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Ambry Genetics, Looking to Entice Pharma, Rolls out CHO Cell Expression Array

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This story has been updated to include additional comments from Ambry Genetics and Sigma-Aldrich.

By Justin Petrone

Ambry Genetics recently expanded its menu of custom-designed microarrays by launching its CHO Cell Expression Array. The company said it designed the new array to target pharmaceutical companies that produce recombinant proteins in Chinese hamster ovary, or CHO, cells.

"The majority of pharmaceutical companies mass produce recombinant proteins in CHO hamster cells," Aaron Elliott, director of genomic services at Ambry, told BioArray News. "In fact, over 70 percent of recombinant proteins are produced in CHO cells, resulting in annual therapeutic sales of over $30 billion worldwide," he said. Elliott's figures were supported by a recent CHO Consortium report.

Ambry, based in Aliso Viejo, Calif., designed its new array in collaboration with Genotypic, a Bangalore, India-based genomic services provider. Elliot said that Genotypic requested the array because it is interested in post-translational protein modification pathways in CHO cells. Genotypic is an Agilent-certified service provider for microarray-based applications.

"For recombinant proteins to be functional, specific protein modification processes have to occur properly such as protein folding and glycosylation," said Elliott. "It is extremely important to monitor the gene expression levels of various protein modification genes and determine which CHO lines produce the highest yield of functional recombinant proteins," he said.

According to Elliott, Ambry is in the process of launching the array, which is already advertised on its website. The chip will be targeted to all pharmaceutical and biotech companies producing recombinant proteins in CHO cells, he said.

Agilent Technologies is manufacturing Ambry's new array. Elliott said that it is available in an Agilent format that provides eight 60,000-marker arrays on a slide and "contains probes that correspond to the most updated CHO cell information." Ambry is pricing the array at $500 per sample. Elliott also said that customers might wish to use the new array in combination with the firm's RNA-seq services offering for studying CHO cells.

Ambry is one of a handful of companies to either offer a catalog CHO cell microarray or to have developed one for internal use. Affymetrix has offered a number of consortia-developed CHO microarrays since 2006 and in a paper published last year in Biotechnology Letters, Pfizer scientists detailed the design of a CHO cell array for the study of 3,500 sequences.

Meanwhile, SAFC Biosciences, a division of Sigma-Aldrich, has developed a CHO cell microarray for internal use. According to a 2009 scientific poster, Agilent Technologies manufactures the array on its 4X44K platform. SAFC R&D scientist Scott Bahr told BioArray News this week that the company has "done some proprietary work" using CHO cell arrays, but its design is not going to be made publicly available. "It will only beavailable as an internal research tool and to our customers with which we collaborate," Bahr said.

Furthermore, a group at Dublin University City in Ireland last year reported the use of array-based gene expression profiling of CHO cells to identify transcriptional modules associated with growth and productivity. Another group at the University of Bielefeld in Germany last year described the development of a custom CHO cell expression array after sequencing the cell lines using Roche 454 Life Sciences' next-generation sequencing platform.

Elliott said that Ambry's array is competitive with other offering "due to the multiplexing that Affy does not offer" and because it is "up to date with the current sequencing information."

Expanding Menu

Ambry is a certified service provider for both Agilent and Roche NimbleGen microarrays. The company jumped into the array market when it introduced a chromosomal microarray analysis service in 2009, and has since launched a number of focused chips (BAN 6/9/2009).

In 2010, it introduced StemArray, an Agilent-made comparative genomic hybridization chip designed for labs characterizing human embryonic stem cells or induced pluripotent stem cells and looking for higher resolution in their studies than conventional karyotyping can provide (BAN 1/19/2010).

And last year, the firm launched its CancerArray, a 180,000-probe array offering genome-wide probe coverage at an average resolution of 20 kilobases with higher-density coverage in more than 400 known cancer-associated genes. That array partially includes content from the Wellcome Trust Sanger Institute's Cancer Gene Census, a catalogue of genes for which mutations have been causally implicated in cancer (BAN 9/13/2011).

Ardy Arianpour, Ambry's vice president of business development, told BioArray News this week that demand has been "very high" for both the StemArray and CancerArray.

He noted that Ambry partnered last year with Cell Line Genetics, allowing Cell Line to offer StemArray to its customers, as "they have access to numerous customers that are doing karyotyping in the regenerative medicine space" (BAN 6/21/2011).

Arianpour added that the Ambry's CancerArray has been an "early winner" for the firm. "Both pharmaceutical companies and institutions conducting cancer research have utilized it for their studies," he said.

Arianpour said that Ambry has some other custom design arrays in development that will be launched later this year, but did not elaborate.

Elliott said that the firm continues to make custom arrays for customers. "The majority of the custom designs we offer are for specific clients who request various organisms," he said. "If sequencing information is available we can typically make an array for it."


Have topics you'd like to see covered inBioArray News? Contact the editor at jpetrone [at] genomeweb [.]com

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