Microarrays pp 189-211 | Cite as

Methods in High-Resolution, Array-Based Comparative Genomic Hybridization

  • Mark R. McCormick
  • Rebecca R. Selzer
  • Todd A. Richmond
Part of the Methods in Molecular Biology™ book series (MIMB, volume 381)


A method of high resolution, array-based comparative genomic hybridization is described for the mapping of copy-number changes associated with chromosomal amplifications, deletions, and translocations. The method involves the design of whole-genome or targeted, fine-tiling arrays for synthesis on a high-density digital microarray-synthesis platform. The arrays can span entire eukaryotic genomes or be targeted to specific chromosomal regions for high-resolution identification of copy-number changes and the corresponding breakpoint locations. The methods described include the bioinformatics required for array design, and the protocols for DNA fragmentation, dual-color labeling, microarray hybridization, and array scanning. The processes for data extraction, normalization, and segmentation analysis are also described.

Key Words

Amplification breakpoint cancer CGH, comparative genomic hybridization copy number deletion DNA microarray segmentation translocation 


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Copyright information

© Humana Press Inc., Totowa, NJ 2007

Authors and Affiliations

  • Mark R. McCormick
    • 1
  • Rebecca R. Selzer
    • 1
  • Todd A. Richmond
    • 1
  1. 1.NimbleGen Systems Inc.Madison

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