DNA Microaray Technology and Data Analysis in Cancer Research

by Li, Shaoguang

• ISBN13: 9789812790453
• ISBN10: 9812790454
• Edition: 1st
• Format: Hardcover
• Copyright: 2009-03-01
• Publisher: World Scientific Pub Co Inc

Summary

DNA microarray technology has become a useful technique in gene expression analysis for the development of new diagnostic tools and for the identification of disease genes and therapeutic targets for human cancers. Appropriate control for DNA microarray experiment and reliable analysis of the array data are key to performing the assay and utilizing the data correctly. The most difficult challenge has been the lack of a powerful method to analyze the data for all genes (more than 30,000 genes) simultaneously and to use the microarray data in a decision-making process. In this book, the authors describe DNA microarray technology and data analysis by pointing out current advantages and disadvantages of the technique and available analytical methods. Crucially, new ideas and analytical methods based on the authors' own experience in DNA microarray study and analysis are introduced. It is believed that this new way of interpreting and analyzing microarray data will bring us closer to success in decision-making using the information obtained through the DNA microarray technology.

Table of Contents

Preface	p. v
Introduction of Authors	p. vii
DNA Microarray Technology	p. 1
Experimental Procedure	p. 2
Experimental Design	p. 4
Quality Control	p. 6
Interpretation of DNA Microarray Data	p. 8
Advantages and Disadvantages	p. 8
Applications of DNA Microarray Technology in Cancer Research	p. 11
Solid Tumors	p. 11
Blood Cancers	p. 12
Our DNA Microarray Study Using Mouse Model of BCR-ABL-Induced Leukemia	p. 13
Leukemia mouse model study	p. 15
Cell line study	p. 19
Current Analytical Methods of DNA Microarray Data	p. 21
Experimental Design	p. 21
Method	p. 21
Robust multi-chip averaging (RMA)	p. 21
iterPLIER	p. 22
Quality Control Diagnostics	p. 25
Saturation	p. 25
Transformed intensities across arrays	p. 28
Normalized intensities across arrays	p. 29
Scatterplot of normalized intensities	p. 30
Average MA plot of normalized intensities	p. 31
Statistical Analysis	p. 32
Analysis of variance (ANOVA) model	p. 32
Contrasts	p. 33
Coefficient of Variation Analysis	p. 36
A Novel Method for DNA Microarray Data Analysis: SDL Global Optimization Method	p. 37
Research Subjects	p. 38
Experimental Design	p. 39
Rationale	p. 39
Fold Change Analysis	p. 40
More Information on SDL Global Optimization	p. 51
Genetic algorithms (GAs)	p. 53
SDL global optimization algorithms	p. 54
Applications of the SDL Global Optimization Method in DNA Microarray Data Analysis	p. 55
Leukemia Cell Line Study	p. 55
Introduction	p. 55
Datasets	p. 55
Analysis strategies	p. 55
Discussion and conclusion	p. 62
Analyses of Publicly Available Human Microarray Data	p. 63
Introduction	p. 63
Datasets	p. 70
Overall Methodology	p. 71
Orthogonal arrays (OAs) and sampling procedure	p. 71
Objective function	p. 74
Search space reduction for global search	p. 76
Mathematical form of SDL optimization	p. 80
Multi-subset class predictor	p. 82
Validation (predicting through a voting mechanism)	p. 83
Experimental Results	p. 83
Discussion	p. 90
Conclusion	p. 99
General Discussion and Future Directions	p. 101
References	p. 105
Index	p. 117
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