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Ambry Genetics Uses Baylor-Designed Chip to Enter Array-Based Cyto-Testing Market

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Ambry Genetics, a clinical-service lab based in Aliso Viejo, Calif., last week debuted its chromosomal microarray analysis service, thereby entering a growing market dominated by Baylor College of Medicine, Signature Genomic Laboratories, and CombiMatrix Molecular Diagnostics.

The market has also sparked interest from array vendors like Agilent Technologies, Affymetrix, and Illumina, which seek to play in it as platform providers.

The centerpiece of Ambry's service is the Ambry CMA 105K Oligo Array, which has been designed to identify chromosomal abnormalities associated with more than 270 genetic disorders. According to Ambry, the array uses 105,000 probes to cover 270 disease loci, with probes at an average resolution of 30 kilobases along the human genome to detect copy number variations.

Ambry licensed its chip from Baylor — a competitor in the market — and the firm is counting on the school's expertise, support, and reference archive of 20,000 patient samples to help it establish itself in the space.

According to Steven Keiles, director of genetic services at Ambry, the firm chose to license Baylor's design instead of licensing from a different source or designing its own because Baylor "is experienced and can support the platform." Additionally, the array is manufactured by Agilent Technologies, whose instrumentation is open and can be used with other array platforms without need for modification, Keiles said.

"Now we are coming into the game with database of more than 20,000 patient samples that will give us the experience that very few people can rival," Keiles told BioArray News last week. "Also, the Agilent scanner can run multiple platforms, so we could bring in different arrays for other applications, as different arrays can be run at that scanner," he said. "We are not limited to just Agilent chips."

Array-based cytogenetic testing is a departure for Ambry. The firm, founded in 2000, runs a Clinical Laboratory Improvement Acts-compliant lab that specializes in sequencing-based testing methods for conditions such as pulmonary disease, pancreatitis, and diabetes.

In April, Ambry was certified by Illumina to offer its Genome Analyzer second-generation sequencer as part of its pharmacogenomic services. Ambry has also adopted Roche NimbleGen sequence-capture arrays as part of that service (see BAN 3/24/2009). Keiles said the introduction of a CMA service was partially due to familiarity with microarray technology.

"We have been a CLIA lab for almost 10 years offering sequencing-based testing as well as some SNP panels but, as we have expanded, we have expanded our research activities and brought in alternative platforms," Keiles said. "Microarray seemed like one of the obvious technologies that would accompany our sequencing tests so we could offer more of a full service to our customers. This technology is getting more popular and we think it has tremendous potential to help our clients."

To become a "full genomic services company," some of Ambry's research staff members have focused on array-related projects, and the firm has hired more personnel to process samples for the service. Still, Ambry decided to offer a CMA service last year and began surveying possible platforms in the fall.

"We basically looked at all the different platforms, decided on the platform, brought the platform in house, and set it up," said Keiles. "We looked for partners, went into a validation phase, completed it, and now we are launching," he said. "It took us about six months from when the equipment was delivered to when we launched the test."

'Business to Go Around'

That speedy adoption time is partially due to choosing Baylor's chip. But even though Baylor also runs a CMA service, Keiles dismissed the idea that Ambry and Baylor would soon be at war for market share. "Baylor is also offering a service like us, but there is more than enough business to go around for multiple labs," Keiles said. "There is little overlap in our client base, so we won't be in direct competition with Baylor."

Art Beaudet, chair of molecular and human genetics at Baylor, similarly does not see such licensing deals as a threat to the school's business. "Many labs are committed to setting up testing in their own shop, some academic and some commercial, but if they are going to set up themselves, we are not going to receive samples from them or their users," Beaudet told BioArray News in an e-mail this week.

Beaudet said that Baylor has invested "years of effort" in designing its arrays and can offer prospective licensees its internally developed software and access to data on 20,000 cases that is "valuable for interpretation." In return for licensing its technology, Baylor receives a "modest fee and they can provide a higher quality service," Beaudet said. Baylor also offers training and back-up services.

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Lisa Shaffer, CEO of Spokane, Wash.-based Signature Genomic Labs, said that the Ambry-Baylor deal is part of a larger trend across the industry of licensing out chip designs. "Allowing other labs to use an array design is becoming more common," she told BioArray News this week, noting that Signature "has more than 40 laboratories" that use its design. Shaffer declined to name them, but noted that Signature this month will host a scientific microarray conference that is geared mainly for such clinical users.

According to Shaffer, Signature has "various models" on how it shares its chip designs, some of which are also manufactured by Agilent. Most labs that use the firm's design incorporate its Genoglyphix display software and receive access to its database of abnormal results. Like Baylor, Signature doesn't view its "lab partners as competitors," Shaffer said. "We do all that we can to support their efforts," she added.

Part of the reason that bigger labs like Signature and Baylor are willing to share is because there is a widely held belief that the market is big enough to reciprocate all the interest it has been receiving. In November, for example, Illumina estimated the entire cyto market — including traditional technologies such as fluorescence in situ hybridization and molecular karyotyping — to be worth "about $2 billion," though the firm estimates that array-based cytogenetic tests make up $200 million of that and are growing 20 percent per year (see BAN 11/18/2008).

Charles Strom, medical director of the genetic testing center of Quest Diagnostics' Nichols Institute, told BioArray News this week that the reason the market has attracted so much interest is because there are a large number of cases where no diagnosis has been made that array-based technologies can help rectify. Quest launched its ClariSure array-based cytogenetic testing service in 2007. It received a license to offer its service in New York in April (see BAN 4/7/2009).

"We are not talking about a year's worth of cases," said Strom of the market potential. "There is a 60-year backlog of cases where no diagnosis has been made that all of these firms are burning through, and it will take years to address all of those patients," he said. Strom said the market will also eventually evolve into other application areas, such as oncology testing.

At the moment, Strom said that Quest — which opted to design its own ClariSure array rather than in-license a design — is "quite happy" with its business, despite the increasing numbers of labs offering a similar service.

'Slow Growth' Prenatal

"I think the [cyto-testing] market will continue to get bigger," said Ambry's Keiles. He particularly singled out the prenatal-testing market as being untapped. "There are millions of women having amniocenteses each year that are not having an array with their amnio," said Keiles. "At some point, this technology will replace standard karyotyping and the numbers will go up dramatically.

"So, we think there is a big market and we also think we provide better service than many out there, so that's how we think we can increase our business," he added.

Others in the space have similar projections for the market, but are less convinced of prenatal testing as a growth driver in the market.

"As to the growth of the market, it is definitely growing rapidly for pediatric and adult diagnosis, but … the prenatal market is not taking off," said Baylor's Beaudet. Baylor has been offering prenatal testing services since 2005 (see BAN 12/14/2005).

"This is unfortunate [as] many very severe disorders could be diagnosed," he said. According to Beaudet, getting the market to increase is "largely a matter of educating [obstetricians] and insurance companies and driving the [array-based test] price down so that there is no difference in cost for the patient or the insurance company for an array versus a karyotype."

Signature's Shaffer also said that the prenatal market is "slowly growing." She attributed the lukewarm market response to its offering, which became available in 2007 (see BAN 4/3/2007), to initial low volumes that have delayed the ability for end users to see what she calls the "benefits" of microarray analysis for prenatal testing.

"The benefits are now being demonstrated in that arrays discover more abnormalities than traditional cytogenetics, [but] results [showing] unclear clinical significance varies from lab to lab because of the design [of the array]and genomic coverage," Shaffer said. "Arrays may replace karyotyping in prenatal testing, but we are not there yet."

Shaffer added that arrays should replace the "majority" of neonatal testing in children with mental retardation or developmental disabilities or birth defects. "Prenatal may be a growth opportunity, but I wouldn't put all of my resources into just that market," she said.

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