Microarray Analysis of the Physical Genome

About this book

In the early years of microarray technology, efforts were directed mainly at profiling expressed genes, while recently the microarray platform has been adapted into diverse applications directed toward the investigation of the physical genome. In Microarray Analysis of the Physical Genome: Methods and Protocols, experts in the field cover DNA microarray applications for the detection and characterization of genomic DNA-associated copy number alteration, loss of heterozygosity (LOH), cytosine methylation, protein binding sites, regulatory elements, and replication timing, with an emphasis on higher eukaryote (animal) and cancer genomes. Written in the highly successful Methods in Molecular Biology™ series format, chapters include a brief introduction to their respective subjects, lists of the necessary materials and reagents, step-by-step protocols, and time-saving notes on troubleshooting and avoiding known pitfalls.

Authoritative and easy-to-use, Microarray Analysis of the Physical Genome: Methods and Protocols is of great value to the molecular biologist or computational biologist interested in understanding the principles of these analyses or in planning future experiments using microarrays to characterize the physical genome.

Written for: Molecular biologists and computational biologists

Keywords:

• Cancer genomes
• Cytosine methylation
• Heterozygosity (LOH)
• Higher eukaryote genomes
• Protein binding sites
• Replication timing

Table of contents

Chapter 1. Introduction
Jonathan R. Pollack

Chapter 2. Comparative Genomic Hybridization on BAC Arrays
Bradley P. Coe, William W. Lockwood, Raj Chari, and Wan L. Lam

Chapter 3. Comparative Genomic Hybridization on Spotted Oligonucleotide Microarrays
Young H. Kim and Jonathan R. Pollack

Chapter 4. Comparative Genomic Hybridization by Representational Oligonucleotide Microarray Analysis
Robert Lucito, and James Byrnes

Chapter 5. Application of Oligonucleotides Arrays for Coincident Comparative Genomic Hybridization, Ploidy Status and Loss of Heterozygosity Studies in Human Cancers
John K. Cowell, and Ken C. Lo

Chapter 6. Molecular Inversion Probe Assay for Allelic Quantitation
Katrina Welch, and Hanlee Ji

Chapter 7. A Whole Genome Amplification Protocol for a Wide Variety of DNAs, Including those from Formalin-Fixed and Paraffin-Embedded Tissue
Pamela L. Paris

Chapter 8. Algorithms for Calling Gains and Losses in Array CGH Data
Pei Wang

Chapter 9. Methylation Analysis by Microarray
Daniel E. Deatherage, Dustin Potter, Pearlly S. Yan, Tim H.-M. Huang, and Shili Lin

Chapter 10. Methylation Analysis by DNA Immunoprecipitation (MeDIP)
Emily A. Vucic, Ian M. Wilson, Jennifer M. Campbell, and Wan L. Lam

Chapter 11. Combining Chromatin Immunoprecipitation and Oligonucleotide Tiling Arrays (ChIP-Chip) for Functional Genomic Studies
Jérôme Eeckhoute, Mathieu Lupien, and Myles Brown

Chapter 12. ChIP-Chip: Algorithms for Calling Binding Sites
Clifford A. Meyer and X. Shirley Liu

Chapter 13. Mapping Regulatory Elements by DNaseI Hypersensitivity Chip (DNase-Chip)
Yoichiro Shibata, and Gregory E. Crawford

Chapter 14. Microarray Analysis of DNA Replication Timing
Neerja Karnani, Christopher M. Taylor, and Anindya Dutta

Chapter 15. Integration of Diverse Microarray Data Types
Keyan Salari and Jonathan R. Pollack