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OGT Sees New Medical Research Exome Array as 'Perfect Complement' to Next-gen Sequencing Workflows

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NEW YORK (GenomeWeb) — Oxford Gene Technology has launched a new microarray product that it believes will be attractive to medical research laboratories that use targeted, next-generation sequencing panels.

The CytoSure Medical Research Exome Array contains enhanced coverage of 4,600 genes relative to medical research and grouped into disease- and syndrome-specific panels, as well as backbone coverage of the human genome. According to the Oxford, UK-based company the chip is highly targeted and exon-focused, and should enable users to detect microdeletions and microduplications relevant to their research.

"It is now commonly accepted that targeted sequencing panels, while excellent at identifying point mutations, are still a long way off providing reliable copy number information," James Clough, vice president of commercial activities at OGT, told BioArray News in an email this week.

"Array comparative genomic hybridization is the gold standard for copy number detection, making the CytoSure Medical Research Exome Array the perfect complement to the NGS workflow for comprehensive analysis of the full mutation spectrum," Clough said.

According to Clough, OGT's new chip was borne of a market need for one array containing "hand-curated, medically relevant genes" that could enable the detection of single or multiple exonic copy number variations. Providing such information to researchers can help them better understand how mutations in multiple genes can contribute to diverse disorders, he noted.

Agilent Technologies manufactures the million-marker array on a single slide. OGT customers can order their own designs based on the array content in Agilent's different multiplex microarray formats, including its 2x400K format, where one slide contains two 400,000-marker arrays; its 4x180K format, where each slide supports four 180,000-marker arrays; and its 8x60K format, where there are eight 60,000-marker arrays printed on each slide. Users can analyze the data using OGT's CytoSure Interpret software.

OGT developed the array in cooperation with partners at Emory Genetics Laboratory in Atlanta. The company introduced the product via an early access program earlier this year.

"Our early adoption program has been invaluable for further developing the array to suit the marketplace," said Clough. While some laboratories want to use the full array — commonly to complement their exome sequencing studies — other laboratories want smaller, more specific array panels that correlate to specific diseases or syndromes, he said.

"Laboratories in the latter category often test the full array to validate the approach before working with us to develop customized array panels," said Clough. It is in OGT's custom array offering where its relationship with EGL comes particularly into play.

"The clinical research expertise and extensive testing provided by EGL means that we have a large database of pre-validated probes that can be integrated into any array design or format," said Clough. "The partnership with Emory also ensures that the latest gene content can be made available to all OGT customers as additional disease-causing genes or mutations are identified."

Madhuri Hegde, executive director at EGL, said that her lab developed the new array with OGT as a "follow up to detect deletions and duplications that are currently not detected by exome sequencing with high confidence."

Hegde told BioArray News in an email that EGL now uses the new OGT array as a "reflex test" for clinical exome sequencing. She noted that other microarrays on the market that contain exon-focused content often have "holes" in terms of coverage of medically relevant genes, whereas the new OGT array "has filled in the gaps."

OGT and EGL have been collaborating for years, and together have designed a menu of CytoSure Molecular Arrays that target genes associated with two dozen diseases and disorders, such as Duchenne muscular dystrophy. Hegde said that EGL continues to use these lower-density targeted arrays, pairing the copy number information they provide with next-generation sequencing. She spoke extensively with BioArray News about EGL's combined use of arrays and sequencing last year.

"There is a lot of hype around next-generation sequencing," Hegde said at the time. "Next-gen sequencing is not the only solution as it does not detect all types of mutations," she said. "There are many complementary assays that go with it."

Hegde will be giving a talk during OGT's workshop at the American Society of Human Genetics meeting later this month in San Diego. The workshop is titled "Arrays and NGS — High Resolution Analysis of the Medical Exome." OGT CEO Mike Evans is also slated to speak.

Clough noted that partnerships with CytoSure Medical Research Exome Array adopters, in addition to the company's relationship with EGL, could lead to the creation of new catalog arrays.

"A number of our early access customers are interested in utilizing this gene content to create smaller, more cost-effective array panels for their specific diseases or syndromes of interest," said Clough. "Collaboration with such experts offers the potential to develop additional catalog products that address various important disease areas," he said.

The product also complements OGT's Genefficiency next-generation sequencing services.

"While the array is available as a product, we can also offer both array and targeted NGS services through our high-throughput Genefficiency Genomic Services laboratory," said Clough. "Some of our early access customers have utilized our Genefficiency services to validate the CytoSure Medical Research Exome Array with their own samples prior to bringing it in house," he said. "This is an excellent option for researchers whose internal resources may be stretched."

Clough told BioArray News earlier this year that the market for the new chip lies largely in US medical genetics laboratories, such as EGL. OGT opened a North American sales office outside of New York two years ago.

"If you look at the genetics testing market, North America leads," Clough said at the time. "I don't know what the number of exomes being run clinically in the UK is, but it is a trivial number compared to the number run by large centers in the US," he said. "I have had people tell me they are going to do 10,000 exomes this year," Clough added. "There aren't 10,000 exomes being done in the whole of Europe."

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