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Roche NimbleGen, Preparing Cyto Array FDA Submission, Eyes Opportunities in Oncology Dx

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By Justin Petrone

After years of serving the life science research market, Roche NimbleGen is now preparing for its entry into the molecular testing space with an initial focus on the diagnosis of genetic abnormalities. At the same time, it is looking at developing tests for other indications, such as in oncology.

CEO Frank Pitzer told BioArray News recently that the Madison, Wis.-based firm intends to drive its NimbleGen array platform into the diagnostics market, where it will develop "important, valuable applications," the first of which will be in the field of cytogenetics.

"We are in the process of preparing for a submission. However, the timeline is dependent on a few things and the final decision is with the [US Food and Drug Administration], not with us," Pitzer said. "The first application will be in the important field of cytogenetics, however, this will not be the last one," he said. "Additional applications do not have to be in cytogenetics as there are numerous other areas which could benefit from the value our products provide."

Indeed, Pitzer said that the company could develop cancer-themed diagnostics. "A lot of content has yet to be discovered, but every day research brings us more and more data, and thus potential diagnostic content, which will open up interesting opportunities for microarrays in this market in areas such as oncology," he said. Pitzer said that Roche is relying on its connections to the medical and scientific community to feed its pipeline with future diagnostic content.

Roche paid $272 million to acquire NimbleGen Systems in 2007, and over the past three years, Roche NimbleGen has rolled out a new workflow, including instrumentation, as well as high-density chips for a number of applications, including comparative genomic hybridization and copy number variation studies. While the company has always touted the diagnostic potential of its platform, the increased focus on the diagnostics market is a shift for NimbleGen.

For Pitzer, who joined Roche NimbleGen in March and previously served as a member of Roche's Global Diagnostic Executive Committee in the Swiss firm's Basel headquarters, Roche's current objective is to take the array firm, which has to date derived most of its revenue from sales to researchers, into the diagnostics space.

"The diagnostic division of Roche is the market leader in in vitro diagnostics in markets such as molecular and professional diagnostics," Pitzer said. "Two of the strategic drivers, or core competencies, that we bring in this market are testing efficiency and medical value," he said. "We will apply this same strategy and these same strengths to Roche NimbleGen, which has previously focused on providing array workflow and service solutions for the life science research market."

The firm's choice of cytogenetics as a primary diagnostic indication is not unique. Over the past year, other companies that manufacture arrays that are used by cytogeneticists to diagnose constitutional abnormalities, including Affymetrix, Agilent Technologies, and Illumina, have similarly acknowledged discussions with the FDA about the potential clearance of their platforms (BAN 4/13/2010).

Illumina, for instance, in January said it would submit its iScan system plus its HumanCytoSNP-12 and HumanOmni1-Quad BeadChips to the regulatory agency as part of the FDA's preliminary investigational device exemption process, where test makers send analytical or clinical protocols for review and comment before proceeding with studies (BAN 1/26/2010).

While the FDA has confirmed that it will require that makers of arrays used in cytogenetics seek clearance for their platforms, it has not yet settled on what criteria its review process will entail. The FDA's Office of In Vitro Diagnostic Device Evaluation and Safety hosted a meeting last month with test providers, array manufacturers, and other experts to address this issue (BAN 7/6/2010).

Donna Roscoe, a scientific reviewer in the division of immunology and hematology at the FDA's Center for Devices and Radiological Health, said at the meeting that array-based cytogenetic tests, which look across a patient's genome to identify causes of certain phenotypes, "challenged FDA's regulation strategy" because they provide an "undefined number of outputs open to interpretation." Because of this, FDA is now looking to create "standards for manufacturers seeking to bring assays for approval," and to ensure that array-based cytogenetic tests are "safe and effective," Roscoe said.

Like its rivals, Roche NimbleGen has provided arrays to cyto labs for years. In 2009, Spokane, Wash.-based cytogenetics testing provider Signature Genomics, now part of PerkinElmer, announced its adoption of Roche's array platform (BAN 11/10/2009). Roche's deal with Signature enabled it to launch Signature-designed NimbleGen CGX arrays for genome-wide analysis of chromosomal abnormalities.

The arrays are available in formats of three samples per slide, six samples per slide, and 12 samples per slide. The whole-genome oligonucleotide arrays enable users to survey more than 200 cytogenetically relevant regions, over 675 functionally significant genes, 5 megabases of telomeric and pericentric regions covered with one oligo every 10 kilobases, pseudoautosomal regions covered with one oligo every 10 kb, and whole-genome backbone coverage of one oligo every 35 kb. While NimbleGen CGX arrays are supported by the firm's reagents and instrumentation, NimbleGen customers get access to Signature's Genoglyphix data-analysis software.

Pitzer said that Roche NimbleGen's FDA submission will likely be different from its current offering, especially with regards to workflow. "Initially, the workflow will be based on the existing platform but of course we will develop it further to move it forward, keeping pace with the requirements of the diagnostics market," said Pitzer. "We will take special considerations to ensure that relevant requirements and demands from diagnostic laboratories are implemented, including automation, ease of use, and robustness."

Pitzer said that Roche Diagnostics' "expertise" will be "key" as Roche NimbleGen seeks to streamline its array workflow for diagnostic use. "This is a place where we are very competitive not only because of the advantages of our technology, but also because of the advantages of the years of experience that Roche Diagnostics can provide as a leading solutions provider in this market," he said.

Though Roche NimbleGen is increasingly focused on the diagnostics market, sales to researchers still comprise the bulk of its revenues. Roche does not break out sales figures for its array business. An independent market survey conducted by JP Morgan's Life Science Tools & Diagnostics group in April estimated that Roche sold $36.7 million worth of arrays in 2009 and predicted the firm would sell $49.6 million worth of arrays this year (BAN 5/18/2010).

Pitzer said that Roche NimbleGen is interested in increasing sales to pharmaceutical researchers, who use the company's platform to screen and identify biomarkers. Given Roche's dual roles as a drug maker and diagnostics company, Pitzer said that Roche NimbleGen is in a "unique position" to execute such sales to other pharmas. "One of the true values of Roche is the combination of a large diagnostics organization and pharma organization under one roof," said Pitzer. "We will better be able to understand the needs of pharma and deliver solutions that fit their specific requirements."

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