Over the past year, the cytogenetics testing market has become increasingly attractive to array vendors large and small.

In March 2008, Affymetrix debuted its Cytogenetics Solution, which paired its 1.8-million-marker SNP 6.0 Array and internally developed software with the cytogeneticist in mind (see BAN 3/25/2008).

Last November, Illumina followed suit, launching its Infinium High-Density HumanCytoSNP-12 DNA Analysis BeadChip and accompanying KaryoStudio software package (see BAN 11/18/2008).

Also recently, Oxford Gene Technology and BlueGnome have released new arrays for cytogenetic use, while companies that offer array-based cytogenetic testing, like Signature Genomic Laboratories, have announced plans to expand their product lines.

During Illumina's annual Analyst Day meeting, which was webcast on Nov. 6, CEO Jay Flatley estimated the cyto testing market at about $2 billion, and Illumina expects it to double by 2012.

While the bulk of cytogenetics testing still employs fluorescent in situ hybridization and molecular karyotyping, Flatley estimated that array-based cytogenetic tests make up $200 million of the overall cyto-testing market and are growing 20 percent per year (see BAN 11/18/2008).

According to users familiar with the technology, including the heads of several cytogenetics labs, they generally welcome the breadth of available platforms. However, some say that when it comes to the new cytogenetic arrays, there is room for improvement.

Columbia University

For example, Brynn Levy, director of the Clinical Cytogenetics Laboratory at Columbia University in New York, said he is using Affymetrix SNP genotyping arrays for both research and clinical purposes.

"In terms of research, we use it to look for new regions of gain and loss that could potentially uncover oncogenes or tumor-suppression genes or other genes that are playing a role in the initiation and progression of the cancer we are investigating," Levy told BioArray News last week.

Levy said he is also using the arrays to help detect gains and losses in very limited specimens, like single cells. "We are looking at single cells that can be taken from circulation during pregnancy as a means to develop a non-invasive, prenatal diagnostic test, and also for pre-implantation testing," he said.

Clinically, Levy's lab uses Affy's Cytogenetic Solution as a "reflex" to G-banding, a widely used, genome-wide technique used in cytogenetics to produce a visible karyotype by staining condensed chromosomes. If a karyotype for a patient exhibiting characteristics potentially caused by a chromosomal abnormality comes back normal, Levy's lab will then perform a genome-wide analysis to search for smaller chromosomal gains and losses in the patient's genome.