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University of Colorado Cancer Center

University of Colorado Cancer Center, A National Cancer Institute-designated Comprehensive Cancer Center


1. Cell Culture and Harvesting - Culture of mammalian cells, harvest and fixation of samples for further evaluation by FISH or karyotyping.
2. Tailored Slide Making – Dropping of fixed cell pellets onto slides for evaluation by metaphase and interphase FISH or G banding and spectral karyotyping.

3. Ploidy Evaluation – Counting of chromosomes in metaphase spreads of any species.
4. Classical Karyotyping – G-banded staining, analysis, interpretation and reporting of simple and complex karyotypes in human and rodent metaphase cells.

    Figure 2. Normal mouse G-banding karyotype       Figure 3. Abnormal G-banded human karyotype

5. SKY Multicolor Karyotyping – Assay, analysis, interpretation and reporting of Spectral Karyotyping (SKY) technology for simple and complex karyotypes of human and mouse specimens.

             Figure 4. HiSKY spectral (left), Classified (center), and Inverted-DAPI (right) images. 

6. FISH probe preparation for enumeration and rearrangements – Development and analytical validation of DNA FISH probes for human and mouse species, including probe design, DNA cloning, DNA labeling in multiple formats, characterization of variability of the patterns in normal and abnormal specimens, definition of scoring systems, identification of optimal cut-offs for specimen classification, and determination of accuracy and reproducibility.

7. DNA Amplification –Whole genome amplification of specific DNA sequences from human and mouse specimens.

8. DNA Labeling and preparation of probe panels – Sizing of DNA fragments and direct incorporation of fluorochromes by nick translation for laboratory-developed reagents and combination of laboratory-developed and commercial reagents in multiple formats, such as 2 targets/2 colors, 3 targets/3 colors, 4-targets/4-colors, 6-targets/2-colors.
              Figure 5 – 4-color ALK/ROS1 break-apart probe set in lung tumor with AK rearrangement. 

9. Preparation of external controls for FISH assays using commercially available and laboratory-developed probes. Identification of specimens positive and negative for the specific characteristics tested and construction of preps with the adequate formats for external controls.

10. FISH in FFPE tissue sections and cell suspensions - Performance of FISH assays in a variety of biological specimens including Carnoy’s fixed cell suspensions, FFPE of tissue sections, cell blocks from cytology and aspirate specimens and arrayed tissue cores (TMAs). 

     Figure 6 (above) – 2 color ALK break-apart probe set in lung cancer with normal ALK gene.     

     Figure 7 (above) - 2 color FGFR1/CEP 8 enumeration probe set in breast cancer with FGFR1 gene 

11. Design and performance of experiments for small to large research projects – Investigation of genomic anomalies such as gene fusions, gene amplifications and homozygous or hemizygous genomic losses in cohorts of tumors of pre-malignant specimens.

12. Preparation of Figures - Acquisition of high resolution microscope images and preparation of high-quality figures illustrating representative results.

13. Archival of experimental records and microscope images – Secure and HIPAA complient storage of electronic data including microscope field images for an extended period of time (7 years or more upon specific request).

14. Consulting – Provide assistance in identifying best technical approach to resolve specific scientific questions. Provide high-quality scientific and technical guidance for experimental design, interpretation of lab-generated or literature data, comparison of results, and troubleshooting of assays. Provide assistance for methodological aspects in grant writing and manuscripts preparation. Provide high quality figures and tables for oral presentations or written documents.

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