Molecular cytogenetic technologies have become vitally important in the analysis of chromosomes for both diagnostics and research applications. Technologies such as fluorescent in situ hybridization (FISH) and microarrays are replacing traditional karyotyping.

FISH uses fluorescent probes that bind to the complementary DNA sequence on a chromosome. The samples are typically placed on a glass slide, and a pathologist uses a fluorescent microscope or digital imager to see where the probes imbed on the chromosome in order to detect malignancies, such as cancer or genetic disorders.

The overall market for FISH is predominantly a consumables business. However, advances in digital imaging and software have advanced the instrument technology and lead to greater acceptance. Aperio, which was acquired by Leica Biosystems in 2012, offers the ScanScope FL, which provides whole-slide images for samples stained with multiple fluorochromes. The system is targeted at multiplex applications and features advanced illumination, autoexposure and autofocus capabilities, which eliminate the need for trial-and-error image capture and minimize the occurrence of photobleaching.

Although FISH is the standard technique for molecular cytogenetic applications, it is a low resolution technique that is highly dependent on a pathologist’s experience. As a result, microarray technology is becoming the preferred technique in many pathology labs. Array-based comparative genome hybridization (aCGH) essentially performs thousands of FISH experiments in a single assay. ACGH measures copy number variations (CNV), providing high resolution information about deletions or duplications of a large DNA segment in comparison to a normal genome. Leading aCGH vendors include Affymetrix and Agilent Technologies.

Affymetrix offers the CytoScan HD Cytogenetics solution, a high density microarray solution that runs on the FDA-cleared and CE-IVD registered GeneChip Scanner 3000Dx v2. High density aCGH arrays provide larger genomic coverage and content, eliminating the need for further analysis or the possibility of missing the detection of significant aberrations.

Agilent offers the SurePrint CGH microarrays and SureScan Dx microarray scanner, which is CE marked for IVD use in Europe. BlueGnome, which Illumina acquired in 2012 (see IBO 9/30/12), specializes in cytogenetics and offers the CytoChip microarrays and ClearScan microarray scanner.

The market for molecular cytogenetics is one of the fastest growing segments of the tissue diagnostics market. Probes, kits and other consumables represent the lion’s share of the market. Annual sales of instruments, such as FISH digital imaging and microarray scanners, is estimated to be about $25 million.

Molecular Cytogenetics at a Glance:

Leading Suppliers

• Leica Biosystems

• Agilent Technologies

• Affymetrix

Largest Markets

• Hospitals/Clinical

• Reference Labs

• Academia/Government

Instrument Cost

• $100,000–$300,000