Cancer Biomarkers Analytical Techniques for Discovery

by ; ;
Edition: 1st
Format: Hardcover
Pub. Date: 2007-02-09
Publisher(s): Wiley-Interscience
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Summary

Tools, techniques, and progress in cancer biomarkers discovery The completion of a number of gene sequencing projects, recent advances in genomic and proteomic technologies, and the availability of powerful bioinformatics tools have led to promising new avenues and approaches in the search for cancer biomarkers. This book provides a comprehensive overview of current methodologies and technologies. It discusses biomarker discovery as a whole, rather than focusing on one specific marker or cancer. With information on both existing and potential biomarkers, Cancer Biomarkers: Analytical Techniques for Discovery: * Provides insights into the current technological platforms for biomarker discovery, including mass spectrometry combined with multidimensional chromatography, DIGE, and various chip technologies * Includes a detailed discussion of protein networks and protein phosphorylation in cancer * Details the use of imaging mass spectrometry, laser capture microdissection, serial analysis of gene expression, enzyme-linked immunosorbent assays, protein microarrays, antibody-based microarrays, and bioinformatics * Covers the emerging role of surface-enhanced laser desorption ionization (SELDI) and various tagging and labeling strategies * Discusses related regulatory and ethical issues With a wealth of information that can be applied to a broad spectrum of biomarker research projects, this is a core reference for biomarker researchers, scientists working in proteomics and bioinformatics, pharmaceutical scientists, oncologists, biochemists, biologists, and chemists.

Author Biography

MAHMOUD H. HAMDAN, PhD, FInstP, is the head of the Mass Spectrometry and Separation Technologies Laboratory at GlaxoSmithKline in Verona, Italy. He is a coauthor of Proteomics Today: Protein Assessment and Biomarkers Using Mass Spectrometry, 2D Electrophoresis, and Microarray Technology, also from Wiley.

Table of Contents

Preface
Acknowledgments
Introduction
Overview
Introduction
Cancer Biomarkers
Phases of Biomarkers Development
New Approach to Biomarkers Discovery
New and Powerful Technologies
Promising Sources for Biomarkers
DNA Methylation
Mitochondrial DNA Mutations
Phosphatidylinositol-3 Kinases (PI3Ks)
Profi ling Tyrosine Phosphorylation
Proteins Expression
Initiatives Relevant to Biomarkers Discovery
Initiatives of the Human Proteome Organization (HUPO)
Data Mining in Cancer Research
Concluding Remarks
References
Proteomic Platforms for Biomarkers Discovery
Surface Enhanced Laser Desorption Ionization
Some Basic Considerations
Protein Capture Surfaces
Enrichment/prefractionation Prior to SELDI Analysis
Combinatorial Affi nity
Magnetic Beads
Stacked Sorbents
Organic Solvent Extraction
Bioinformatics in SELDI
Some Representative SELDI Applications
Addressing Reproducibility in SELDI Analysis
Limitations and Other Open Questions Regarding Current SELDI
Other Open Questions
Outlook
Two-dimensional Polyacrylamide Gel Electrophoresis
Sample Preparation
Reducing Sample Complexity
Various Nomenclatures In-gel Analysis
Multiple-gels Two-dimensional Analyses
Two-dimensional DIGE Analysis
Multiphoton Detection Imaging
Stable-isotope Labeling with Amino Acids in Cell Culture (SILAC)
Laser Capture Microdissection
MS Analysis of Gel-separated Proteins
Representative Applications of 2-DE for Biomarkers Discovery
Protein Microarrays
Analytical Protein Microarrays
Substrates and Protein Attachment Methods
Detection Strategies
Surface Plasmon Resonance (SPR)
Atomic Force Microscopy (AFM)
Enzyme-linked Immunosorbent Assay (ELISA)
Radio Isotope Labeling
Fluorescence Detection
Functional Protein Microarrays
Reverse-phase Protein Microarrays
Future Prospects
Multidimensional Liquid Chromatography Coupled to MS
Protein Labeling
Labeling a Specifi c Amino Acid
Stable Isotope Incorporation
Limitations of Labeling
Chromatographic Separation
Three Dimensional Separation
Two-dimensional Chromatography
Basic Considerations Regarding MudPIT
Mass Spectrometry and Data Analysis
Data Analysis and Interpretation
Application of Multidimensional Chromatography/MS
Outlook for Multidimensional LC/MS
Imaging Mass Spectrometry
Tissue Preparation and Matrix Application
MS Acquisition
Some Representative Applications of Imaging MS
Current Limitations and Potential Developments
References
Some Existing Cancer Biomarkers
Introduction
Historic Glimpse at PSA
Prostate-specifi c Antigen
PSA as a Screening Marker
Improving the Specifi city of PSA
Free/Complexed PSA
PSA Isoforms
Impact of Age, Race, and PSA Velocity
Looking for Other Solutions
Genetic Alterations
Phosphorylated Akt
Concluding Remarks
Existing Biomarkers for Ovarian Cancer
Table of Contents provided by Publisher. All Rights Reserved.

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