Table of Contents s492

T A B L E O F C O N T E N T S

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...... 32 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...... 35 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 Biomarkers in the urinary proteome...... 61 Peptides in body fluids and tissues as biomarkers of disease...... 61 Analysis of peptides in bodily fluids...... 61 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...... 66 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 Fluorescent indicators for biomarkers...... 69 Molecular imaging technologies...... 70 Computer tomography...... 70 Magnetic resonance imaging...... 70 Positron emission tomography...... 71 Advantages of imaging biomarkers...... 71 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...... 73 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...... 75 Quantum dot molecular labels...... 76 Bioconjugated QDs for multiplexed profiling of biomarkers...... 77 Magnetic nanotags for multipley detection of biomarkers...... 77 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...... 79 Nucleoprotein nanodevices for detection of cancer biomarkers...... 80 Future prospects of application of nanobiotechnology for biomarkers...... 80 Bioinformatics...... 80 Biomarker Workflow Guide...... 81 Analysis of microarray data for selecting useful biomarkers...... 81 Role of bioinformatics in discovery of protein biomarkers...... 81 Role of bioinformatics in detection of cancer biomarkers...... 82 Biomarker databases...... 82 Gene networks as biomarkers...... 83

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 Q-PCR...... 88 Combined PCR-ELISA...... 88 Non-PCR methods...... 88 Linked Linear Amplification...... 89 Transcription mediated amplification...... 89 Rapid analysis of gene expression...... 89 WAVE nucleic acid fragment analysis system...... 89 DNA probes with conjugated minor groove binder...... 90 Rolling circle amplification technology...... 90 Gene-based diagnostics through RCAT...... 91 RCAT-immunodiagnostics...... 91 RCAT-biochips...... 92 RCAT-pharmacogenomics...... 92 Circle-to-circle amplification...... 92 Biochips and microarrays...... 92 Applications of biochips/microarrays...... 93 Role of biochip/microarrays in discovery of biomarkers...... 93 Biomarkers and high throughput molecular screening...... 94 Detection and expression profiling of miRNA...... 94 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...... 95

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...... 114 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...... 116 Drug development in neurological disorders...... 116 Future prospects of biomarker-based drug development...... 117 The Biomarker Alliance...... 117 Molecular Libraries and Imaging Roadmap of NIH...... 117 Biomarkers Consortium...... 118 Pharmacogenomic biomarker information in drug labels...... 119

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 Lack of C-peptide as biomarker of complications of diabetes type 1...... 126 Serum retinol binding protein 4 as biomarker of insulin resistance...... 127 Biomarkers of metabolic syndrome...... 127 Adiponectin...... 127 Biomarkers in immune disorders...... 128 Biomarkers relevant to organ transplantation...... 128 Biomarkers of graft versus host disease...... 128 Biomarkers of renal allograft failure...... 130 Biomarkers of renal transplant tolerance...... 131 Biomarkers of lung transplant rejection...... 131 Systemic lupus erythematosus...... 132 Current management and need for biomarkers...... 132 Role of collaborative efforts and databases of SLE biomarkers...... 132 C4d-bearing reticulocytes...... 133 Adiponectin...... 133 CB-CAPS...... 133 Genetic loci of SLE...... 133 Epigenetic biomarkers of SLE...... 133 Biomarkers of musculoskeletal disorders...... 134 Biomarkers of rheumatoid arthritis...... 134 Circulating cytokines in RA...... 134 Serum CRP in RA...... 134 Assays for biomarkers of RA...... 135 Biomarkers of spondylarthritis...... 135 Biomarkers of osteoarthritis...... 136 Biomarkers of osteoporosis...... 137 Dual x-ray absorptiometry...... 137 Bone imaging with quantitative CT and MRI...... 137 Assays for detection of biomarkers of osteoporosis...... 138 Biomarkers of infectious diseases...... 138 Chemokines as biomarkers of infection...... 139 Circulating CPS-1 as biomarkers of organ damage in sepsis...... 139 Endotoxin...... 140 Procalcitonin...... 140 Application of proteomics for discovering biomarkers of infections...... 141 Systemic inflammatory response syndrome...... 141 Nitric oxide as a biomarker of sepsis...... 142 Tuberculosis...... 142 Conventional diagnosis of tuberculosis...... 143 Molecular diagnostics for tuberculosis...... 143 Biomarkers for tuberculosis...... 143 Biomarkers of pulmonary tuberculosis in the breath...... 144 Biomarkers of viral infections...... 144 Viral hepatitis...... 144 Biomarkers of SARS...... 146 Biomarkers of HIV...... 147 Biomarkers in parasitic infections...... 147 Role of biomarkers in malaria...... 147 Identification of biomarkers in Schistosomiasis infections...... 148 Biomarkers of liver disease...... 149 Breath biomarkers of liver disease...... 149 Biomarkers of viral hepatitis B and C...... 149 Biomarkers of liver injury...... 150 Biomarkers of liver cirrhosis...... 150 FibroMax...... 150 Biomarkers of pancreatitis...... 151 Biomarkers of renal disease...... 151 Biomarkers of lupus nephritis...... 152 Biomarkers of diabetic nephropathy...... 152 Cystatin C as biomarker of glomerular filtration rate (GFR)...... 152 Estimated GFR and albuminuria as biomarkers of chronic kidney disease...... 152 Proteomic biomarkers of acute kidney injury...... 153 Biomarkers of pulmonary diseases...... 153 Biomarkers of oxidative stress in lung diseases...... 154 Biomarkers of survival in acute respiratory distress syndrome...... 154 Urinary NO as biomarker...... 154 Plasma biomarkers related to inflammation...... 154 Pulmonary surfactant proteins as biomarkers for lung diseases...... 155 Cytokine/chemokine biomarkers of SARS...... 155 Biomarkers of chronic obstructive pulmonary disease...... 155 Increased expression of PIGF as a biomarker of COPD...... 156 Chromagranin A (CgA) as biomarker of airway obstruction in smokers...... 156 BNP as a biomarker of chronic pulmonary disease...... 156 Alpha1-antitrypsin gene polymorphisms predisposing to emphysema...... 157 Biomarkers of asthma...... 157 Comparison of biomarkers of asthma and COPD...... 157 Exaled NO as a biomarker of asthma...... 157 Cytokines as biomarkers of asthma severity...... 158 Biomarker for rhinovirus-induced asthma exacerbation...... 158 Biomarkers for predicting response to corticosteroid therapy...... 159 IgE as guide to dosing of omalizumab for asthma...... 159 Endothelin-1 in exhaled breath as biomarker of asthma...... 159 Biomarkers for cystic fibrosis...... 160 Biomarkers of pulmonary embolism...... 160 Biomarkers in gynecology and obstetrics...... 161 Biomarkers of menopause...... 161 Biomarkers of premenstrual dysphoric disorder...... 161 Biomarkers of endometriosis...... 162 Biomarkers for preeclampsia...... 162 Protein biomarker of preeclampsia in urine...... 163 Protein biomarkers of preeclampsia in CSF...... 163 Protein HtrA1 as biomarker for preeclampsia...... 163 sFlt1 and soluble endoglin as biomarkers of preeclampsia...... 164 RNA biomarkers...... 164 Biomarkers of premature birth...... 165 Biomarkers of oxidative stress in complicated pregnancies...... 165 Fetal biomarkers in maternal blood...... 165 Biomarkers for genetic disorders...... 166 Biomarkers for Down’s syndrome...... 166 Biomarkers for muscular dystrophy...... 166 Biomarkers of phenylketonuria...... 167 Genetic biomarkers for psoriasis...... 167 Biomarkers of lysosomal storage disorders...... 168 Biomarkers of aging...... 169 Effect of calorie restriction on biomarkers of longevity...... 170 Genes as biomarkers of aging...... 170 Mitochondrial mutations as biomarkers of aging...... 170 Telomere attrition as aging biomarker...... 171 Gene variants as determinants of biological age...... 171 Genetic signatures of longevity...... 171 Low serum thyroid hormone level as biomarker of longevity...... 172 Role of bioinformatics in search for biomarkers of aging...... 172 Study of biomarkers of aging in a genetically homogeneous population...... 172 Biomarkers of miscellaneous disorders...... 173 Biomarkers of chronic fatigue syndrome...... 173 Biomarkers of inflammatory bowel disease...... 173 Biomarkers of erectile dysfunction...... 174 Biomarkers of heat stroke...... 174 Nasal nitric oxide as a biomarker of response to rhinosinusitis therapy...... 175 Biomarkers common to multiple diseases...... 175 Vitamin D as a biomarker of disease...... 175 Biomarkers and nutrition...... 176 Biomarkers in nutritional epidemiology...... 176 Biomarkers of nutritional status...... 176 Biomarkers of branched chain amino acid status...... 177 Biomarkers of caloric restriction...... 177 Biomarkers of malnutrition...... 177 Proteomic biomarkers and nutrition...... 177 Biomarkers of gene-environmental interactions in human disease...... 178

6. Biomarkers of Cancer...... 179 Introduction...... 179 The ideal biomarker for cancer...... 179 Single vs multiple biomarkers of cancer...... 180 Types of cancer biomarkers...... 180 HER3 as biomarker of cancer...... 181 DNA repair biomarkers...... 181 miRNAs as biomarkers in cancer...... 181 Circulating miRNAs for cancer detection...... 183 Diagnostic value of miRNA in cancer...... 183 Biomarkers of epigenetic gene silencing in cancer...... 183 Immunologic biomarkers of cancer...... 184 Molecular diagnostic techniques for cancer...... 184 Technologies for detection of cancer biomarkers...... 185 Genomic technologies for cancer biomarkers...... 185 Cold-PCR...... 185 Genome analysis at the molecular level...... 186 Sequencing-based approaches for detection of cancer biomarkers...... 186 Early detection of tumor suppressor gene mutations...... 186 Biomarkers of PTEN tumor suppressor gene status...... 187 HAAH as a biomarker for cancer...... 187 KRAS as a biomarker of cancer...... 188 Telomerase as a biomarker of cancer...... 188 Digital karyotyping for cancer biomarkers...... 188 LigAmp for detection of gene mutations in cancer...... 189 Mitochondrial DNA as a cancer biomarker...... 189 Tissue microarrays for study of cancer biomarkers...... 189 Molecular fingerprinting of cancer...... 190 Biomarkers of inflammation in cancer...... 191 Proteomic technologies for detecting biomarkers of cancer...... 191 2D PAGE...... 192 Antibody-based detection of protein biomarkers...... 192 Aptamer-based molecular probes for cancer biomarker discovery...... 193 Cancer immunomics to identify autoantibody signatures...... 193 Desorption electrospray ionization for detection of cancer biomarkers...... 194 Detection of circulating nucleosomes in serum of cancer patients...... 194 Detection of tumor markers with ProteinChip technology...... 194 eTag assay system for cancer biomarkers...... 195 Glycoprotein biomarkers of cancer...... 195 HER-2/neu oncoprotein as biomarkers for cancer...... 196 Humoral proteomics...... 196 Laser capture microdissection...... 196 Membrane-type serine protease-1...... 197 Phage display technology...... 197 Proteomic analysis of cancer cell mitochondria...... 197 Proteomic technologies for detection of autoimmune biomarkers...... 198 SELDI-TOF MS...... 198 Serum proteome analysis for early detection of cancer...... 198 Tissue proteomics for discovery of cancer biomarkers...... 199 Metabolomic biomarkers of cancer...... 199 Choline phospholipid biomarkers of cancer...... 199 Hypoxia-inducible factor-1...... 200 Detection of drug resistance in cancer by metabolic profiling...... 200 Epitomics for the early detection of cancer...... 200 Detection of biomarkers of DNA methylation...... 201 PCR with bisulfite for detecting DNA methylation biomarkers in cancer...... 202 MDScan microarray technology...... 203 Rubicon MethylPlex technology...... 203 Epigenomics Marker Machine for DNA methylation biomarkers...... 204 Sequenom’s integrated genetic analysis platform...... 204 Histone deacetylase...... 204 Mucins as epigenetic biomarkers in epithelial cancers...... 205 Nanobiotechnology for early detection of cancer to improve treatment...... 205 Selective expression of biomarkers by cancer compared with normal tissues...... 205 Ultrasound radiation to enhance release of a tumor biomarker...... 206 In vivo imaging of cancer biomarkers...... 206 Computer tomography...... 206 Optical systems for in vivo molecular imaging of cancer...... 206 Positron emission tomography...... 207 Imaging of tumor oxygenation and microvascular permeability by MRI...... 207 Xenon-enhanced MRI...... 207 Kallikrein gene family and cancer biomarkers...... 208 Circulating cancer cells in blood as biomarkers of cancer...... 208 Applications of cancer biomarkers...... 209 Use of biomarkers for cancer classification...... 209 Cancer classification using microarrays...... 209 Proteomic classification of cancer...... 210 Use of biomarkers for early detection of cancer...... 210 Applications of biomarkers for cancer diagnosis...... 210 Methylated DNA sequences as cancer biomarkers...... 210 MicroRNA expression profiling for diagnosis of human cancers...... 211 MUC4 as a diagnostic biomarker in cancer...... 211 Applications of biomarkers for cancer diagnosis and therapy...... 212 Asparagine synthetase as biomarker for therapy with L-asparaginase...... 212 Peptide-based agents for targeting cancer biomarkers...... 213 Biomarkers for assessing efficacy of cancer therapy...... 213 ERCC1-XPF expression as a biomarker of response to chemotherapy...... 213 P53 expression level as biomarker of efficacy of cancer gene therapy...... 213 Biomarkers of angiogenesis for developing antiangiogenic therapy...... 213 Biomarkers of response to antiangiogenic agent brivanib alaninate...... 214 Circulating endothelial cells as targets for antiangiogenic drugs...... 214 DCE-MRI biomarkers for evaluation of antiangiogenic agents...... 214 Combination of soluble biomarkers of angiogenesis with imaging...... 215 Tumor endothelial markers...... 215 VEGF signalling inhibitors as biomarkers...... 216 Biomarkers of prognosis in cancer treatment...... 216 Biomarkers of drug resistance in cancer...... 216 A systems approach to biomarkers of innate drug resistance...... 217 Epithelial membrane protein-1 as a biomarker of gefitinib resistance...... 217 Methylation biomarkers of drug resistance in cancer...... 217 Biomarkers of radiation exposure and response...... 218 Role of biomarkers in drug development in oncology...... 218 Molecular imaging of tumor as a guide to drug development...... 219 Use of PET to assess response to anticancer drugs...... 219 Use of MRI to assess response to anticancer drugs...... 220 Biomarkers in plucked hair for assessing cancer therapy...... 220 Molecular targets of anticancer drugs as biomarkers...... 221 Safety biomarkers in oncology studies...... 221 Role of biomarkers in phase I clinical trials of anticancer drugs...... 221 Biomarkers according to location/type of cancer...... 222 Bladder cancer biomarkers...... 222 Detection of FGFR3 mutations in urine for diagnosis of bladder cancer...... 222 NMP22 BladderChek...... 222 Urinary telomerase as biomarker for detection of bladder cancer...... 222 Concluding remarks abut biomarkers of urinary cancer...... 223 Brain cancer biomarkers...... 223 Biomarkers to predict response to EGFR inhibitors...... 223 CD133 as biomarker of resistance to radiotherapy...... 224 Circulating microvesicles as biomarkers...... 224 CSF protein profiling...... 224 CSF attractin as a biomarker of malignant astrocytoma...... 225 Methylation profiling of brain tumors...... 225 Metabolite biomarkers of brain tumors...... 226 miRNAs as biomarkers of brain tumors...... 226 MRI biomarker for response of brain tumor to therapy...... 227 Multigene predictor of outcome in GBM...... 227 Neuroimaging biomarkers combined with DNA microarray analysis...... 227 Receptor protein tyrosine phosphatase  as biomarker of gliomas...... 228 Serum protein fingerprinting...... 228 VEGF-R2 as biomarker of angiogenesis in brain tumors...... 228 Breast cancer biomarkers...... 228 Biomarkers of breast cancer in breath...... 230 Biomarkers for breast cancer in nipple aspiration fluid...... 230 Circulating nucleic acid biomarkers of breast cancer...... 230 Flow cytometry for quantification of biomarker expression patterns...... 230 Plasma proteomics for biomarkers of breast cancer...... 231 Quantitative realtime PCR assays for biomarker validation...... 231 Cdk6 as a biomarker of breast cancer...... 232 Centromere protein-F...... 232 Carbonic anhydrase IX...... 232 COX-2 as a biomarker of breast cancer...... 233 Glycomic biomarkers of breast cancer...... 233 HER-2/neu oncoprotein...... 233 High mobility group protein A2...... 235 Hypermethylated genes as biomarkers of metastatic breast cancer...... 235 Lipocalin 2 as biomarker of breast cancer progression...... 235 Long intervening non-coding RNAs...... 236 Mammaglobin...... 236 miRNA biomarkers of breast cancer...... 236 p27 expression as biomarker for survival after chemotherapy...... 237 Podocalyxin...... 237 Progranulin as a biomarker of breast cancer...... 238 Proliferating cell nuclear antigen...... 238 Protein kinase C as a predictive biomarker of metastatic breast cancer...... 238 Retinoblastoma tumor suppressor gene as a biomarker...... 238 Riboflavin carrier protein...... 239 Risk of invasive cancer after diagnosis of ductal carcinoma in situ...... 239 Serum CA 15-3 as biomarker of prognosis in advanced breast cancer...... 240 Suppressor of deltex protein...... 240 Tumor microenvironment as biomarker of metastasis in breast cancer...... 240 Type III TGF- receptor as regulator of cancer progression...... 240 Diagnostic tests based on breast cancer genes...... 241 Prognostic role of breast cancer genes...... 242 Protein biomarkers for breast cancer prevention...... 243 Biomarkers to evaluate efficacy of chemoprevention...... 243 Biomarkers of response to chemotherapy of breast cancer...... 243 Cervical cancer biomarkers...... 244 Gastrointestinal cancer biomarkers...... 245 Esophageal cancer biomarkers...... 246 Gastric cancer biomarkers...... 246 Colorectal cancer biomarkers...... 247 Head and neck cancer...... 251 Leukemia biomarkers...... 252 Chromosome translocations in leukemias...... 252 DNA methylation biomarkers in leukemia...... 253 Gene mutations as biomarkers in leukemia...... 253 Molecular diagnostic techniques for leukemia...... 254 Proteomic technologies for discovering biomarkers of leukemia...... 254 Biomarkers of chronic lymphocytic leukemia...... 255 Biomarkers of chronic myeloid leukemia...... 255 Biomarkers of drug resistance in leukemia...... 256 Biomarkers of myelodysplasitic syndromes...... 256 Lymphoma biomarkers...... 256 Liver cancer biomarkers...... 256 Lung cancer biomarkers...... 257 Autoantibodies as biomarkers in lung cancer...... 258 Biomarkers associated with neuroendocrine differentiation in NSCLC...... 259 Biomarkers of chronic inflammation in lung cancer...... 259 Biomarkers for predicting sensitivity to chemotherapy in lung cancer...... 259 Biomarkers for prediction of sensitivity to EGFR inhibitors...... 260 Circulating tumor cells as biomarkers...... 261 Gene expression profiling for biomarkers of lung cancer...... 261 Methylation biomarkers of lung cancer...... 262 miRNA biomarkers in lung cancer...... 262 Proteomic biomarkers in exaled breath condensate...... 263 Serum protein biomarkers of lung cancer...... 263 tNOX as biomarker of lung cancer...... 263 Tumor-derived DNA and RNA markers in blood...... 264 Volatile organic compounds in the exhaled breath...... 264 Malignant pleural mesothelioma...... 264 Melanoma biomarkers...... 265 Nasopharyngeal carcinoma biomarkers...... 266 Proteomic biomarkers of nasopharyngeal cancer...... 267 miRNA biomarkers of nasopharyngeal carcinoma...... 268 Oral cancer biomarkers...... 268 Ovarian cancer biomarkers...... 269 Epitomics approach for ovarian cancer biomarkers in serum...... 270 Gene expression studies in ovarian cancer...... 270 HtrA1 as a biomarker of response to chemotherapy in ovarian cancer...... 271 Mutation of genes in ovarian cancer...... 271 Serum biomarkers of ovarian cancer prognosis...... 271 Serum albumin-associated peptides and proteins...... 272 Multiplex assays for biomarkers of ovarian cancer...... 272 Concluding remarks on biomarker-based tests of ovarian cancer...... 273 Pancreatic cancer biomarkers...... 273 Discovery and validation of pancreatic cancer biomarkers...... 274 Cancer stem cells as biomarkers of pancreatic cancer...... 275 Histone modifications used as biomarkers in pancreatic cancer...... 275 miRNA biomarkers of pancreatic cancer...... 275 Proteomic biomarkers of pancreatic cancer...... 276 Prostate cancer...... 277 Adipose tissue-derived biomarkers of obesity-related prostate cancer...... 278 B7-H3 as biomarker of prostate cancer...... 278 Detection of prostate cancer biomarkers in urine...... 279 Detection of prostatic intraepithelial neoplasia...... 280 Epigenetic biomarkers of prostate cancer...... 280 Gene expression analysis of prostate cancer...... 280 Genetic biomarkers of prostate cancer...... 281 Huntingtin Interacting Protein 1 overexpression in prostate cancer...... 281 Id proteins expression in prostate cancer...... 281 Identification of prostate cancer mRNA biomarkers...... 282 Integrative genomic and proteomic profiling of prostate cancer...... 282 LCM for diagnosis of prostate cancer...... 282 Loss of p27 as predictor of recurrence of prostate cancer...... 283 Microarray for diagnosis of prostate cancer...... 283 miRNA biomarkers of prostate cancer...... 283 Prostate cancer biomarkers in semen...... 284 PSA as biomarker of prostate cancer...... 284 ProPSA as biomarker of prostate cancer...... 284 Prostate Health Index...... 285 PSMA as biomarker of prostate cancer...... 285 Sarcosine as a metabolic biomarker of prostate cancer...... 285 Serum HAAH as biomarker of prostate cancer...... 285 Silenced CDH13 gene as a biomarker of cancer...... 286 Serum-protein fingerprinting...... 286 Tests for prostate cancer based on genetic dislocations...... 286 Concluding remarks on biomarkers of prostate cancer...... 287 Renal cancer biomarkers...... 287 Gene expression profile of RCC for biomarkers...... 287 miRNA biomarkers of renal cancer...... 287 Use of proteomics for detection of RCC biomarkers...... 288 Use of RCC biomarkers for prognosis and therapy...... 288 Thyroid cancer biomarkers...... 289 Gene expression biomarkers of thyroid cancer...... 289 Multiple endocrine neoplasia type 2B as risk factor for thyroid cancer...... 290 miRNA biomarkers of thyroid cancer...... 290 Biochemical biomarkers of thyroid cancer...... 290 Role of the NCI in molecular diagnosis of cancer...... 290 The Cancer Genome Anatomy Project...... 291 Molecular profiling of cancer...... 291 Cancer Genome Atlas...... 291 Cancer Genetic Markers of Susceptibility Project...... 292 Oncology Biomarker Qualification Initiative...... 292 Role of NCI in cancer biomarker development and validation...... 293 COBRED project for cancer biomarker research in Europe...... 294 Future prospects for cancer biomarkers...... 295 Cancer biomarker research at academic institutions...... 295 Future prospects and challenges in the discovery of cancer biomarkers...... 295

7. Biomarkers of Disorders of the Nervous System...... 297 Introduction...... 297 Discovery of biomarkers for neurological disorders...... 297 Biomarker identification in the CSF using proteomics...... 298 Biomarker identification in the CSF using lipidomics...... 298 Cerebral microdialysis for the study of biomarkers of cerebral metabolism...... 298 Detection of protein biomarkers of CNS disorders in the blood...... 299 Brain imaging for detection of biomarkers...... 299 Biomarkers of the aging brain...... 300 Cellular biomarker of aging of the brain...... 300 Protein aggregation as a biomarker of aging brain...... 300 Data mining for biomarkers of neurological disorders...... 300 Antibodies as biomarkers in disorders of the nervous system...... 301 Biomarkers of neural regeneration...... 301 Biomarkers of disruption of blood-brain barrier...... 301 Biomarkers of neurotoxicity...... 302 Glial fibrillary acidic protein as biomarker of neurotoxicity...... 302 Single-stranded DNA as a biomarker of neuronal apoptosis...... 302 Biomarkers of neurogenetic disorders...... 303 Charcot-Marie Tooth disease...... 303 Duchenne and Becker muscular dystrophy...... 304 Fragile X syndrome...... 305 Hereditary neuropathy with liability to pressure palsies...... 305 Hereditary metabolic storage disorders with neurologic manifestations...... 305 Gaucher disease...... 306 Pompe’s disease...... 306 Mitochondrial disorders affecting the nervous system...... 306 Spinal muscular atrophy...... 307 Biomarkers of neurodegenerative disorders...... 307 Biomarkers of Alzheimer’s disease...... 307 The ideal biomarker for AD...... 309 Protein biomarkers of AD in CSF...... 310 Amyloid precursor protein...... 311 Tau proteins in CSF...... 312 Tests for the detection of A in CSF...... 312 Monitoring of synthesis and clearance rates of A in the CSF...... 313 Tests combining CSF tau and A...... 313 CSF sulfatide as a biomarker for AD...... 314 Glycerophosphocholine as CSF biomarker in AD...... 314 CSF Reelin as biomarker of AD...... 314 Urine tests for AD...... 315 Plasma protein biomarkers of AD...... 315 A serum protein-based algorithm for the detection of AD...... 316 Protein kinase C in red blood cells...... 316 Detection of aggregated misfolded proteins in the blood...... 316 Lymphocyte Proliferation Test...... 316 A biomarker-based skin test for AD...... 317 Radioiodinated clioquinol as a biomarker for Aβ...... 317 Nanotechnology to measure A-derived diffusible ligands...... 317 Simultaneous measurement of several biomarkers for AD...... 318 Use of biomarkers to predict AD in patients with MCI...... 318 Genetic tests for AD...... 319 Gene expression patterns in AD...... 319 Magnetic resonance spectroscopy in AD...... 320 MRI for biomarkers of AD...... 320 PET scanning for biomarkers of AD...... 321 Targeting of chemokine receptor as biomarker for brain imaging...... 323 Plasma biomarkers of drug response in AD...... 323 PredictAD project...... 323 Concluding remarks about biomarkers for AD...... 324 Biomarkers of Parkinson’s disease...... 324 Biomarkers of PD based on gene expression in blood...... 325 Cardiac denervation as a biomarker of PD...... 325 Imaging biomarkers of PD...... 325 Metabolic brain networks as biomarkers...... 326 Metabonomic biomarker profile for diagnosis and monitoring of PD...... 326 Protein biomarkers of PD...... 327 Serum vitamin D as a biomarker of PD...... 327 Future prospects for biomarkers of PD...... 327 Biomarkers of Huntington's disease...... 328 Quantitative MRI measurement of brain atrophy as biomarker of HD...... 328 Biomarkers of Wilson’s disease...... 329 Biomarkers of amyotrophic lateral sclerosis...... 329 Biomarkers of neuroinflammation in ALS...... 330 Detection of ALS biomarkers in blood vs CSF...... 330 Ideal biomarker of ALS...... 330 Imaging biomarkers of ALS...... 331 Metabolomic biomarkers of ALS...... 331 Proteomic biomarkers of ALS...... 331 Future prospects of biomarkers of ALS...... 332 Biomarkers of dementia in HIV-1-infected patients...... 332 Biomarkers of prion diseases...... 332 14-3-3 protein and tTau/P-Tau ratio...... 332 Bioluminescence imaging as a surrogate biomarker of prion infectivity...... 333 Biomarkers of multiple sclerosis...... 333 Antibodies in multiple sclerosis...... 334 Antibodies to galactocerebroside...... 334 Antibodies to myelin oligodendrocyte glycoprotein...... 334 Detecting autoantibodies in multiple sclerosis...... 335 CSF Cystatin C as a biomarker of multiple sclerosis...... 335 T cells as biomarkers of multiple sclerosis...... 335 Matrix metalloproteinases as biomarkers in multiple sclerosis...... 336 Gelsolin as a biomarker of multiple sclerosis...... 336 Gene expression profiling of biomarkers in multiple sclerosis...... 336 Serum proteomic pattern analysis in multiple sclerosis...... 337 Biomarkers of remyelination and repair...... 337 Myelin imaging by PET...... 337 Biomarkers of response to therapy of multiple sclerosis...... 337 DNA motifs in the blood as biomarkers of response to treatment...... 338 Concluding remarks and future perspective for biomarkers of multiple sclerosis...... 338 Biomarkers of stroke...... 339 Biomarkers of intracerebral hemorrhage...... 340 Biomarkers of hypoxic brain damage...... 341 Brain natriuretic peptide as a biomarker for cardioembolic stroke...... 341 Brain lactate and N-acetylaspartate as biomarkers of stroke...... 341 CRP as biomarker of risk of stroke...... 341 Intercellular adhesion molecule 1 as biomarker of ischemic stroke...... 342 Lp-PLA2 and CRP as biomarkers for stroke...... 342 Neuroserpin polymorphisms as a biomarker of stroke...... 342 NMDA receptors as biomarkers of excitotoxicity in stroke...... 343 Nucleosomes as biomarkers of stroke...... 343 PARK7 and nucleoside diphosphate kinase A as biomarkers of stroke...... 343 Visinen-like protein 1...... 344 Gene expression in blood following ischemic stroke...... 344 Biomarker panel for stroke...... 344 Future prospects for biomarkers of stroke...... 344 Biomarkers of traumatic brain injury...... 345 Technologies for identification of biomarkers of TBI...... 346 Proteomic technologies for biomarkers of TBI...... 346 Cerebral microdialysis for study of biomarkers of TBI...... 347 Biomarkers of TBI...... 347 C-tau as biomarker of TBI...... 347 Hyperphosphorylated axonal neurofilament protein...... 348 IL-6 and nerve growth factor as biomarkers of TBI...... 348 Serum S100B as biomarker of TBI...... 348 Biomarkers of inflicted TBI in infants...... 349 Clinical applications of biomarkers of TBI...... 349 Biomarkers of CNS infections...... 349 Biomarkers of CNS HIV infection...... 349 Biomarkers of bacterial meningitis...... 350 Biomarkers of epilepsy...... 350 Genetic epilepsies...... 351 Biochemical markers of epilepsy...... 351 Imaging biomarkers of epilepsy...... 351 Biomarkers of normal pressure hydrocephalus...... 352 Biomarkers of retinal disorders...... 352 Biomarkers of age-related macular degeneration...... 352 Biomarkers for autism...... 353 Biomarkers of sleep disorders...... 354 Biomarker of excessive daytime sleepiness...... 354 Biomarkers of obstructive sleep apnea...... 354 Biomarkers of restless legs syndrome...... 355 Biomarkers of pain...... 355 Biomarkers of neuropathic pain...... 355 Brain insular glutamate as biomarker of fibromyalgia...... 356 Biomarkers of visceral pain...... 356 Biomarkers of migraine...... 357 Biomarkers of psychiatric disorders...... 357 Biomarkers of depression...... 357 Biomarkers of psychosis...... 358 Biomarkers of schizophrenia...... 358 Genetic biomarkers of schizophrenia...... 358 Gene expression analysis of blood for biomarkers of schizophrenia...... 358 Proteomic studies for biomarkers of schizophrenia...... 359 Metabolic biomarkers of schizophrenia...... 359

8. Biomarkers of Cardiovascular Disorders...... 361 Introduction...... 361 Epidemiology of cardiovascular disease...... 361 Biomarkers of cardiovascular diseases...... 361 Genetic biomarkers of cardiovascular disorders...... 363 Methods for identification of cardiovascular biomarkers...... 364 Application of proteomics for biomarkers of cardiovascular disease...... 364 Detection of biomarkers of myocardial infarction in saliva by a nanobiochip...... 364 Metabolomic technologies for biomarkers of myocardial ischemia...... 365 Imaging biomarkers of cardiovascular disease...... 365 Annexin A5 as an imaging biomarker of cardiovascular disease...... 365 Cardiovascular MRI...... 365 Myocardial perfusion imaging...... 366 Applications of biomarkers of cardiovascular disease...... 366 Biomarkers for ischemic heart disease and myocardial infarction...... 366 Troponin...... 367 Natriuretic peptide...... 368 Copeptin...... 369 Creatine kinase muscle brain...... 369 Myoglobin...... 369 Fatty acid binding protein...... 369 High density lipoprotein 2...... 370 Cripto-1 as a biomarker of myocardial infarction...... 370 Cataract as a biomarker of ischemic heart disease...... 370 Plasma fetuin-A levels and the risk of myocardial infarction...... 371 Biomarkers of congestive heart failure...... 371 Angiogenesis biomarkers...... 371 beta-2a protein as a biomarker of heart failure...... 371 Desmin...... 372 Galectin-3 as biomarker of acute heart failure...... 372 G protein-coupled receptor kinase-2 as biomarker of CHF...... 372 KIF6 gene as biomarker of CHF...... 373 NT ProBNP as biomarker of CHF...... 373 Oxidative stress as biomarker of heart failure...... 373 Future prospects for biomarkers of heart failure...... 374 Biomarkers for atherosclerosis...... 374 Adipocyte enhancer-binding protein 1...... 374 Ghrelin as a biomarker of atherosclerosis...... 375 Imaging biomarkers of hypercholesterolemia/atherosclerosis...... 375 Inflammatory biomarkers of atherosclerosis...... 375 Lipid-modified proteins as biomarkers of atherosclerosis...... 376 Lp-PLA2 as biomarker of atherosclerotic heart disease...... 376 Nitric oxide impairment and atherosclerosis...... 376 Oxygen free radicals as biomarkers of atherosclerosis...... 376 Proteomic profiles of serum inflammatory markers of atherosclerosis...... 376 Biomarkers of risk factors for coronary heart disease...... 377 Antibody to oxidized-LDL...... 377 Apolipoproteins as risk factors for coronary heart disease...... 377 CRP as biomarker of risk for coronary heart disease...... 378 Impairment of EPCs by oxidative stress as a biomarker of disease...... 378 Biomarkers for pulmonary arterial hypertension...... 379 Biomarkers of abdominal aortic aneurysm...... 379 Genetic biomarkers for cardiovascular disease...... 380 Genetic biomarkers of atherosclerosis...... 380 IL-1 gene polymorphism as biomarker of cardiovascular disease...... 381 Polymorphisms of the eNOS gene and angina pectoris...... 381 Polymorphisms in the apolipoprotein E gene...... 381 Mutations in the low density lipoprotein receptor gene...... 381 Mutations within several genes that code for ion channel...... 382 Polymorphism in the angiotensinogen gene...... 382 Kallikrein gene mutations in cardiovascular disease...... 382 Kallikrein gene and essential hypertension...... 383 Gene mutations in pulmonary arterial hypertension...... 383 Genetic biomarkers of early onset myocardial infarction...... 383 Gene variant as a risk factor for sudden cardiac death...... 383 Multiple biomarkers for prediction of death from cardiovascular disease...... 384 Role of biomarkers in the management of cardiovascular disease...... 384 Role of biomarkers in the diagnosis/prognosis of myocardial infarction...... 384 Role of biomarkers in the prevention of cardiovascular disease...... 385 Molecular signature analysis in management of cardiovascular diseases...... 385 C-reactive protein as biomarker of response to statin therapy...... 386 Role of circulating biomarkers and mediators of cardiovascular dysfunction...... 386 Use of protein biomarkers for monitoring acute coronary syndromes...... 387 Use of biomarkers for prognosis of recurrent atrial fibrillation...... 387 Use of multiple biomarkers for monitoring of cardiovascular disease...... 387 Use of biomarkers in the management of peripheral arterial disease...... 388 Use of biomarkers in the management of hypertension...... 389 Future prospects for cardiovascular biomarkers...... 389 Cardiovascular Biomarker Consortium...... 389 Systems Approach to Biomarker Research in Cardiovascular Disease...... 389

9. Biomarkers & Personalized Medicine...... 391 Introduction...... 391 Pharmacogenetics...... 391 Biomarkers and pharmacogenetics...... 392 Pharmacogenomics...... 393 Pharmacoproteomics...... 394 Single cell proteomics for personalized medicine...... 394 Role of biomarkers in development of personalized drugs...... 395 Use of biomarkers for developing MAb therapy in oncology...... 395 Biobanking, biomarkers and personalized medicine in EU...... 395 Expression signatures as diagnostic/prognostic tools...... 396 Biomarkers for monitoring response to therapy...... 396 Drug rescue by biomarker-based personalized medicine...... 397 Future role of biomarkers in personalized medicine...... 397

10. Regulatory issues...... 399 Introduction...... 399 Biomarker validation...... 399 FDA criteria for a valid biomarker...... 399 Role of NIST in validation of cancer biomarkers...... 401 Quality specifications for BNP and NT-proBNP as cardiac biomarker assays...... 401 FDA perspective of biomarkers in clinical trials...... 402 FDA and predictive medicine...... 403 Biomarkers and FDA’s Voluntary Genomic Data Submission...... 404 Role of imaging biomarkers in approval of drugs...... 404 FDA Critical Path Initiative and biomarker R&D...... 405 FDA consortium linking genetic biomarkers to serious adverse events...... 405 Oncology Biomarker Qualification Initiative...... 406 Critical Path Initiative...... 407 Predictive Safety Testing Consortium...... 408 From validated biomarker assay to a clinical laboratory diagnostic...... 408 Fast Path programs...... 409 Need for a single federal agency to oversee biomarker field...... 409

11. Markets for Biomarkers...... 411 Introduction...... 411 Biomarker markets according to technologies/applications...... 411 Markets for protein biomarkers...... 411 Biomarker market relevant to drug discovery and development...... 412 Biomarker market relevant to epigenetics...... 412 Biomarket market relevant to bioinformatics...... 412 Biomarker markets according to therapeutic areas...... 412 Geographical distribution of biomarker markets...... 413 Unfulfilled needs in biomarkers...... 413 Drivers for the growth of markets for biomarkers...... 414 Challenges facing the biomarker industry...... 415 Pitfalls in the discovery and development of biomarkers...... 415 Strategies for developing biomarker markets...... 415 Utilization of biomarker research in academic laboratories...... 416 Biomarker discovery at pharmaceutical companies...... 416 Industrial-academic collaborations in biomarkers...... 416 Application of biomarkers in medical practice...... 417 Future role of biomarkers in healthcare...... 417 Applications of biomarkers beyond healthcare...... 418 Combating bioterrorism...... 418 Biomarkers for monitoring human exposure to environmental toxins...... 418 Application of biomarkers in animal health...... 419 Biomarker patents...... 419 Factors that enhance the value of biomarker IP...... 420 US policy on gene patenting relevant to biomarkers...... 420

12. References...... 421 Tables

Table 1-1: Historical landmarks in discovery and development of biomarkers...... 24 Table 1-2: Classification of biomarkers...... 24 Table 1-3: Terminology of biomarkers of disease relevant to clinical development...... 26 Table 1-4: Autoimmune disorders under study for autoantibodies as predictors...... 35 Table 1-5: Comparison of various types of biomarkers...... 35 Table 1-6: Use of “-omic” technologies for discovery of biomarkers...... 37 Table 1-7: Role of biomarkers in translational medicine...... 38 Table 2-1: Classification of methods of gene expression analysis...... 42 Table 2-2: Comparison of proteomic profiling technologies for discovery of biomarkers...... 63 Table 2-3: Companies involved in developing molecular imaging...... 72 Table 3-1: Applications of biochip/microarray technology in relation to biomarkers...... 93 Table 4-1: Companies using metabolomics for drug discovery...... 100 Table 4-2: Causes of failures in clinical trials and their reduction by use of biomarkers...... 114 Table 4-3: Biomarker-based drug development at major pharmaceutical companies...... 115 Table 5-1: Biomarkers of diabetes mellitus...... 124 Table 5-2: Biomarkers of sepsis...... 138 Table 5-3: Biomarkers of pulmonary diseases...... 153 Table 5-4: Biomarkers of aging...... 169 Table 5-5: Examples of biomarkers common to multiple diseases...... 175 Table 6-1: Desirable characteristics of biomarkers for cancer...... 179 Table 6-2: Types of cancer biomarkers...... 180 Table 6-3: A classification of molecular diagnostic methods in cancer...... 184 Table 6-4: Novel biomarkers of prognosis in cancer treatment...... 216 Table 6-5: Biomarkers of brain tumors...... 223 Table 6-6: Biomarkers of breast cancer...... 229 Table 6-7: miRNA associated with breast cancer...... 236 Table 6-8: Biomarkers of colorectal cancer...... 247 Table 6-9: Biomarkers of lung cancer...... 258 Table 6-10: Classification of biomarkers of melanoma...... 265 Table 6-11: Biomarkers of nasopharyngeal carcinoma and potential applications...... 267 Table 6-12: Biomarkers of ovarian cancer...... 269 Table 6-13: Classification of biomarkers of pancreatic cancer...... 274 Table 6-14: Biomarkers of prostate cancer...... 277 Table 7-1: Biomarkers of cerebral metabolism...... 299 Table 7-2: Classification of biochemical markers of AD in blood and CSF...... 308 Table 7-3: Characteristics of an ideal biomarker for Alzheimer disease...... 309 Table 7-4: Biomarkers of Parkinson’s disease...... 325 Table 7-5: Classification of biomarkers of sporadic amyotrophic lateral sclerosis...... 329 Table 7-6: Biomarkers of multiple sclerosis...... 333 Table 7-7: Biomarkers of response to interferon-b in multiple sclerosis...... 337 Table 7-8: Biomarkers of stroke...... 339 Table 7-9: Biochemical biomarkers of traumatic brain injury...... 345 Table 7-10: Biomarkers of epilepsy...... 351 Table 8-1: Classification of biomarkers for cardiovascular diseases...... 362 Table 8-2: Genes that cause cardiovascular diseases...... 363 Table 9-1: Pharmacogenetic vs. pharmacogenomic studies...... 392 Table 9-2: Applications of pharmacoproteomic biomarkers in personalized medicine...... 394 Table 11-1: Biomarker markets according to technologies/applications 2010-2020...... 411 Table 11-2: Biomarker markets according to therapeutic areas 2010-2020...... 413 Table 11-3: Geographical distribution of biomarker markets 2010-2020...... 413 Table 11-4: Factors driving the growth of biomarker industry...... 414

Figures

Figure 1-1: Relation of biomarkers to other technologies and healthcare...... 38 Figure 2-1: The central role of spectrometry in proteomics...... 50 Figure 4-1: Role of biomarkers in drug discovery and development process...... 97 Figure 6-1: Role of proteomics in the discovery of cancer biomarkers...... 192 Figure 6-2: Cancer biomarker development and validation...... 294 Figure 7-1: Discovery and application of biomarkers in neurological diseases...... 297 Figure 9-1: Role of pharmacogenetic biomarkers in personalized medicine...... 393 Figure 9-2: Impact of biomarkers on personalized medicine...... 398 Figure 10-1: Stages and timelines of biomarker discovery, development and marketing...... 399 Figure 10-2: Biomarker qualification pilot process at the FDA...... 401 Figure 10-3: From a validated biomarker assay to a clinical laboratory diagnostic...... 409 Figure 11-1: Unfulfilled needs in biomarkers technologies and applications...... 414