Biomarkers - Technologies, Markets and Companies

NEW YORK, Nov. 30, 2011 /PRNewswire/ -- Reportlinker.com announces that a new market research report is available in its catalogue:

Biomarkers - Technologies,markets and companies

http://www.reportlinker.com/p0203536/Biomarkers---Technologiesmarkets-and-companies.html#utm_source=prnewswire&utm_medium=pr&utm_campaign=Genomics

Summary

This report follows the broad definition of a biomarker as a characteristic that can be objectively measured and evaluated as an indicator of normal biological or pathogenic processes as well as pharmacological responses to a therapeutic intervention. Tests based on biomarkers have been around for more than half a century, but interest in their application for diagnostics and drug discovery as well as development has increased remarkably since the beginning of the 21st century. This report describes different types of biomarkers and their discovery using various "-omics" technologies such as proteomics and metabolomics. Molecular diagnostics technologies are used for the discovery of biomarkers and new tests are also based on biomarker.

Currently the most important applications of biomarkers are in drug discovery and development. The role of biomarkers in various therapeutic areas particularly cancer, cardiovascular diseases and disorders of the central nervous system, is described. Biomarkers are useful not only for diagnosis of some of these diseases but also for understanding the pathomechanism as well as a basis for development of therapeutics.

Biomarkers will facilitate the combination of therapeutics with diagnostics and will thus play an important role in the development of personalized medicine. Biomarkers play a role in use of pharmacogenetics, pharmacogenomics and pharmacoproteomics for development of personalized medicine.

Many of the regulatory issues concerning biomarkers are related to genomics, proteomics, molecular diagnostics and pharmacogenomics/pharmacogenetics. Validation of biomarkers and their role in clinical trials is discussed.

Biomarker markets are estimated from 2010 to 2020 according to share of markets for various technologies and applications: proteomics, metabolomics, molecular diagnostics, drug discovery, clinical trials, and bioinformatics. Market values are further split according to therapeutic applications and major geographical areas. Unfulfilled needs in biomarkers are identified as well as the drivers for biomarker markets. Challenges facing the biomarker industry and strategies for developing biomarker markets are discussed.

A large number of companies with varying technical backgrounds are involved in biomarkers and 277 of these are profiled in part 2 of the report with classification into various categories.These also include major pharmaceutical companies. There is tabulation of 514 collaborations between companies and additional academic collaborations are mentioned in the individual profiles of companies. The report is supplemented by 1,000 references, 66 tables and 13 figures

TABLE OF CONTENTS

0. Executive Summary 21

1. Introduction 23

Definitions 23

Historical aspects of biomarkers 23

Classification of biomarkers 24

Biological marker as response to therapeutic intervention 25

Pharmacokinetic/pharmacodynamics biomarkers 25

Predictive biomarkers 25

Valid biomarkers 26

Types of biomarkers 26

Genes as biomarkers 26

Proteins as biomarkers 27

Proteomics 27

DNA biomarkers 28

Mitochondrial DNA 28

Mitochondrial mutations 28

RNA biomarkers 28

Transcriptomics 29

MicroRNAs 30

Metabolomics 30

Glycomics 30

Single nucleotide polymorphisms 31

Haplotyping 31

Cell biomarkers of disease 32

Stem cell biomarkers 32

Association of stem cell biomarkers with disease 32

Cancer stem cell biomarkers 33

Endoglin as a functional biomarker of stem cells 33

p75NTR as a biomarker to isolate adipose tissue-derived stem cells 33

Protein expression profile as biomarker of stem cells 33

STEMPRO? EZChek? for analysis of biomarkers of hESCs 34

SSEA-4 as biomarker of MSCs 34

Gaseous mediators as biomarkers of disease 34

Autoantibodies as biomarkers of autoimmune diseases 34

Comparison of various types of biomarkers 35

Biomarkers and systems biology 36

Systems biology approach to biomarker identification 37

Relation of biomarkers to other technologies and healthcare 37

Biomarkers and translational medicine 38

Limitations of use of biomarkers in healthcare 38

2. Technologies for Discovery of Biomarkers 41

Introduction 41

The ideal biomarker 41

Genomic technologies 41

Gene expression 41

Whole genome expression array 42

Gene expression profiling on whole blood samples 43

Profiling gene expression patterns of white blood cells 43

Tissue microarrays for study of biomarkers 43

Epigenomic technologies 44

Discovery of methylation biomarkers 44

Proteomic technologies 45

2D GE 46

Biomarker Amplification Filter 47

CellCarta® proteomics platform 47

Isotope-coded affinity tags 48

Liquid chromatography-MS/MS 48

Lucid Proteomics System 48

Magnetics beads for protein biomarker discovery 49

MASStermind™ 49

Mass spectrometry 49

2D PAGE and mass spectrometry 50

Imaging mass spectrometry 50

MALDI mass spectrometry for biomarker discovery 51

Quantitative tandem MS 52

Single-molecule mass spectrometry using a nanopore 52

Requirements for MS-based proteomic biomarker development 53

Protein tomography 53

Protein biochips/microarrays and biomarkers 53

Antibody-based biomarker discovery 54

Detection of biomarkers using peptide array technology 54

Discovery of biomarkers by MAb microarray profiling 54

Protein nanobiochip 55

Gene expression microarray data as a source of protein biomarkers 55

Quantification of protein biomarkers 55

Mass spectrometry for quantification of protein biomarkers 55

Real-time PCR for quantification of protein biomarkers 56

CyTOF for quantification of biomarkers 56

Search for biomarkers in body fluids 56

Challenges and strategies for discovey of protein biomarkers in plasma 57

3-D structure of CD38 as a biomarker 58

BD™ Free Flow Electrophoresis System 58

Isotope tags for relative and absolute quantification 58

Plasma protein microparticles as biomarkers 59

Proteome partitioning 59

Stable isotope tagging methods 60

Technology to measure both the identity and size of the biomarker 60

Targeted proteomic approaches 61

Biomarkers in the urinary proteome 61

Peptides in body fluids and tissues as biomarkers of disease 61

Analysis of peptides in bodily fluids 62

Serum peptidome patterns 62

SISCAPA method for quantitating proteins and peptides in plasma 63

Comparison of proteomic profiling technologies for discovery of biomarkers 63

Verification for interlaboratory reproducibility of protein biomarkers 63

Significance of similar protein biomarkers in different tissues 64

Glycomic technologies 65

Metabolomic technologies 65

Genome-wide association studies for identification of metabolic biomarkers 66

Lipid profiling 66

Mass spectrometry-based kits for discovery of metabolic biomarkers in plasma 66

Role of metabolomics in biomarker identification and pattern recognition 67

Urinary profiling by capillary electrophoresis 67

Validation of biomarkers in large-scale human metabolomics studies 67

Lipidomics 67

Disease biomarkers in breath 68

Portable breath test for volatile organic compounds 68

Detection of breath biomarkers by sensation technology 69

Detection of breath biomarkers optical frequency comb spectroscopy 69

Detection of breath biomarkers by infrared absorption spectroscopy 69

Fluorescent indicators for biomarkers 70

Molecular imaging technologies 70

Computer tomography 70

Magnetic resonance imaging 71

Positron emission tomography 71

Advantages of imaging biomarkers 72

Monitoring in vivo gene expression by molecular imaging 72

Molecular imaging in vivo as a biomarker 72

Challenges and future prospects of molecular imaging 73

Basic research in molecular imaging 73

Imaging intracellular NADH as a biomarker of disease 73

Devices for molecular imaging 74

Imaging biomarkers in clinical trials 74

Molecular imaging in clinical practice 74

Nuclear magnetic resonance 74

Chemical derivatization to enhance biomarker detection by NMR 75

Fluxomics by using NMR 75

Nanobiotechnology 75

Nanomaterials for biolabeling 76

Quantum dot molecular labels 77

Bioconjugated QDs for multiplexed profiling of biomarkers 77

Magnetic nanotags for multipley detection of biomarkers 78

Nanoproteomics and biomarkers 78

High-field asymmetric waveform ion mobility mass spectrometry 78

Nanoparticles for molecular imaging 78

Nanoparticles for discovering biomarkers 79

Nanosensors for measuring biomarkers in blood 79

Nanobiochip sensor technique for analysis of oral cancer biomarkers 80

Nucleoprotein nanodevices for detection of cancer biomarkers 80

Future prospects of application of nanobiotechnology for biomarkers 80

Bioinformatics 81

Biomarker Workflow Guide 81

Analysis of microarray data for selecting useful biomarkers 81

Role of bioinformatics in discovery of protein biomarkers 82

Role of bioinformatics in detection of cancer biomarkers 82

Biomarker databases 83

Gene networks as biomarkers 83

Role of bioinformatics in integrating various data and biomarker discovery 83

Evaluation of biomarker studies 84

3. Biomarkers and Molecular Diagnostics 85

Introduction 85

Molecular diagnostic technologies 85

Polymerase chain reaction 85

Amplification 85

Target selection 86

Detection of amplified DNA 86

Limitations of PCR 86

Real-time PCR systems 87

Limitations of real-time PCR 87

Future applications of real-time qPCR 88

Real-time qPCR for quantification of circulating mtDNA 88

Combined PCR-ELISA 88

Non-PCR methods 89

Linked Linear Amplification 89

Transcription mediated amplification 89

Rapid analysis of gene expression 89

WAVE nucleic acid fragment analysis system 90

DNA probes with conjugated minor groove binder 90

Rolling circle amplification technology 91

Gene-based diagnostics through RCAT 91

RCAT-immunodiagnostics 92

RCAT-biochips 92

RCAT-pharmacogenomics 92

Circle-to-circle amplification 92

Biochips and microarrays 93

Applications of biochips/microarrays 93

Role of biochip/microarrays in discovery of biomarkers 94

Biomarkers and high throughput molecular screening 94

Detection and expression profiling of miRNA 95

Real-time PCR for expression profiling of miRNAs 95

Real-time PCR for expression profiling of miRNAs 95

Use of LNA to explore miRNA 95

Microarrays for analysis of miRNA gene expression 96

4. Biomarkers for Drug Discovery & Development 97

Introduction 97

Biomarker technologies for drug discovery 98

Proteomics-based biomarkers for drug discovery 98

Chemoproteomics 98

Activity-based chemical proteomics 98

Transcriptomics for drug discovery 99

AvalonRx® drug discovery platform 99

Metabolomics for drug discovery 99

Biomarkers and drug safety 100

Biomarkers of adverse drug reactions 100

Applications of biomarkers in drug safety studies 101

Genomic technologies for toxicology biomarkers 101

Proteomic technologies for toxicology biomarkers 102

Metabonomic technologies for toxicology biomarkers 102

Integration of genomic and metabonomic data to develop toxicity biomarkers 102

Toxicology studies based on biomarkers 103

Biomarkers of hepatotoxicity 104

Biomarkers of nephrotoxicity 105

Cardiotoxicity 106

Neurotoxicity 107

Applications of biomarkers for drug development 107

Application of metabonomics/metabolomics for drug development 107

Role of pharmacokinetic/pharmacodynamic biomarkers in drug development 108

Molecular imaging as a biomarker in drug development 109

Molecular imaging in preclinical studies 109

Molecular imaging in clinical trials 110

Prospects of molecular imaging in drug discovery and development 111

Biomarkers in clinical trials 111

NIH recommendations on the use of biomarkers in clinical trials 112

Advantages of biomarkers for drug development 113

Limitations and problems with use of biomarkers in clinical trials 113

Application of biomarkers by the pharmaceutical companies 114

Use of biomarkers in relation to stage of drug discovery and development 115

Drug development in cardiovascular disorders 115

Drug development in neurological disorders 115

Future prospects of biomarker-based drug development 116

The Biomarker Alliance 116

Molecular Libraries and Imaging Roadmap of NIH 117

Biomarkers Consortium 117

Pharmacogenomic biomarker information in drug labels 118

Concluding remarks on the future trends in biomarker development 118

5. Role of Biomarkers in Healthcare 121

Introduction 121

Biomarkers of inflammation 121

ESR and CRP as biomarkers of inflammation 122

Biomarkers of oxidative stress 122

1,4-dihydroxynonane-mercapturic acid 122

Oxidative DNA damage 123

Proteins as biomarkers of oxidative stress in diseases 123

Testing for oxidative stress 123

Biomarkers in metabolic disorders 123

Biomarkers of acute intermittent porphyria 123

Liver X receptors 124

Biomarkers of diabetes mellitus 124

Biomarkers of hyperglycemia 125

Biomarkers of diabetes-associated oxidative stress 125

Biomarkers of inflammation associated with diabetes 126

Biomarkers of renal complications in diabetes mellitus type 2 126

Biomarkers of diabesity 126

Glycosylated hemoglobin in diabetes mellitus 126

Glycated albumin as a biomarker of diabetes mellitus 127

Lack of C-peptide as biomarker of complications of diabetes type 1 127

Serum retinol binding protein 4 as biomarker of insulin resistance 127

Biomarkers of metabolic syndrome 128

Adiponectin 128

Biomarkers in immune disorders 129

Biomarkers relevant to organ transplantation 129

Biomarkers of graft versus host disease 129

Biomarkers of renal allograft failure 130

Biomarkers of renal transplant tolerance 131

Biomarkers of lung transplant rejection 132

Systemic lupus erythematosus 132

Current management and need for biomarkers 132

Role of collaborative efforts and databases of SLE biomarkers 133

C4d-bearing reticulocytes 133

Adiponectin 133

CB-CAPS 133

HMGB1 134

Genetic loci of SLE 134

Epigenetic biomarkers of SLE 134

Biomarkers of musculoskeletal disorders 134

Biomarkers of rheumatoid arthritis 135

Circulating cytokines in RA 135

miRNA biomarkers in RA 135

Serum CRP in RA 136

Assays for biomarkers of RA 136

Biomarkers of spondylarthritis 136

Biomarkers of osteoarthritis 137

Biomarkers of osteoporosis 138

Dual x-ray absorptiometry 139

Bone imaging with quantitative CT and MRI 139

Assays for detection of biomarkers of osteoporosis 139

Biomarkers of infectious diseases 139

Application of proteomics for discovering biomarkers of infections 140

Chemokines as biomarkers of infection 141

Circulating CPS-1 as biomarkers of organ damage in sepsis 141

CoQ10 level reduction in septic shock 141

Endotoxin as biomarker of infection 142

Nitric oxide as a biomarker of sepsis 142

Procalcitonin as a guide to antibiotic therapy in infections 143

Soluble urokinase plasminogen activator receptor 143

Systemic inflammatory response syndrome 144

Tuberculosis 144

Conventional diagnosis of tuberculosis 145

Molecular diagnostics for tuberculosis 145

Biomarkers for tuberculosis 145

Biomarkers of pulmonary tuberculosis in the breath 146

Biomarkers of viral infections 146

Viral hepatitis 146

Biomarkers of SARS 148

Biomarkers of HIV 149

Biomarkers in parasitic infections 149

Role of biomarkers in malaria 150

Identification of biomarkers in Schistosomiasis infections 150

Biomarkers of liver disease 151

Breath biomarkers of liver disease 151

Biomarkers of viral hepatitis B and C 151

Biomarkers of liver injury 152

Biomarkers of liver cirrhosis 152

FibroMax 152

Biomarkers of pancreatitis 153

Biomarkers of renal disease 153

Biomarkers of lupus nephritis 154

Biomarkers of diabetic nephropathy 154

Cystatin C as biomarker of glomerular filtration rate (GFR) 154

Estimated GFR and albuminuria as biomarkers of chronic kidney disease 155

Proteomic biomarkers of acute kidney injury 155

Biomarkers of pulmonary diseases 155

Biomarkers of oxidative stress in lung diseases 156

Biomarkers of acute lung injury and respiratory distress syndrome 156

Cytokine/chemokine biomarkers of SARS 156

Plasma biomarkers related to inflammation 157

Urinary NO as biomarker 157

Biomarkers of interstitial lung disease 157

Pulmonary surfactant proteins as biomarkers for lung diseases 157

Serum KL-6 as biomarker of interstitial lung disease 158

Biomarkers of chronic obstructive pulmonary disease 158

Alpha1-antitrypsin gene polymorphisms predisposing to emphysema 158

BNP as a biomarker of chronic pulmonary disease 158

Chromagranin A (CgA) as biomarker of airway obstruction in smokers 159

Gene expression profile in peripheral blood of patients with COPD 159

Increased expression of PIGF as a biomarker of COPD 159

Biomarkers of asthma 159

Biomarker for rhinovirus-induced asthma exacerbation 159

Biomarkers for predicting response to corticosteroid therapy 160

Comparison of biomarkers of asthma and COPD 160

Cytokines as biomarkers of asthma severity 160

Exaled NO as a biomarker of asthma 161

Endothelin-1 in exhaled breath as biomarker of asthma 162

IgE as guide to dosing of omalizumab for asthma 162

Periostin as a biomarker for treatment of asthma with lebrikizumab 162

Biomarkers for cystic fibrosis 162

Biomarkers of pulmonary embolism 163

D-dimer as biomarker of thromboembolism 163

BNP and cTnT as biomarkers of outcome in pulmonary embolism 163

Biomarkers in gynecology and obstetrics 164

Biomarkers of menopause 164

Biomarkers of premenstrual dysphoric disorder 164

Biomarkers of endometriosis 165

Biomarkers for preeclampsia 165

Protein biomarker of preeclampsia in urine 166

Protein biomarkers of preeclampsia in CSF 166

Protein HtrA1 as biomarker for preeclampsia 166

sFlt1 and soluble endoglin as biomarkers of preeclampsia 167

RNA biomarkers 167

Biomarkers of premature birth 168

Biomarkers of oxidative stress in complicated pregnancies 168

Fetal biomarkers in maternal blood 168

Biomarkers for genetic disorders 169

Biomarkers for Down's syndrome 169

Biomarkers for muscular dystrophy 170

Biomarkers of phenylketonuria 170

Genetic biomarkers for psoriasis 170

Biomarkers of lysosomal storage disorders 171

Biomarkers of aging 172

Effect of calorie restriction on biomarkers of longevity 173

Genes as biomarkers of aging 173

Mitochondrial mutations as biomarkers of aging 174

Telomere attrition as aging biomarker 174

Gene variants as determinants of biological age 174

Genetic signatures of longevity 174

Low serum thyroid hormone level as biomarker of longevity 175

Role of bioinformatics in search for biomarkers of aging 175

Study of biomarkers of aging in a genetically homogeneous population 175

Biomarkers of miscellaneous disorders 176

Biomarkers of inflammatory bowel disease 176

Biomarkers of erectile dysfunction 176

Biomarkers of fever 177

Biomarkers of heat stroke 177

Biomarkers of radiation injury 178

Biomarkers common to multiple diseases 178

Nasal nitric oxide as a biomarker of response to rhinosinusitis therapy 178

Biomarkers and nutrition 179

Biomarkers in nutritional epidemiology 179

Biomarkers of nutritional status 179

Biomarkers of branched chain amino acid status 179

Biomarkers of caloric restriction 180

Biomarkers of malnutrition 180

Proteomic biomarkers and nutrition 180

Vitamin deficiency as biomarker of disease 181

Vitamin D as a biomarker of disease 181

Vitamin B12 deficiency 181

Biomarkers of gene-environmental interactions in human disease 182

6. Biomarkers of Cancer 183

Introduction 183

The ideal biomarker for cancer 183

Single vs multiple biomarkers of cancer 184

Types of cancer biomarkers 184

HER3 as biomarker of cancer 185

DNA repair biomarkers 185

miRNAs as biomarkers in cancer 185

Circulating miRNAs for cancer detection 187

Diagnostic value of miRNA in cancer 187

Biomarkers of epigenetic gene silencing in cancer 187

Immunologic biomarkers of cancer 188

Molecular diagnostic techniques for cancer 188

Technologies for detection of cancer biomarkers 189

Genomic technologies for cancer biomarkers 189

Cold-PCR 189

Genome analysis at the molecular level 190

Sequencing-based approaches for detection of cancer biomarkers 190

Early detection of tumor suppressor gene mutations 190

Biomarkers of PTEN tumor suppressor gene status 191

HAAH as a biomarker for cancer 191

KRAS as a biomarker of cancer 192

Telomerase as a biomarker of cancer 192

Digital karyotyping for cancer biomarkers 192

LigAmp for detection of gene mutations in cancer 193

Mitochondrial DNA as a cancer biomarker 193

Tissue microarrays for study of cancer biomarkers 193

Molecular fingerprinting of cancer 194

Biomarkers of inflammation in cancer 195

Proteomic technologies for detecting biomarkers of cancer 195

2D PAGE 196

Antibody-based detection of protein biomarkers 196

Aptamer-based molecular probes for cancer biomarker discovery 197

Cancer immunomics to identify autoantibody signatures 197

Desorption electrospray ionization for detection of cancer biomarkers 198

Detection of circulating nucleosomes in serum of cancer patients 198

Detection of tumor markers with ProteinChip technology 198

eTag assay system for cancer biomarkers 199

Glycoprotein biomarkers of cancer 199

HER-2/neu oncoprotein as biomarkers for cancer 200

Humoral proteomics 200

Laser capture microdissection 200

Membrane-type serine protease-1 201

Phage display technology 201

Proteomic analysis of cancer cell mitochondria 201

Proteomic technologies for detection of autoimmune biomarkers 202

SELDI-TOF MS 202

Serum proteome analysis for early detection of cancer 202

Triple-quadrupole MS for detection of mutant proteins 203

Targeted MS for validation of cancer biomarkers in plasma 203

Tissue proteomics for discovery of cancer biomarkers 203

Metabolomic biomarkers of cancer 203

Choline phospholipid biomarkers of cancer 204

Hypoxia-inducible factor-1 204

Detection of drug resistance in cancer by metabolic profiling 205

Epitomics for the early detection of cancer 205

Detection of biomarkers of DNA methylation 205

PCR with bisulfite for detecting DNA methylation biomarkers in cancer 207

MDScan? microarray technology 208

Rubicon MethylPlex technology 208

Epigenomics Marker Machine for DNA methylation biomarkers 208

Sequenom's integrated genetic analysis platform 209

Histone deacetylase 209

Mucins as epigenetic biomarkers in epithelial cancers 209

Nanobiotechnology for early detection of cancer to improve treatment 210

Selective expression of biomarkers by cancer compared with normal tissues 210

Ultrasound radiation to enhance release of a tumor biomarker 210

In vivo imaging of cancer biomarkers 211

Computer tomography 211

Optical systems for in vivo molecular imaging of cancer 211

Positron emission tomography 211

Imaging of tumor oxygenation and microvascular permeability by MRI 212

Xenon-enhanced MRI 212

Kallikrein gene family and cancer biomarkers 212

Circulating cancer cells in blood as biomarkers of cancer 213

Applications of cancer biomarkers 214

Use of biomarkers for cancer classification 214

Cancer classification using microarrays 214

Proteomic classification of cancer 214

Use of biomarkers for early detection of cancer 214

Applications of biomarkers for cancer diagnosis 215

Methylated DNA sequences as cancer biomarkers 215

MicroRNA expression profiling for diagnosis of human cancers 216

MUC4 as a diagnostic biomarker in cancer 216

Applications of biomarkers for cancer diagnosis and therapy 216

Asparagine synthetase as biomarker for therapy with L-asparaginase 217

Peptide-based agents for targeting cancer biomarkers 217

Biomarkers for assessing efficacy of cancer therapy 218

ERCC1-XPF expression as a biomarker of response to chemotherapy 218

P53 expression level as biomarker of efficacy of cancer gene therapy 218

Biomarkers of angiogenesis for developing antiangiogenic therapy 218

Biomarkers of response to antiangiogenic agents 219

Circulating endothelial cells as targets for antiangiogenic drugs 219

Imaging biomarkers for evaluation of antiangiogenic agents 219

Tumor endothelial markers 220

VEGF signaling inhibitors as biomarkers 220

VEGF-PET imaging for analysis of angiogenic changes within a tumor 221

Biomarkers of prognosis in cancer treatment 221

Biomarkers of drug resistance in cancer 221

A systems approach to biomarkers of innate drug resistance 222

Epithelial membrane protein-1 as a biomarker of gefitinib resistance 222

Methylation biomarkers of drug resistance in cancer 222

STAT3 and resistance to cisplatin 223

Biomarkers of radiation therapy for cancer 223

Role of biomarkers in drug development in oncology 223

Molecular imaging of tumor as a guide to drug development 224

Use of PET to assess response to anticancer drugs 225

Use of MRI to assess response to anticancer drugs 225

Biomarkers in plucked hair for assessing cancer therapy 225

Molecular targets of anticancer drugs as biomarkers 226

Safety biomarkers in oncology studies 226

Role of biomarkers in phase I clinical trials of anticancer drugs 226

Biomarkers according to location/type of cancer 227

Bladder cancer biomarkers 227

Detection of FGFR3 mutations in urine for diagnosis of bladder cancer 227

NMP22 BladderChek 227

Urinary telomerase as biomarker for detection of bladder cancer 228

Concluding remarks abut biomarkers of urinary cancer 228

Brain tumor biomarkers 228

14-3-3zeta positive expression as a prognostic biomarker for GBM 229

Biomarkers to predict response to EGFR inhibitors 229

CD133 as biomarker of resistance to radiotherapy 229

Circulating microvesicles as biomarkers 230

CSF protein profiling 230

CSF attractin as a biomarker of malignant astrocytoma 230

Methylation profiling of brain tumors 230

Metabolite biomarkers of brain tumors 231

miRNAs as biomarkers of brain tumors 232

MRI biomarker for response of brain tumor to therapy 232

Multigene predictor of outcome in GBM 232

Neuroimaging biomarkers combined with DNA microarray analysis 233

Receptor protein tyrosine phosphatase ? as biomarker of gliomas 233

Serum protein fingerprinting 233

VEGF-R2 as biomarker of angiogenesis in brain tumors 234

Bone tumor biomarkers 234

Cytogenetics for the study of bone and soft tissue tumors 234

Biomarkers of Ewing's tumors 234

Role of biomarkers in the diagnosis of bone tumors 235

Breast cancer biomarkers 235

Biomarkers of breast cancer in breath 236

Biomarkers for breast cancer in nipple aspiration fluid 236

Circulating nucleic acid biomarkers of breast cancer 236

Flow cytometry for quantification of biomarker expression patterns 237

Plasma proteomics for biomarkers of breast cancer 237

Quantitative realtime PCR assays for biomarker validation 237

Cdk6 as a biomarker of breast cancer 238

Centromere protein-F 238

Carbonic anhydrase IX 239

COX-2 as a biomarker of breast cancer 239

Glycomic biomarkers of breast cancer 239

HER-2/neu oncoprotein 240

High mobility group protein A2 241

Hypermethylated genes as biomarkers of metastatic breast cancer 241

Lipocalin 2 as biomarker of breast cancer progression 242

Long intervening non-coding RNAs 242

Mammaglobin 242

miRNA biomarkers of breast cancer 242

p27 expression as biomarker for survival after chemotherapy 243

Podocalyxin 244

Progranulin as a biomarker of breast cancer 244

Proliferating cell nuclear antigen 244

Protein kinase C as a predictive biomarker of metastatic breast cancer 244

Retinoblastoma tumor suppressor gene as a biomarker 245

Riboflavin carrier protein 245

Risk of invasive cancer after diagnosis of ductal carcinoma in situ 246

Serum CA 15-3 as biomarker of prognosis in advanced breast cancer 246

Suppressor of deltex protein 246

Tumor microenvironment as biomarker of metastasis in breast cancer 246

Type III TGF-? receptor as regulator of cancer progression 247

Diagnostic tests based on breast cancer genes 247

Prognostic role of breast cancer genes 248

Protein biomarkers for breast cancer prevention 249

Biomarkers to evaluate efficacy of chemoprevention 250

Biomarkers of response to chemotherapy of breast cancer 250

Concluding remarks and future prospects of breast cancer biomarkers 251

Cervical cancer biomarkers 251

Gastrointestinal cancer biomarkers 252

Esophageal cancer biomarkers 252

Gastric cancer biomarkers 253

Colorectal cancer biomarkers 253

Head and neck cancer 258

Leukemia biomarkers 259

Chromosome translocations in leukemias 259

DNA methylation biomarkers in leukemia 260

Gene mutations as biomarkers in leukemia 260

Molecular diagnostic techniques for leukemia 261

Proteomic technologies for discovering biomarkers of leukemia 261

Biomarkers of chronic lymphocytic leukemia 262

Biomarkers of chronic myeloid leukemia 262

Biomarkers of drug resistance in leukemia 263

Biomarkers of myelodysplasitic syndromes 263

Lymphoma biomarkers 263

Liver cancer biomarkers 264

Lung cancer biomarkers 264

Autoantibodies as biomarkers in lung cancer 266

Biomarkers associated with neuroendocrine differentiation in NSCLC 266

Biomarkers of chronic inflammation in lung cancer 266

Biomarkers for predicting sensitivity to chemotherapy in lung cancer 267

Biomarkers for prediction of sensitivity to EGFR inhibitors 267

Circulating tumor cells as biomarkers 268

Gene expression profiling for biomarkers of lung cancer 269

Methylation biomarkers of lung cancer 269

miRNA biomarkers in lung cancer 270

Proteomic biomarkers in exaled breath condensate 270

Serum protein biomarkers of lung cancer 271

tNOX as biomarker of lung cancer 271

Tumor-derived DNA and RNA markers in blood 271

Volatile organic compounds in the exhaled breath 272

Malignant pleural mesothelioma 272

Melanoma biomarkers 272

Nasopharyngeal carcinoma biomarkers 274

Proteomic biomarkers of nasopharyngeal cancer 275

miRNA biomarkers of nasopharyngeal carcinoma 275

Oral cancer biomarkers 276

Ovarian cancer biomarkers 276

Epitomics approach for ovarian cancer biomarkers in serum 277

Gene expression studies in ovarian cancer 278

HE4 protein in urine as a biomarker for ovarian cancer 278

HtrA1 as a biomarker of response to chemotherapy in ovarian cancer 279

Mutation of genes in ovarian cancer 279

Serum biomarkers of ovarian cancer prognosis 279

Serum albumin-associated peptides and proteins280

Multiplex assays for biomarkers of ovarian cancer 280

Concluding remarks on biomarker-based tests of ovarian cancer 281

Pancreatic cancer biomarkers 281

Discovery and validation of pancreatic cancer biomarkers 282

Cancer stem cells as biomarkers of pancreatic cancer 282

Histone modifications used as biomarkers in pancreatic cancer 283

miRNA biomarkers of pancreatic cancer 283

Proteomic biomarkers of pancreatic cancer 284

Prostate cancer 285

Adipose tissue-derived biomarkers of obesity-related prostate cancer 286

B7-H3 as biomarker of prostate cancer 286

Cancer genetics-guided biomarker signatures of prostate cancer 286

Detection of prostate cancer biomarkers in urine 287

Detection of prostatic intraepithelial neoplasia 288

Epigenetic biomarkers of prostate cancer 288

Gene expression analysis of prostate cancer 289

Genetic biomarkers of prostate cancer 289

Huntingtin Interacting Protein 1 overexpression in prostate cancer 289

Id proteins expression in prostate cancer 290

Identification of prostate cancer mRNA biomarkers 290

Integrative genomic and proteomic profiling of prostate cancer 290

LCM for diagnosis of prostate cancer 290

Loss of p27 as predictor of recurrence of prostate cancer 291

Microarray for diagnosis of prostate cancer 291

miRNA biomarkers of prostate cancer 292

Prostate cancer biomarkers in semen 292

PSA as biomarker of prostate cancer 292

ProPSA as biomarker of prostate cancer 293

Prostate Health Index 293

Prostasomes in blood as biomarker of prostate cancer 293

PSMA as biomarker of prostate cancer 294

Sarcosine as a metabolic biomarker of prostate cancer 294

Serum HAAH as biomarker of prostate cancer 294

Silenced CDH13 gene as a biomarker of cancer 294

Serum-protein fingerprinting 295

Tests for prostate cancer based on genetic dislocations 295

Concluding remarks on biomarkers of prostate cancer 295

Renal cancer biomarkers 296

Gene expression profile of RCC for biomarkers 296

miRNA biomarkers of renal cancer 296

Use of proteomics for detection of RCC biomarkers 296

Use of RCC biomarkers for prognosis and therapy 297

Thyroid cancer biomarkers 298

Detection of BRAF mutation 298

Gene expression biomarkers of thyroid cancer 298

Multiple endocrine neoplasia type 2B as risk factor for thyroid cancer 298

miRNA biomarkers of thyroid cancer 299

Biochemical biomarkers of thyroid cancer 299

Role of the NCI in molecular diagnosis of cancer 299

The Cancer Genome Anatomy Project 300

Molecular profiling of cancer 300

Cancer Genome Atlas 300

Cancer Genetic Markers of Susceptibility Project 301

Oncology Biomarker Qualification Initiative 301

Role of NCI in cancer biomarker development and validation 302

Projects for cancer biomarker research in Europe 303

COBRED project 303

COLTHERES consortium 304

PREDICT Consortium 304

Future prospects for cancer biomarkers 304

Cancer biomarker research at academic institutions 304

Future prospects and challenges in the discovery of cancer biomarkers 305

7. Biomarkers of Disorders of the Nervous System 307

Introduction 307

Discovery of biomarkers for neurological disorders 307

Biomarker identification in the CSF using proteomics 308

Biomarker identification in the CSF using lipidomics 308

Cerebral microdialysis for the study of biomarkers of cerebral metabolism 309

Detection of protein biomarkers of CNS disorders in the blood 309

Brain imaging for detection of biomarkers 309

Biomarkers of the aging brain 310

Cellular biomarker of aging of the brain 310

CSF F2-isoprostanes as biomarker of aging brain 310

Protein aggregation as a biomarker of aging brain 310

Data mining for biomarkers of neurological disorders 311

Antibodies as biomarkers in disorders of the nervous system 311

Biomarkers of neural regeneration 311

Biomarkers of disruption of blood-brain barrier 312

Biomarkers of neuro

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