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9780387399775

Microarray Technology and Cancer Gene Profiling

by
  • ISBN13:

    9780387399775

  • ISBN10:

    0387399771

  • Edition: 1st
  • Format: Hardcover
  • Copyright: 2006-12-30
  • Publisher: Landes Bioscience
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Summary

Cancer is a heterogeneous disease in most respects, including its cellularity, different genetic alterations and diverse clinical behaviors. Traditional molecular analyses are reductionist, assessing only one or a few genes at a time, thus working with a biologic model too specific and limited to confront a process whose clinical outcome is likely to be governed by the combined influence of many genes. The potential of functional genomics is enormous, because for each experiment, thousands of relevant observations can be made simultaneously. Accordingly, DNA array, as other high throughput technologies, might catalyze and ultimately accelerate the development of knowledge in tumor cell biology. Although in its infancy, the implementation of DNA array technology in cancer research has already provided investigators with novel data and intriguing new hypotheses on the molecular cascade leading to cancerogenesis, tumor aggressiveness and sensitivity to antineoplastic agents. Given the revolutionary implications that the use of this technology might have in the clinical management of cancer patients, principles of DNA array-based tumor gene profiling need to be clearly understood for the data to be correctly interpreted and appreciated. In the present book, written by leading experts in each field, the technical features characterizing this powerful laboratory tool are discussed, and the applications so far described in the field of oncology are reviewed.

Table of Contents

Microarray Technology
Manufacturing of Microarraysp. 1
Abstractp. 1
Introductionp. 1
Nomenclaturep. 1
The DNA Microarray Libraryp. 2
Robotic Printersp. 3
Printing Pinsp. 5
Microarray Slide Substratesp. 8
Personnelp. 10
Conclusionsp. 10
Technological Platforms for Microarray Gene Expression Profilingp. 12
Abstractp. 12
Principles of Gene Microarray Technologyp. 12
Target Preparation and Hybridizationp. 14
Image Acquisition and Quantificationp. 16
Principles of Gene Microarray Data Analysisp. 19
Abstractp. 19
Introductionp. 19
Study Design and Data Analysisp. 20
Data Collection and Normalizationp. 23
Comparing Expression Datap. 24
Gaining Weights...and Feeling Good About It!p. 31
Abstractp. 31
A Light Introductionp. 31
P-Value Weightingp. 32
Within-Spot Pixel Variance Weightingp. 35
A Weighty Discussionp. 37
Complementary Techniques: RNA Amplification for Gene Profiling Analysisp. 39
Abstractp. 39
Introductionp. 39
Source Material Collection and RNA Isolationp. 40
Single-Strand cDNA Synthesisp. 41
Double-Stranded cDNA (ds-cDNA) Synthesisp. 41
RNA Amplificationp. 42
Target Labeling for cDNA Microarray Using Amplified RNAp. 45
RNA Amplification Protocolp. 46
Complementary Techniques: Laser Capture Microdissection-Increasing Specificity of Gene Expression Profiling of Cancer Specimensp. 54
Abstractp. 54
Microdissection Technologies: The Past and the Presentp. 54
Why Microdissection?p. 59
Slide Preparation for Microdissectionp. 62
In Our Laboratoryp. 63
Conclusionsp. 64
Complementary Techniques: Validation of Gene Expression Data by Quantitative Real Time PCRp. 66
Abstractp. 66
PCR-Based Analysis of Gene Quantitationp. 66
Principlesp. 67
Main Issuesp. 68
Messenger RNA Cell Sourcep. 71
Applications in the Oncology Field
Microarrays for Cancer Diagnosis and Classificationp. 74
Abstractp. 74
Introductionp. 74
Revealing Expression Profiles for Cancer Diagnosis and Classificationp. 75
Using Expression Profiles in the Clinicp. 79
Perspectivep. 83
Gene Profiling for the Prediction of Tumor Response to Treatment: The Case of Immunotherapyp. 86
Experimental Models, Human Polymorphisms and Cancer Heterogeneityp. 86
Gene Profiling and T-Cell Phenotypesp. 87
Interactions between Tumor Cells and TA-Specific T-Cellsp. 88
The Tumor Microenvironmentp. 89
Influence of Genetic Background and Cancer Heterogeneity on Immune Responsivenessp. 89
Gene Profiling of Anticancer Immune Responsesp. 90
Conclusionsp. 92
Identification of Molecular Determinants of Tumor Sensitivity and Resistance to Anticancer Drugsp. 95
Abstractp. 95
Introductionp. 95
Correlation of Gene Expression Data from DNA Arrays with Response to Anticancer Agentsp. 97
Conclusionsp. 102
SNP and Mutation Analysisp. 105
Abstractp. 105
Introductionp. 105
Enzymatic Approachp. 106
Polymerase Chain Reaction (PCR)p. 106
Microarray Approachesp. 107
Invader Assayp. 108
Mass Spectrometryp. 110
Sequencingp. 111
Summaryp. 115
Cancer Development and Progressionp. 117
Abstractp. 117
Cancer Developmentp. 117
Science/Technologyp. 120
Complementary Approachp. 123
In Vitro/Preclinical Research Using Microarrayp. 125
Clinical Studiesp. 127
Gene Expression Profiling in Malignant Lymphomasp. 134
Abstractp. 134
Introductionp. 134
Gene Expression Profilingp. 135
Gene Expression Analysisp. 135
The Applications of Gene Expression Profiling to Leukemia and Lymphomap. 136
Tumor Immunologyp. 147
Abstractp. 147
Tumor Immunology and the Post-Genomic Erap. 147
Tumor Immune Escapep. 148
New Targets for Tumor Immunotherapyp. 149
Dendritic Cell Biologyp. 150
T Cell Biologyp. 150
Tumor Microenvironmentp. 151
Concluding Remarksp. 154
Indexp. 157
Table of Contents provided by Ingram. All Rights Reserved.

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