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NanoString Plans to Take Second-Gen nCounter Technology through FDA

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By Justin Petrone

Inching closer to having a US Food and Drug Administration-cleared offering on the market, NanoString Technologies last week debuted its second-generation nCounter Analysis System, upon which it will submit tests to the agency for review, according to a company official.

"It is the basis for our diagnostic platform," Chris Grimley, the Seattle-based company's vice president of marketing, said last week.

He noted that while the new nCounter system is not a diagnostic platform per se, it is manufactured according to standard 13485 of the International Organization for Standardization and Good Manufacturing Practice, guidelines created for producing in vitro diagnostics products, and contains the hardware that will be included in future FDA submissions.

Grimley spoke with BioArray News at the American Society of Human Genetics annual meeting, held in Montreal last week.

NanoString was founded in 2003. It launched its first-generation nCounter Analysis System in 2008 and subsequently introduced applications for gene expression, miRNA analysis, and copy number variation. The system is based on technology licensed from the Institute for Systems Biology and enables researchers to measure gene expression in a multiplexed fashion using sets of color-coded molecular barcodes and single-molecule imaging to detect and count hundreds of unique transcripts in a single reaction.

Grimley said that the new nCounter system differs from the original in terms of footprint, throughput, and ease of use.

"The digital analyzer is two-thirds the size of the original one; the key benefit is that it is designed for more ambitious studies," Grimley said, Specifically, he said it has a 50 percent higher throughput, with customers able to run 108 relatively complex assays, compared to 72 lower-complexity assays before. "We are close to producing 100,000 data points per day," said Grimley.

That should embolden its customers running applications like gene expression profiling to conduct larger studies, Grimley added.
"It really means that they can look at projects that are bigger and complete them in the amount of time that they want to complete them in," he said. "We are starting to see people come with large projects — tens of thousands. The higher the throughput [of] our system, the faster that project will be completed, and the more amenable our technology is."

Grimley said that besides the reduced size and increased throughput, the new platform contains "small changes to make the instrument more robust so that when you are running large projects, the overall goal is to spend less time generating data and to have more time to analyze the data and figure out what it means, and [whether] the hypothesis [is] correct."

NanoString has also introduced its nSolver software package that allows users to check quality control, normalize, and analyze their nCounter data and transfer results to third-party software packages for data visualization or cross-platform analysis.

Grimley said that there is no exchange program in place for existing customers to trade in their first-generation nCounters for the new instrument. The price for the new system is the same as for the first: $235,000.

NanoString has traditionally positioned its technology as a complement to microarray-based approaches, while Grimley made it clear that quantitative PCR is a rival technology.

He said that with NanoString's approach, there is "no need to run replicates as each data point is really an answer, whereas with qPCR you probably have to divide a data point by two or three because you run replicates to get actually meaningful data points."

Grimley said that the firm's higher-throughput platform also "enables people to consider bigger projects and allows them to complete them faster" than would be possible with qPCR.

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Taking another swipe at qPCR, he noted that the firm can analyze formalin-fixed, paraffin-embedded samples following "basic deparaffinization," requiring no other purification steps. Analyzing FFPE samples is "more challenging with qPCR where you have to do the purification steps," he claimed.

First adopters of the new system include the Broad Institute, which has ordered two next-gen nCounters, and a "large commercial company in Europe that has also purchased two." Grimley declined to name the firm.

In a statement, Aviv Regev, a core member at the Broad, said that the institute has used NanoString's platform in "areas as diverse as genome analysis, epigenomics, infectious disease, metabolic disease, and cancer." Nir Hacohen, a senior associate member at the Broad, added that the institute is "looking forward" to using the new nCounter system to "accelerate some of our larger projects."

PAM50

In the same statement, NanoString CEO Brad Gray called the introduction of "IVD-quality hardware" an "important milestone" on the firm's path toward developing nCounter-based molecular diagnostics.

NanoString's main test in development is its Breast Cancer Intrinsic Subtyping Assay. NanoString last year launched a version of the assay for research purposes. The assay is based on the PAM50 gene signature that the company exclusively licensed last year from Bioclassifier, a consortium of cancer experts from four institutions.

NanoString announced earlier this year that it had initiated the first in a series of studies to evaluate the clinical utility of the assay. The initial investigation will rely on approximately 1,000 samples from the TransATAC study to evaluate whether the assay can quantitate the probability of cancer recurrence in individual post-menopausal women with hormone receptor-positive, early-stage breast cancer who have been treated with hormonal therapy (BAN 8/16/2011).

TransATAC is a translational study group that has used the tissue and data from the Arimidex, Tamoxifen, Alone or in Combination, or ATAC, trial to study the molecular characteristics of tumors in patients with ESBC.

The firm has not yet targeted a launch date for the clinical version of the assay.

Grimley said last week that the trial is "ongoing" and that the firm will have more to discuss in the future. In terms of other tests in its pipeline, Grimley said that NanoString's focus is the breast cancer test.

"As a small company, we have to make sure we put our focus onto specific products," said Grimley. The firm's two focuses are "PAM50 and the life science tools business," he said.


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

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