Microarray analysis of the physical genome : methods and protocols / edited by Jonathan R. Pollack. — Dordrecht ; London : Humana Press, c2009. – (58.17/M592/v.556)

Contents

    Contents
    
    Preface
    Contributors
    1 Introduction
    2 Comparative Genomic Hybridization on BAC Arrays
    3 Comparative Genomic Hybridization on Spotted Oligonucleotide Microarrays
    4 Comparative Genomic Hybridization by Representational Oligonucleotide Microarray Analysis 33
    5 Application of Oligonucleotides Arrays for Coincident Comparative Genomic Hybridization， Ploidy Status and Loss of Heterozygosity Studies in Human Cancers 47
    6 Molecular Inversion Probe Assay for Allelic Quantitation 67
    7 A Whole-Genome Amplification Protocol for a Wide Variety of DNAs， Including Those from Formalin-Fixed and Paraffin-Embedded Tissue 89
    8 Algorithms for Calling Gains and Losses in Array CGH Data 99
    9 Methylation Analysis by Microarray 117
    10 Methylation Analysis by DNA Immunoprecipitation (MeDIP) 141
    11 Combining Chromatin Immunoprecipitation and Oligonucleotide Tiling Arrays (ChIP-Chip) for Functional Genomic Studies
    12 ChIP-Chip: Algorithms for Calling Binding Sites
    13 Mapping Regulatory Elements by DNaseI Hypersensitivity Chip (DNase-Chip) 177
    14 Microarray Analysis of DNA Replication Timing 191
    15 Integration of Diverse Microarray Data Types
    Index