Tumor Biomarker Discovery, Softcover reprint of hardcover 1st ed. 2009 Methods and Protocols Methods in Molecular Biology Series, Vol. 520

Biomarkers are molecular indicators of a biological status and, as biochemical species, can be interrogated to evaluate disease status and therapeutic interventions. Biomarkers may be detectable in the blood, other body fluids, or tissues. The expectation is that the level of an informative biomarker is related to the specific type of disease present in the body. Hence, disease-relevant biomarkers can be used to measure the presence, progress, or intensity of disease. Through a variety of mechanisms, cancer cells provide the biomarker material for their own detection. Tumor biomarkers include cancer-specific mutations or changes in gene expression, both of which can result in aberrant protein expression. These variant or abundant proteins can be detectable in the circulation as the free proteins or as novel autoantibodies to those proteins, the latter indicating that the immune system can provide an exquisitely sensitive sensor of disease. Because cancer cells shed DNA in the circu- tion, an event rarely seen in healthy individuals, tumor-specific genetic changes, such as promoter methylation or gene mutations, are detectable in DNA prepared from plasma or other body fluids. Cancer-related biochemical changes often effect measurable me- bolic variations within a cell or organism. In addition, these biochemical changes result in posttranslational modification of proteins via glycosylation or phosphorylation providing a plethora of opportunity for biomarker discovery.

Identification of Tumor-Associated Antigens as Diagnostic and Predictive Biomarkers in Cancer.- Autoantibodies Against Cancer Antigens.- Discovery of Antibody Biomarkers Using Protein Microarrays of Tumor Antigens Cloned in High Throughput.- Analysis of Glycans on Serum Proteins Using Antibody Microarrays.- Glycoproteomic Analysis by Two-Dimensional Electrophoresis.- All-Liquid Separations, Protein Microarrays, and Mass Spectrometry to Interrogate Serum Proteomes: An Application to Serum Glycoproteomics.- Reverse-Phase Protein Microarrays for Theranostics and Patient Tailored Therapy.- Serum Proteomics Using Mass Spectrometry.- Hormones as Biomarkers: Practical Guide to Utilizing Luminex Technologies for Biomarker Research.- High-Throughput Analysis of Serum Antigens Using Sandwich ELISAs on Microarrays.- Tissue Microarrays as a Tool in the Discovery and Validation of Tumor Markers.- Quantitative, Fluorescence-Based In-Situ Assessment of Protein Expression.- Tumor Marker Discovery by Expression Profiling RNA from Formalin Fixed Paraffin Embedded Tissues.- High-Throughput Mutation Screening Using a Single Amplification Condition.- DNA Sequencing of Cancer-Related Genes for Biomarker Discovery.- Analysis of Loss of Heterozygosity in Circulating DNA.- Pharmacogenomics.- Study Designs in Genetic Epidemiology.- Developing Classifiers for the Detection of Cancer Using Multi-Analytes.- Metabolomics of Cancer.- MRI and MRS of Human Brain Tumors.- Magnetic Resonance Spectroscopy of Living Tissues.

Provides a detailed overview of the range of biomarker technologies as written by leading researchers in the field Useful both for researchers interested in new tumor biomarkers and physicians seeking familiarity with new technologies in the clinical setting Covers a wide range of biomarker assay formats and systems Presents alternative approaches to similar forms of biomarkers, covering a variety of detection technologies and approaches to data analysis Comprehensive guide to pitfalls of biomarker discovery and validation technologies