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.

1. Identification of Tumor-Associated Antigens (TAAs) as Diagnostic and Predictive Biomarkers in Cancer Jian-Ying Zhang, Kok Sun Looi, and Eng M. Tan 2. Autoantibodies against Cancer Antigens Sacha Gnjatic, Lloyd J. Old, and Yao-Tseng Chen 3. Discovery of Antibody Biomarkers Using Protein Microarrays of Tumor Antigens Cloned in High-Throughput Madhumita Chatterjee, Jerzy Wojciechowski, and Michael A. Tainsky 4. Analysis of Glycans on Serum Proteins Using Antibody Microarrays Songming Chen and Brian B. Haab 5. Glycoproteomic Analysis by Two Dimensional Electrophoresis Mary Ann Comunale and Anand Mehta 6. All-Liquid Separations, Protein Microarrays and Mass Spectrometry to Interrogate Serum Proteomes: An Application to Serum Glycoproteomics Tasneem H. Patwa, Yinghua Qiu, Jia Zhao, Diane M. Simeone, and David M. Lubman 7. Reverse Phase Protein Microarrays for Theranostics and Patient Tailored Therapy Virginia Espina, Lance A. Liotta, and Emanuel F. Petricoin III 8. Serum Proteomics Using Mass Spectrometry Brian L. Hood, David E. Malehorn, Thomas P. Conrads, and William L. Bigbee 9. Hormones as Biomarkers: Practical Guide to Utilizing Luminex Technolgies for Biomarker Research Faina Linkov, Zoya Yurkovetsky, and Anna Lokshin 10. High-Throughput Analysis of Serum Antigens Using Sandwich ELISAs on Microarrays Shannon L. Servoss, Rachel Gonzalez, Susan Varnum, and Richard C. Zangar 11. Tissue Microarrays as a Tool in the Discovery and Validation of Tumor Markers Stephen M. Hewitt 12. Quantitative, Fluorescence-Based In-Situ Assessment of Protein Expression Christopher B. Moeder, Jennifer M. Giltnane, Sharon Pozner Moulis, and David L. Rimm 13. Tumor Marker Discovery by Expression Profiling RNA from Formalin Fixed Paraffin Embedded Tissues Maureen T. Cronin, Debjani Dutta, Mylan Pho, Anhthu Nugyen, Jennie Jeong, and Mei-Lan Liu 14. High-Throughput Mutation Screening Using a Single Amplification Condition Lijia Shi and John E. Landers 15. DNA Sequencing of Cancer-Related Genes for Biomarker Discovery Lisa M. Farwell and Victoria A. Joshi 16. Analysis of Loss of Heterozygosity in Circulating DNA Takeshi Nakamura, Eiji Sunami, and Dave S. B. Hoon 17. Pharmacogenomics Shilong Zhong and Marjorie Romkes 18. Study Designs in Genetic Epidemiology Michele L. Cote 19. Developing Classifiers for the Detection of Cancer Using Multi-Analytes Adi Laurentiu Tarca, Sorin Draghici, and Roberto Romero 20. Metabolomics of Cancer Natalie J. Serkova and Kristine Glunde 21. MRI and MRS of Human Brain Tumors Bob L. Hou and Jiani Hu 22. Magnetic Resonance Spectroscopy of Living Tissues Natalie J. Serkova, Kendra M. Hasebroock, and Susan L. Kraft

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