The Importance of Cytogenomics in the Diagnostic Pathway

Changes in chromosomes number or structure helps us to diagnose disease states, such as cancer and congenital disorders. Cytogenomics explores 2 aspects of human DNA to guide a diagnostic process: chromosome evaluation and molecular testing, such as Fluorescence In-Situ hybridization (FISH). Chromosomes are a “macro” look at the 23 paired compliments of human DNA.

Chromosome analysis

Cytogenomic analysis can be ordered from a variety of cell sources, including peripheral blood lymphocytes, bone marrow, ascites, skin, and solid tumors. Each of these specimen types are grown, or cultured, in different ways in the Cytogenomics laboratory to obtain metaphase spreads for chromosome analysis and/or FISH. Cultured cells are processed and “fixed” with a 1:1 methanol:acetic acid solution, then dropped onto glass slides under consistent humidity to allow the chromosomes to spread for visualization. The glass slides with the chromosome spreads are then colored with a contrasting stain and visualized under a light microscope. Some solid tumors are not cultured and are embedded in a wax paraffin block. Those blocks are then cut into thin sections and placed on a positively charged glass slide and used specifically for FISH assays. Chromosome analysis is performed by a highly trained technologist and assisted with a digital imaging system using highly intuitive chromosomal software. Utilization of digital solutions increase efficiencies and can be easily integrated with high speed slide scanning systems and automated analysis software platforms to speed the time to result to treating clinicians.

FISH analysis

Fluorescence In-Situ Hybridization, or  FISH, assays can be done on several types of specimens, cultured chromosomes slides, as described above, or Formalin Fixed Paraffin Embedded Tissue (FFPET). Chromosome  FISH is performed on cells captured in metaphase or interphase cycles of division. Metaphase cells will have dividing chromosomes on which we can visualize fluorescent probes. Interphase  FISH will not offer mitotic cells, but probes can still be visualized for diagnostic analysis. FISH is analyzed on a florescent microscope with a digital imaging system, like chromosomes.

FFPET FISH is more complex in preparation and in analysis. Some solid tumors are not cultured and are embedded in a wax paraffin block. Those blocks are then cut into thin sections and placed on a positively charged glass slide and used specifically for FISH assays. FFPET slides must be deparaffinized, pretreated, denatured, and hybridized for FISH probes to be applied and analyzed. This historically has been a time-consuming, highly manual process with great variation in techniques and results. Automation has had a great impact on this area of FISH diagnostics, offering both fully-automated and semi-automated paraffin FISH processing. These automated solutions have greatly improved quality and efficiencies of performing FFPET  FISH assays by decreasing the variability of temperatures, timing of solution changes, and manual handling.

Cytogenomic diagnostics- why is it important?

Chromosomes and  FISH results work together to inform the clinical team that the team makes complex diagnostic treatment determinations. The insight Cytogenomic analysis yields powerful and clinically significant documentation of chromosomal states that could indicate disease and clarify management pathways. Cytogenomics has the duty to skillfully examine, analyze, and summarize data to expedite the diagnostic pathway.