University of Colorado Cancer Center Cytogenetics Core

FISH

Aneusomies for EGFR (red) and centromere 7 (green) sequences detected in formalin-fixed, paraffin embedded lung cancer tissue sections

The UCCC Cytogenetics Core Laboratory provides classic and molecular cytogenetics services, including fluorescence in situ hybridization (FISH). We have experience with commercially available and researcher-provided probes, such as:

• chromosome enumeration probes
• painting probes
• translocation probes
• single copy or locus-specific probes
• nick-translated DNA fragments

We also provide consulting services and training for non-assisted lab use.

Our Services

Single and dual color fluorescence in situ hybridization (FISH) assays

• Differentiation of mammalian chromosomes or DNA sequences translocated to rodent chromosomes and monitoring established cell lines using human genomic or Cot-1 DNA probes.
• Identification of specific aneuploidies in metaphase spreads and interphase nuclei, in  preparations from diffuse or solid tissues using satellite and locus-specific DNA probes.
• Identification of particular human chromosomes or chromosome fragments in complex rearrangements and/or marker chromosomes using whole chromosome-specific painting probes (WCP) or a region-specific probe (Partial Chromosome Probes). WCPs are used also for identification of human chromosomes in hybrid cells.
• DNA clone mapping (phage, cosmid, P1, PAC, BAC, and YAC) on metaphase chromosomes of human, rat, mouse and hamster cells.
• Investigation of genomic deletion, duplication or amplification in metaphase and in interphase nuclei in fresh or preserved biological preparations using DNA clones.
• Detection of chromosome translocations in metaphase or interphase cells using probes encompassing or closely associated with the breakpoints.

Multicolor-FISH assay

• Simultaneous hybridization of several probes to extended chromatin to determine the orientation and overlap of the tested sequences.
• Analysis of multiple probes in a given cell for more accurate definition of its genomic status. 
  

  Spectral Karyotyping

  Spectral karyotype of a cell representative of the small cell lung carcinoma cell line UMC19.

Comparative Genomic Hybridization (CGH) assay

• Analysis of DNA sequence copy numbers of cultured or uncultured human, mouse and rat specimens.
• Multicolor Karyotyping using spectral karyotyping in human, mouse and rat specimens (SKY) and multiplex-FISH (M-FISH) in human specimens.

Unbanded chromosome analysis

• Breakage evaluation.
• Cell proliferation index (mitotic index).
• Ploidy evaluation

Giemsa-trypsin (GTG) banded chromosome analysis

• Karyotype characterization of human, mouse, rat, and hamster specimens or cell lines in metaphase or prometaphase cells.
• Determination of cell line homogeneity and evolution using metaphase analysis.
• Identification of parental species in hybrid cell lines.

Additional procedures

Tissue culture

Initiation, maintenance, harvest, and freezing of cell cultures for cytogenetic purposes.

Establishment of immortal cell lines from lymphocytes

DNA labeling by nick-translation for FISH assays

Lab staff performs nick translation labeling. DNA fragments may be genomic DNA, cDNA or vector DNA. Due to sensitivity limitations of our current instrumentation, we need unique sequence probes larger than 2.5 kb for mapping studies. If the probe is known to be amplified, we can use probes >1.0 kb.

How to Use This Core Lab

Testing and instrumentation are available by appointment only. Turnaround time is highly dependent on the specimen or project. Please contact Dr. Varella-Garcia to schedule your project and discuss turnaround times.