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OGT Plans to Put New Consortium-Designed Arrays 'Forward First' to Cyto Customers

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By Justin Petrone

Oxford Gene Technology this week said it sees its new menu of International Standard Cytogenomic Array Consortium-designed microarrays as its top offering for the cytogenetics research community, which it said may favor the standardized arrays in an increasingly competitive market.

Spencer Howell, director of cytogenetics at OGT, told BioArray News this week that the Oxford, UK-based firm is seeing "massive uptake" in the cytogenetics market, and that customers "prefer a standard design" over other designs available today. "The first recommendation we will make is the ISCA designs," he said.

The ISCA arrays, launched last week, were designed in collaboration with the International Standard Cytogenomic Array consortium, a group of clinical and molecular genetics laboratories, that seeks to standardize the use of arrays and interpretation of array results in cytogenetics research.

OGT's CytoSure ISCA aCGH arrays are manufactured by Agilent Technologies in the Santa Clara, Calif.-based firm's new, million-feature G3 format. They are available in three formats: eight arrays on a slide with 60,000 probes each; four arrays on a slide with 180,000 probes each; and four arrays on a slide with 44,000 probes each. The arrays, which offer whole-genome coverage, focus particularly on disease and syndrome-associated genome regions.

OGT already has a number of designs for the cyto market. Since 2007, the firm has launched Syndrome Plus, a chip containing two, 105,000-probe arrays that include markers for over 200 syndromes; a chromosome X chip with four, 44,000-probe arrays as well as a higher-density chromosome X chip targeting genes, exons, miRNAs, rRNAs and snRNAs on the X chromosome; and, most recently, a chip with four, 44,000-probe arrays for detecting mutations in the dystrophin gene that are responsible for Duchenne muscular dystrophy (see BAN 11/18/2008, BAN 11/3/2009).

To develop the ISCA chips, OGT developed several iterations of ISCA's design using different probe sets from its Oligome probe bank of 20,000,000 validated probes. The firm selected the best-performing probes from those sets for the arrays, said Howell.

According to Howell, OGT will from now on "put the ISCA arrays forward first" to customers, meaning the company will steer its cytogenetics customers first to the ISCA chips. "Straight away, we can point them to the consortium," he said. "They can understand the aims of the consortium. There are such high-profile experts on the [ISCA's] steering committee and most people will say that ISCA is the way forward for us."

"The important thing with array CGH in constitutional disorders is if you look at yield from karyotyping it's something on the order of 5 to 8 percent," James Clough, vice president of clinical and genomic solutions of OGT, told BioArray News this week. "We are now getting yields from oligo arrays heading into 25 percent. Part of the challenge ISCA wants to address is, 'What is that other 75 percent?'"

According to Clough, OGT has been working with ISCA for "many years," and the firm views the chips as a "step forward" as the consortium grows. "There are more than 60 [ISCA-affiliated] labs around the world and it's a good step forward for them," he said of OGT's offering.

Two ISCA members that have worked with OGT to design its arrays include David Ledbetter of Emory University and John Crolla, head of prenatal and molecular cytogenetics at Wessex Regional Genetics Laboratory in the UK. Crolla is also a CytoSure ISCA customer, according to Clough.

Some OGT customers, too, have contributed to the company's efforts to develop the CytoSure ISCA, including helping it select the content for its Syndrome Plus array.

According to Howell, there are "a lot of similarities in the designs" between the two chips, and there are a few reasons why customers might prefer one over the other.

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'One Size Doesn't Fit All'

According to Howell, ISCA members are likely to adopt CytoSure ISCA arrays because "they want to use what other members are using." He also said that the UK's National Health Service is "moving from a karyotype-based to an array-based approach as a frontline test" in cytogenetics," and labs that offer the higher-density ISCA designs will get the "maximum return for the funding they get" as they can run eight samples on a slide that contains eight 60,000-probe arrays.

At the same time, Clough said OGT's eight-by-60K and four-by-180K CytoSure ISCA designs will require a higher-resolution scanner. However, he noted that most labs should be able to use their existing scanners with a Syndrome Plus array.

"Many labs have got something like the Axon GenePix scanner, which will scan the older format arrays," said Clough. "To move to the G3 arrays, they've got to spend £100,000 ($157,000) on a new scanner."

Clough added that there are different camps within the cytogenetics research community that are interested in particular areas.

"Some labs are interested in particular areas, others are more general," said Clough. "I think it's the same with our chromosome X arrays. One size doesn't fit all."

According to Howell, OGT plans to release more cytogenetics products this year, particularly in the molecular genetics area. "There are several groups looking at single-gene disorders. We have identified that as a growth area," he said. "We'll have a cytogenetics part of the CytoSure range, but also a molecular genetics part of the CytoSure range as we go forward."

OGT is also investing in data analysis. The firm launched a new analysis tool called CytoSure Interpret at the end of 2009 (see BAN 11/3/2009) that is designed to offer users access to visualization tools, imported and external annotation information, databasing capabilities, and standardized formatting.

According to Howell, OGT's informatics offering "is developing all the time. The idea is to help guide people processing these samples from acquiring results to interpretation. Analysis is the bottleneck."

Clough added that OGT is working with labs to move them from karyotyping to CGH. OGT last year became the European distributor for Sunnyvale, Calif.-based array instrumentation provider SciGene, a move that could enable the company help customers outfit their labs and ramp up processing of samples.

"Moving from karyotyping to array CGH requires a different skill set," said Clough. "Array CGH is a high-value process. You need to make sure you are getting the best results."

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