Comparative Molecular Cytogenetics Core Facility

Chromosome Fluorescence in Situ Hybridization (FISH)

The FISH technique uses fluorescently labeled probes to target specific genes or a particular chromosomal region in order to detect abnormalities that cannot be identified by conventional banding methods. Some advantages of FISH include detection of microdeletions, chromosomal rearrangements, aneuploidy, and the ability to analyze non-dividing cells. Recently, it has been widely used to validate micro-array data by confirming amplification/gain or deletion/loss of chromosomal regions of interest. The drawback of FISH analysis is that it requires knowledge of the loci involved in an aberration.

The basic steps of FISH involve creating and labeling the probe, preparing slides with the desired target sample, hybridizing the probe to the sample, and visualizing the signal using a fluorescent microscope. FISH can be performed on cell nuclei or metaphase preparations that have been properly fixed and applied to slides, or on paraffin-embedded tissues.

Investigator responsibilities:

1. Provide fixed, tissue section slides (formalin fixation for at least 24 hours and no longer than 48 hours is critical for tissue sections).
2. Provide actively growing cells.

Testing Options
Identifies chromosomal aberrations
Translocations (balanced)	Yes
Translocations (unbalanced)	Yes
Copy number changes	Yes
Additions (>10MB)	Yes
Deletions (>10MB)	Yes
Deletions of specific genes/loci	Yes
Inversions	Yes
Insertions	Yes
Identifies presence of markers	Yes
Distinguishes between double minutes and homogeneously staining regions	Yes
Identifies chromosomal origins	Yes
Identifies specific p/q arms/bands	Yes
Requires specifically labeled probes	Yes
More than two probes at one time	Sometimes
Requires viable material	Sometimes
Requires metaphase spreads	Yes
Applicable to interphase nuclei	Yes
Applicable to DNA extracted from paraffin embedded tissue	Yes
Affected by normal tissue contamination	Yes
Identifies tumor heterogeneity	Yes
Applicable for studies in other species	Yes

Sample Requirements:

• Peripheral blood: 5-10 mls in Heparin container
• Culture: Culture must be actively growing with media supplied. A T-75 flask is preferred. Tissue culture flask must not be vented. This prevents spillage and contamination during transit. Do not fill beyond recommendation of flask i.e. (to the absolute top of flask or tube).
• Interphase FISH: Offered only for non-dividing samples.

Please inquire if your sample varies from the listed recommendations. Please inquire for likely turnaround time.