149

4. Pharmacogenomics 151

Introduction 151

Basics of pharmacogenomics 152

Pharmacogenomics and drug discovery 152

Preclinical prediction of drug efficacy 154

Pharmacogenomics and clinical trials 154

Impact of genetic profiling on clinical studies 155

Limitations of the pharmacogenomic-based clinical trials 156

Pharmacogenomic aspects of major therapeutic areas 157

Oncogenomics 157

Oncogenes 157

Tumor suppressor genes 158

Cardiogenomics 159

Neuropharmacogenomics 161

Pharmacogenomics of Alzheimer's disease 161

Pharmacogenomics of depression 162

Pharmacogenomics of schizophrenia 162

Companies involved in neurogenomics-based drug discovery 163

5. Role of Pharmacoproteomics 165

Basics of proteomics 165

Proteomic approaches to the study of pathophysiology of diseases 165

Single cell proteomics for personalized medicine 166

Diseases due to misfolding of proteins 166

Therapies for protein misfolding 167

Significance of mitochondrial proteome in human disease 168

Proteomic technologies for drug discovery and development 168

Role of reverse-phase protein microarray in drug discovery 168

Role of proteomics in clinical drug safety 168

Toxicoproteomics 169

Application of pharmacoproteomics in personalized medicine 170

6. Role of Metabolomics in Personalized Medicine 171

Metabolomics and metabonomics 171

Metabolomics bridges the gap between genotype and phenotype 171

Metabolomics, biomarkers and personalized medicine 172

Metabolomic technologies 172

Urinary profiling by capillary electrophoresis 173

Lipid profiling 173

Role of metabolomics in biomarker identification and pattern recognition 174

Validation of biomarkers in large-scale human metabolomics studies 174

Pharmacometabonomics 174

Metabonomic technologies for toxicology studies 175

Metabonomics/metabolomics and personalized nutrition 175

7. Personalized Biological Therapies 177

Introduction 177

Recombinant human proteins 177

Therapeutic monoclonal antibodies 177

Cell therapy 178

Autologous tissue and cell transplants 178

Stem cells 178

Role of stem cells derived from unfertilized embryos 178

Cloning and personalized cell therapy 179

Use of stem cells for drug testing 179

Gene therapy 179

Personalized vaccines 180

Personalized vaccines for viral diseases 180

Personalized cancer vaccines 180

Antisense therapy 180

RNA interference 181

MicroRNAs 182

8. Personalized Medicine in Major Therapeutic Areas 183

Introduction 183

Management of infections 184

Management of HIV 184

CD4 counts as a guide to drug therapy for AIDS 184

Drug-resistance in HIV 184

Genetics of human susceptibility to HIV infection 185

Measurement of Replication Capacity 186

Personalized vaccine for HIV 186

Prevention of adverse reactions to antiviral drugs 186

Pharmacogenetics and HIV drug safety 187

Pharmacogenomics of antiretroviral agents 187

Role of diagnostic testing in HIV 188

Role of genetic variations in susceptibility to HIV-1 188

Personalized treatment of hepatitis B 188

Personalized treatment of hepatitis C 189

Personalized management of tuberculosis 190

Psychiatric disorders 191

Psychopharmacogenetics 191

COMT genotype and response to amphetamine 191

Genotype and response to methylphenidate in children with ADHD 192

Personalized antipsychotic therapy 192

Personalized antidepressant therapy 194

EEG to predict adverse effects and evaluate antidepressant efficacy 195

Individualization of SSRI treatment 195

Vilazodone with a test for personalized treatment of depression 197

Neurological disorders 197

Personalized management of Alzheimer's disease 197

Personalized management of Parkinson's disease 198

Discovery of subgroup-selective drug targets in PD 199

Personalized management of Epilepsy 199

Choice of the right AED 200

Pharmacogenetics of epilepsy 200

Pharmacogenomics of epilepsy 200

Drug resistance in epilepsy 201

Future prospects for management of epilepsy 202

Personalized management of migraine 203

Individualization of use of triptans for migraine 203

Personalized management of stroke 204

Brain imaging in trials of restorative therapies for stroke 204

Decisions for evacuation of intracerebral hemorrhage 204

Revascularization procedures in chronic post-stroke stage 205

Personalized treatment of multiple sclerosis 205

Immunopathological patterns of demyelination for assessing therapy 206

Personalizing mitoxantrone therapy of multiple sclerosis 206

Fusokine method of personalized cell therapy of multiple sclerosis 207

MBP8298 207

Pharmacogenomics of IFN-? therapy in multiple sclerosis 207

T cell-based personalized vaccine for MS 209

Cardiovascular disorders 209

Role of diagnostics in personalized management of cardiovascular disease 209

Testing in coronary heart disease 209

SNP genotyping in cardiovascular disorders 210

Cardiovascular disorders with a genetic component 210

Gene variant as a risk factor for sudden cardiac death 212

KIF6 gene test as a guide to management of heart disease 212

SNP Chip for study of cardiovascular diseases 213

Pharmacogenomics of cardiovascular disorders 213

Modifying the genetic risk for myocardial infarction 213

Management of heart failure 214

?-blockers 214

Bucindolol 214

BiDil 214

Management of hypertension 215

Pharmacogenomics of diuretic drugs 215

Pharmacogenomics of ACE inhibitors 216

Management of hypertension by personalized approach 216

Prediction of antihypertensive activity of rostafuroxin 217

Pharmacogenetics of lipid-lowering therapies 218

Polymorphisms in genes involved in cholesterol metabolism 218

Role of eNOS gene polymorphisms 219

The STRENGTH study 219

Personalized management of women with hyperlipidemia 220

Thrombotic disorders 221

Factor V Leiden mutation 221

Anticoagulant therapy 221

Antiplatelet therapy 222

Nanotechnology-based personalized therapy of cardiovascular diseases 222

Project euHeart for personalized management of heart disease 223

Concluding remarks 223

Personalized management of pulmonary disorders 223

Role of genetic ancestory in lung function 224

Personalized therapy of asthma 224

Biomarkers for predicting response to corticosteroid therapy 224

Genetic polymorphism and response to ?2-adrenergic agonists 225

Genotyping in asthma 225

IgE as guide to dosing of omalizumab for asthma 226

Lebrikizumab for personalised treatment of asthma 226

Personalized management of chronic obstructive pulmonary disease 226

Personalized management of skin disorders 227

Genetic testing for personalized skin care 227

Management of hair loss based on genetic testing 228

Personalized therapy of rheumatoid arthritis 228

DIATSTAT™ anti-cyclic citrullinated peptides in rheumatoid arthritis 229

Personalization of COX-2 inhibitor therapy 229

Personalization of infliximab therapy 230

Personalized approaches in immunology 230

Role of Mannose-binding lectin in personalized medicine 231

Pharmacogenetics and pharmacogenomics of immunosuppressive agents 231

Personalized management of patients with lupus erythematosus 231

Personalized management of pain 232

Pharmacogenetics/pharmacogenomics of pain 232

Mechanism-specific management of pain 233

Preoperative testing to tailor postoperative analgesic requirements 233

Personalized analgesics 234

Management of genetic disorders 234

Personalized treatment of cystic fibrosis 234

Personalized management of gastrointestinal disorders 235

Personalized therapy of inflammatory bowel disease 235

Personalized management of lactose intolerance 236

Personalized approaches to improve organ transplantation 236

Personalization of kidney transplantation 236

Personalization of cardiac transplantation 237

Prediction of rejection to tailor anti-rejection medications 237

Personalized immunosuppressant therapy in organ transplants 238

Role of immunological biomarkers in monitoring grafted patients 239

Improved matching of blood transfusion 239

Personalized approach to addiction 239

Pharmacogenetics of drug addiction 239

Genetic polymorphism and management of alcoholism 240

Personalized therapy for smoking cessation 240

Antidepressant therapy for smoking cessation 241

Effectiveness of nicotine patches in relation to genotype 241

Personalized approaches to miscellaneous problems 241

Hormone replacement therapy in women 241

Personalized treatment of malaria 242

Personalized management of renal disease 242

Gene associated with end-stage renal disease 243

Personalized care of trauma patients 243

Personalized anticoagulation 244

Personalized Hyperbaric oxygen therapy 244

Personalized preventive medicine 245

Personalized nutrition 245

Nutrigenomics 246

Genomics of vitamin D and calcium supplementation 246

Nutrigenomics and functional foods 247

Nutrigenetics and personalized medicine 247

Nutrigenomics and personalized medicine248

Nutrition and proteomics 248

Personalized diet prescription 248

9. Personalized Therapy of Cancer 251

Introduction 251

Challenges of cancer classification 251

Relationships of technologies for personalized management of cancer 251

Impact of molecular diagnostics on the management of cancer 252

AmpliChip P53 as companion diagnostic for cancer 253

Analysis of RNA splicing events in cancer 253

Analysis of chromosomal alterations in cancer cells 253

Cancer classification using microarrays 253

Detection of loss of heterozygosity 254

Diagnosis of cancer of an unknown primary 255

Diagnostics for detection of minimal residual disease 255

DNA repair biomarkers 255

Fluorescent in situ hybridization 256

Gene expression profiling 256

Gene expression profiles predict chromosomal instability in tumors 257

Isolation and characterization of circulating tumor cells 258

Modulation of CYP450 activity for cancer therapy 258

Personalized therapies based on oncogenic pathways signatures 259

Quantum dot-based test for DNA methylation 259

Role of molecular imaging in personalized therapy of cancer 259

Functional diffusion MRI 260

FDG-PET/CT for personalizing cancer treatment 260

Image-guided personalized drug delivery in cancer 261

Tumor imaging and elimination by targeted gallium corrole 261

Future prospects of molecular imaging in management of cancer 261

Unraveling the genetic code of cancer 262

Cancer prognosis 262

Detection of mutations for risk assessment and prevention 263

Impact of biomarkers on management of cancer 263

HER-2/neu oncogene as a biomarker for cancer 263

L-asparaginase treatment of cancer guided by a biomarker 264

Oncogene GOLPH3 as a cancer biomarker 264

Predictive biomarkers for cancer 264

Sequencing to discover biomarkers to personalize cancer treatment 265

Systems biology approach to discovery of radiation sensitivity biomarkers 265

VeraTag™ assay system for cancer biomarkers 266

Determination of response to therapy 266

ChemoFx cell culture assay for predicting anticancer drug response 266

Ex vivo testing of tumor biopsy for chemotherapy sensitivity 267

Genomic approaches to predict response to anticancer agents 267

Gene expression patterns to predict response of cancer to therapy 267

Genomic analysis of tumor biopsies 268

Genotype-dependent efficacy of pathway inhibition in cancer 268

Mutation detection at molecular level 268

Role of genetic variations in susceptibility to anticancer drugs 269

Non-genetic factors for variations in response of cancer cells to drugs 269

Proteomic analysis of tumor biopsies to predict response to treatment 269

Real-time apoptosis monitoring 270

Serum nucleosomes as indicators of sensitivity to chemotherapy 270

Targeted microbubbles to tumors for monitoring anticancer therapy 271

PET imaging for determining response to chemotherapy 271

Tissue systems biology approach to personalized management of cancer 271

Targeted cancer therapies 272

Targeting glycoproteins on cell surface 272

Targeting pathways in cancer 272

Functional antibody-based therapies 272

Personalized cancer vaccines 274

Antigen-specific vaccines 274

Active immunotherapy based on antigen specific to the tumor 274

Tumor-derived vaccines 275

MyVax 275

OncoVAX 275

Tumor cells treated with dinitrophenyl 276

Prophage 276

Melacine 276

Patient-specific cell-based vaccines 277

Dendritic cell-based vaccines 277

Adoptive cell therapy 278

Combination of antiangiogenic agents with ACT 280

Genetically targeted T cells for treating B cell malignancies 280

Genetic engineering of tumor cells 280

Hybrid cell vaccination 281

Personalized peptide cancer vaccines 281

Current status and future prospects of personalized cancer vaccines 281

Personalized radiation therapy 283

Molecular diagnostics combined with cancer therapeutics 284

Aptamers for combined diagnosis and therapeutics of cancer 284

Role of nanobiotechnology in personalized management of cancer 285

Design of future cancer therapies 286

Screening for personalized anticancer drugs 286

Role of epigenetics in development of personalized cancer therapies 286

Personalized therapy of cancer based on cancer stem cells 287

Role of oncoproteomics in personalized therapy of cancer 287

Cancer tissue proteomics 287

Role of sequencing in personalized therapy of cancer 288

Pharmacogenomic-based chemotherapy 288

Whole genome technology to predict drug resistance 288

Anticancer drug selection based on molecular characteristics of tumor 288

Testing microsatellite-instability for response to chemotherapy 289

Pharmacogenetics of cancer chemotherapy 289

CYP 1A2 290

Thiopurine methyltransferase 290

Dihydropyrimidine dehydrogenase 291

UGT1A1 test as guide to irinotecan therapy 291

Role of computational models in personalized anticancer therapy 292

A computational model of kinetically tailored treatment 292

Mathematical modeling of tumor mivroenvironments 292

Molecular profiling of cancer 293

Drug resistance in cancer 293

Detection of drug resistance in cancer by metabolic profiling 294

Determination of chemotherapy response by topoisomerase levels 294

Anaplastic lymphoma kinase 295

Management of drug resistance in leukemia 295

Overexpression of multidrug resistance gene 295

P53 mutations 296

A chemogenomic approach to drug resistance 296

Systems biology approach to personalizing therapy for drug-resistant cancer 296

Examples of personalized management of cancer 297

Personalized management of brain cancer 297

Biosimulation approach to personalizing treatment of brain cancer 297

Genetics and genomics of brain cancer 297

Prognosis of glioblastoma multiforme based on its genetic landscape 299

Molecular diagnostics for personalized management of brain cancer 299

Personalized chemotherapy of brain tumors 301

Personalized therapy of oligodendroglial tumors (OTs) 302

Personalized therapy of neuroblastomas 303

Personalized therapy of medulloblastomas 303

Personalized management of germ cell brain tumors 304

Personalized management of breast cancer 304

Developing personalized drugs for breast cancer 304

Gene expression plus conventional predictors of breast cancer 305

Her2 testing in breast cancer as a guide to treatment 306

HER2/neu-derived peptide vaccine for breast cancer 308

Molecular diagnostics in breast cancer 308

Pharmacogenetics of breast cancer 310

Proteomics-based personalized management of breast cancer 310

Predicting response to chemotherapy in breast cancer 310

Prediction of resistance to chemotherapy in breast cancer 313

Prediction of adverse reaction to radiotherapy in breast cancer 314

Prediction of recurrence in breast cancer for personalizing therapy 314

Prognosistic tests for breast cancer 316

Racial factors in the management of breast cancer 318

RATHER consortium to study personalized approach to breast cancer 318

TAILORx (Trial Assigning Individualized Options for Treatment) 318

Trends and future prospects of breast cancer research 319

Understanding tumor diversity in mouse mammary cancer model 319

Personalized management of ovarian cancer 319

Early diagnosis of ovarian cancer 320

Determining response to chemotherapy in ovarian cancer 320

Recurrent and drug-resistant ovarian cancer 320

Pathway targeted therapies for ovarian cancer 321

Personalized management of hematological malignancies 322

Personalized management of acute lymphoblastic leukemia 322

Personalized management of acute myeloid leukemia 323

Personalized management of chronic lymphocytic leukemia 324

Personalized management of multiple myeloma 324

Personalized management B cell lymphomas 325

Personalized vaccine for follicular lymphoma 326

Personalized management of myelodysplastic syndrome 327

Personalized management of hepatocellular carcinoma 327

Personalized management of gastrointestinal cancer 327

Personalized management of esophageal cancer 327

Personalized management of gastric cancer 328

Personalized management of colorectal cancer 328

A systems biology approach to drug resistance in colorectal cancer 331

Personalized management of liver cancer 331

Personalized management of lung cancer 332

Determination of outcome of EGFR tyrosine kinase inhibitor treatment 332

Crizotinib for personalized management of NSCLC 334

Testing for response to chemotherapy in lung cancer 334

Testing for prognosis of lung cancer 335

Testing for recurrence of lung cancer 335

Role of a new classification system in the management of lung cancer 335

Personalized management of malignant melanoma 336

Therapy for inhibiting BRAF mutation in melanoma 336

Vaccine for malignant melanoma based on heat shock protein 336

Personalized management of pancreatic cancer 337

Biomarkers of pancreatic cancer 337

Histone modifications predict treatment response in pancreatic cancer 338

Personlized management of prostate cancer 338

Diagnostics for guiding therapy of prostate cancer 338

Early detection of cancer recurrence and guiding treatment 339

Effects of of lifestyle changes shown by gene expression studies 339

Personalized peptide vaccine for prostate cancer 340

Future of cancer therapy 340

Challenges for developing personalized cancer therapies 340

Cancer Genome Atlas 341

COLTHERES consortium 341

Computer and imaging technologies for personalizing cancer treatment 341

Genomic Cancer Care Alliance 342

Integrated genome-wide analysis of cancer for personalized therapy 342

International Cancer Genome Consortium 342

PREDICT Consortium 343

Companies involved in developing personalized cancer therapy 344

10. Development of Personalized Medicine 347

Introduction 347

Non-genomic factors in the development of personalized medicine 347

Personalized medicine based on circadian rhythms 347

Cytomics as a basis for personalized medicine 348

Intestinal microflora 348

Gut microbiome compared to human genome 348

Metabolic interactions of the host and the intestinal microflora 349

Role of drug delivery in personalized medicine 349

Personalized approach to clinical trials 350

Use of Bayesian approach in clinical trials 350

Individualzing risks and benefits in clinical trials 350

Clinical trials of therapeutics and companion diagnostics 351

Players in the development of personalized medicine 351

Personalized Medicine Coalition 351

European Personalized Medicine Diagnostics Association 352

Role of pharmaceutical industry 353

Production and distribution of personalized medicines 353

Role of biotechnology companies 354

Role of life sciences industries 354

Role of molecular imaging in personalized medicine 355

Molecular imaging for personalized drug development in oncology 355

Molecular imaging and CNS drug development 357

Companies involved in molecular imaging 358

Role of the clinical laboratories 358

Role of the US government in personalized medicine 359

Department of Health and Human Services and personalized medicine 360

Agency for Healthcare Research and Quality 360

Comparative effectiveness research 361

Role of the US Governmen

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