Chromosome Orientation Fluorescence In Situ Hybridization or Strand-Specific FISH

  • Susan M. BaileyEmail author
  • Eli S. Williams
  • Michael N. Cornforth
  • Edwin H. Goodwin
Part of the Methods in Molecular Biology book series (MIMB, volume 659)


Chromosome Orientation FISH (CO-FISH) is a technique that can be used to extend the information obtainable from standard FISH to include the relative orientation of two or more DNA sequences within a chromosome. CO-FISH can determine the absolute 5′-to-3′ direction of a DNA sequence relative to the short arm-to-long arm axis of the chromosome, and so was originally termed “COD-FISH” (Chromosome Orientation and Direction FISH). CO-FISH has been employed to detect chromosomal inversions associated with isochromosome formation, various pericentric inversions, and to confirm the origin of lateral asymmetry. More recent and sophisticated applications of CO-FISH include distinction between telomeres produced via leading- vs. lagging-strand DNA synthesis, identification of interstitial blocks of telomere sequence that result from inappropriate fusion to double-strand breaks (telomere-DSB fusion), discovery of elevated rates of mitotic recombination at chromosomal termini and sister chromatid exchange within telomeric DNA (T-SCE), establishing replication timing of mammalian telomeres throughout S-phase (ReD-FISH) and to identify chromosomes, in combination with spectral karyotyping (SKY-CO-FISH).

Key words



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Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Susan M. Bailey
    • 1
    Email author
  • Eli S. Williams
    • 2
  • Michael N. Cornforth
    • 3
  • Edwin H. Goodwin
    • 4
  1. 1.Department of Environmental & Radiological Health SciencesColorado State UniversityFort CollinsUSA
  2. 2.Drug Discovery ProgramH. Lee Moffitt Cancer Centre and Research InstituteTampaUSA
  3. 3.Department of Radiation OncologyUniversity of Texas Medical BranchGalvestonUSA
  4. 4.Kroma TiD Inc.Fort CollinsUSA

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