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Rivals Say the More the Merrier as CMDX Joins Signature, Baylor in Nascent CGH Dx Market

This month CombiMatrix Molecular Diagnostics became the latest player to enter the array comparative genomic hybridization-based constitutional genetic testing market.
The firm began offering its Constitutional Genetic Array Test, its first, through its CLIA-approved labs in Irvine, Calif. According to CMDX, the single assay can identify over 50 common genetic disorders. The array has been sold through Array Genomics in Europe since last spring (see BAN 4/25/2006).
By targeting the CGH-based genetic testing market, which specifically serves children and adults born with chromosomal abnormalities that lack positive diagnosis, CMDX will be competing in the same space as Signature Genomic Laboratories and Baylor College of Medicine.
Still, rivals this month welcomed CMDX’s entry as a sign that the CGH-based constitutional testing market is healthy and growing.
“I think the market’s big and there’s plenty of room for other players,” said Lisa Shafer, scientific director of Spokane, Wash.-based Signature Genomic Labs. Shaffer said that she had no hard numbers to support this estimate, but that the number of patients Signature works with has grown steadily since the service was launched in 2004.
Shaffer noted that “every year there’s approximately 120,000 children born with birth defects in this country. And almost all of them need a chromosomal analysis whether they get it or not. So that’s what we call the renewable market,” Shaffer told BioArray News this month.
“Then there’s the legacy market. Approximately 3 percent of the population has a form of mental retardation. So there’s this huge market out there where they would benefit from having an array CGH analysis,” Shaffer said.
However, rather than creating a new market, Shaffer said that companies like Signature and CMDX will transform the existing market for cytogenetic testing, which is currently served by fluorescence in situ hybridization and karyotyping.
“I would say that there are at least 200 cytolabs in the US and they are all pulling from the same market. So as we start eliminating karyotyping analysis there’s plenty of room for others to get into this market,” Shaffer said.
That’s an assessment shared by CombiMatrix CEO Amit Kumar. “The market is served primarily today through karyotyping and there are probably 300,000-400,000 kids diagnosed with developmental disorders out there,” he told BioArray News earlier this month.

“The current technology doesn’t catch all the disorders. About 70 percent of them are not diagnosed. Of the remaining 30 percent that are diagnosed, roughly half of them are misdiagnosed,” he said.

“We think our chip will migrate much of karyotyping and FISH testing over to CGH arrays. So the market for us is 50,000 to several hundred thousand assays,” he added.

Peter Papenhausen, national director of cytogenetics at Laboratory Corporation of America, offered that “most diagnostic cases in the literature are now including array data along with cytogenetic and clinical descriptions.”
According to Papenhausen, LabCorp “has been running aCGH for about a year with the resolution gradually increasing.”
Less FISH, More CGH?
From the perspective of CMDX and Signature, replacing older cytogenetic technologies, like FISH and karyotyping, is part of the narrative of the spread of array CGH-based testing. However, both firms agree that their technology doesn’t do everything.

“If you have a true balanced translocation you’re not going to see that on a microarray, so you have to use FISH or G-banding. It’s important to remember that nothing does everything.”

“Is this going to replace karyotyping and FISH? I believe it is. Microarrays are going to replace cytogenetics,” said Shaffer. “Now when I say array CGH is going to replace cytogenetics and FISH, it’s not 100 percent. But anything that results in a gain or loss of DNA should be detectable by array CGH,” she said.

Mansoor Mohammed, chief scientific officer at CMDX, said this month that CGH would more likely transform the way different technologies are used in cytogenetics, rather than replace any technology in particular.  “I do not believe that array CGH will replace traditional cytogenetics,” he told BioArray News, “but do I think it’s a transformative technology? Yes.”

Still, questions remain among cytogeneticists about what role array CGH will play in the future. According to Jannine Cody, a research assistant professor at the University of Texas’ Chromosome 18 Clinical Research Center, her colleagues in the cytogenetics community are moving towards array CGH, but the technology still has its limitations, especially when it comes to identifying balanced chromosomal translocations — when genetic material is evenly transferred between non-homologous chromosomes.

“With the arrays the resolution is wonderful. But it only tells you what is out of balance,” Cody told BioArray News. “If you have a true balanced translocation you’re not going to see that on a microarray, so you have to use FISH or G-banding. It’s important to remember that nothing does everything,” she added.

LabCorp’s Papenhausen said that the community in general has been moving towards array CGH and that his peers have “largely embraced the new technology.”

Still, he warned that array CGH “should not be viewed as a replacement technology, since both karyotyping and FISH have a place in clinical diagnostics.”

“Even in the area of developmental delay, best suited for these arrays, there are some limitations associated with mosaicism and balanced rearrangements,’ he told BioArray News in an e-mail. “Those limitations are easily outweighed by the broad-spectrum, high-resolution capabilities incumbent in arrays that are necessary for many diagnostic cases,” he added. So “a comprehensive analysis should include both chromosome analysis and CGH,” Papenhausen said.

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