Seattle startup NanoString Technologies last week said it has signed on Baylor College of Medicine and the University of Miami’s Miller School of Medicine as early-access partners for its nCounter digital gene-expression platform.
Terms of the early-access program call for Baylor’s Microarray Core Facility in Houston and Miami’s Sylvester Comprehensive Cancer Center to use the nCounter. NanoString placed the nCounter at the University of Washington and the California Institute of Technology late last year (see BAN 12/11/2007).
According to Lianne McLean, vice president of marketing at NanoString, the Baylor and Miami deals have emboldened the company to prepare the nCounter for a full commercial launch in the second quarter.
“We have placed all of our early-access systems and are now collecting feedback from those sites,” McLean told BioArray News via e-mail this week.
“We want to get overall impressions and feedback from the customers about the software user interface on the system, our training processes, and data analysis.”
The company is now ready to take its first orders for the nCounter for delivery in May.
Each nCounter system costs $235,000 and additional prep stations can be purchased for $65,000 from NanoString. The company’s main competitor is Applied Biosystems, whose TaqMan quantitative real-time PCR assays are widely used for array data validation. However, NanoString only envisions itself displacing TaqMan and other qPCR platforms at certain sample throughput levels.
“In general, once you are looking at more than a few genes the pricing is often less than TaqMan and as the number of samples increases, the pricing relative to TaqMan savings are even greater,” she said.
To reach its intended market, McLean said that NanoString is targeting academic and pharmaceutical core labs as well as service labs. The company is reaching out to microarray and broad genomic core labs that offer a variety of technologies.
The technology behind nCounter was developed at the Institute for Systems Biology in Seattle and works by attaching color-coded tags to target molecules that enable scientists to produce digital gene-expression data.
While the nCounter does not use array technology, it is being marketed to array users as a replacement for quantitative PCR, a technology that is frequently used to validate gene sets obtained through larger gene-expression studies.
“It has become clear that all array data has to be verified by a method that is more linear and has a greater dynamic range, like qPCR.”
This week, the firm announced that a paper co-authored with ISB and CalTech that compares the nCounter to both TaqMan PCR and real-time PCR will appear in the March 7th issue of Nature Biotechnology.
The paper describes experiments using the nCounter to profile the expression of 509 human genes in a single multiplexed assay, analysis of a gene set that overlaps with the Microarray Quality Control gene expression study, and quantitation of transcript levels for 21 sea urchin genes across 7 embryo samples. According to the paper, the results of the study demonstrate a “remarkable correlation in the pattern of gene expression between NanoString technology and real-time PCR at all transcript levels.”
According to McLean, the system is best positioned for biomarker validation. Though it has been widely reported that pharma R&D spending has been conservative and the National Institutes of Health budget is unlikely to increase through 2009, McLean said the firm sees the uptake of recent next-generation sequencing platforms, like ABI’s SOLiD system and Illumina’s Genome Analyzer, as promising.
“Complaints exist about the lack of funding, yet lots of next-gen sequencers are being placed,” said McLean. “If a new system offers a better way of doing science, we believe the funding will be there.”
An Alternative to qPCR?
From the perspective of NanoString’s early-access customers, the main rationale for adopting the nCounter platform is its ability to save users time and money when validating array data analysis.
“I believe that there’s an empty space between the high-throughput whole-genome array platforms and what conceivably can be done using qPCR, at least with the systems I have,” said Lisa White, director of Baylor’s microarray core.
White told BioArray News last week that the “medium area” between qPCR and arrays sold by vendors like Affymetrix and Illumina is “very interesting” to users that have started projects using the whole-genome arrays and would like to scale their studies to look at expression in a smaller number of tissue and other samples.
Still, White said that NanoString users will mostly benefit from that sweet spot in sample throughput size. “I think someone that just wants to do qPCR on a small number of genes on few samples probably won’t benefit” from using the system, she said. “If I have five sample and five genes, I can easily do that with qPCR. It’s once you get up into 20, 40, 60 samples with qPCR that you start racking up the money and the time and nCounter would make sense.”
Toumy Guettouche, manager of the Oncogenomics Core Facility at the University of Miami, agreed. “I believe that NanoString offers a technology that can compete with qPCR,” he told BioArray News this week. “For certain applications, like large-scale gene-expression projects, NanoString technology seems superior.”
He said that it is unlikely the nCounter will cut into areas currently dominated by array-based applications. “It has become clear that all array data has to be verified by a method that is more linear and has a greater dynamic range, like qPCR,” Guettouche said.
“The drawback of qPCR is that it is quiet labor intensive, even in highly automated settings,” he said. This limits the number of ‘gene hits’ that can be verified by qPCR.”