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Chromatin Protocols pp 67–94Cite as

Analysis of Genomic Aberrations Using Comparative Genomic Hybridization of Metaphase Chromosomes

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1288))

Abstract

Comparative genomic hybridization (CGH) allows the global screening of copy number aberrations within a sample. Specifically, large (>20 mb) deletions and amplifications are detected, based on utilization of test and reference (karyotypically normal) DNA. These samples are whole-genome amplified by DOP-PCR and then differentially labeled with fluorophores via nick translation. Test and reference samples are competitively hybridized to normal metaphase chromosomes. The relative amount of each DNA that binds to a chromosomal locus is indicative of the abundance of that DNA. Thus, if a chromosomal region is amplified, the test DNA will out-compete the reference DNA for binding and fluorescence will indicate amplification. Conversely, if a region is deleted, more reference DNA will bind and fluorescence will indicate a deletion. The following chapter outlines the protocols used for CGH analysis of metaphase chromosomes. These protocols include metaphase chromosome slide preparation, DNA extraction (from blood, cell lines, and microdissected formalin-fixed paraffin-embedded tissue), DOP-PCR, nick translation, in situ hybridization, and fluorescence microscopy and image analysis.

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Author information

Authors and Affiliations

  1. Texas Biomedical Research Institute, 7620 N. W. Loop 410 (at Military Drive), 760549, San Antonio, TX, 78245-0549, USA

    Melanie A. Carless Ph.D.

Authors
  1. Melanie A. Carless Ph.D.
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Correspondence to Melanie A. Carless Ph.D. .

Editor information

Editors and Affiliations

  1. H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA

    Srikumar P. Chellappan

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Carless, M.A. (2015). Analysis of Genomic Aberrations Using Comparative Genomic Hybridization of Metaphase Chromosomes. In: Chellappan, S. (eds) Chromatin Protocols. Methods in Molecular Biology, vol 1288. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2474-5_6

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  • DOI: https://doi.org/10.1007/978-1-4939-2474-5_6

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-2473-8

  • Online ISBN: 978-1-4939-2474-5

  • eBook Packages: Springer Protocols

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