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Seeking to Court Academics, HTG to Debut Mid-Density, Whole-Genome Arrays in 2009

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SAN DIEGO — Looking to provide more upstream research tools to its pharmaceutical and academic customers, High Throughput Genomics plans to launch mid-density arrays during the first quarter of 2009, and hopes to make whole-genome arrays available by the end of next year, according to a company official.
 
Chief Scientific Officer Bruce Seligmann said this week that the company plans to introduce the mid-density and whole-genome arrays in order to complement its existing offering, the ArrayPlate 96-16, which enables customers to survey 16 genes per well on HTG’s platform.
 
The planned debuts are also part of the company’s new objective to move beyond its pharma base, and the mid-to-high-density array formats may help win converts, especially in academia.
 
Seligmann spoke with BioArray News following his presentation at IBC Life Sciences’ Discovery2Diagnostics conference, held here this week.
 
“All of our clients have come to us and said that they need a high-density array that gives the same quality data as the microplate assay does today,” Seligmann said. “What they want is a whole-genome array so that they can produce, for example, a whole-genome dose response curve.
 
“This makes it a consistent platform,” he added. “The same assay will be done to identify genes as is performed in downstream applications.”
 
HTG’s flagship platform is its ArrayPlate 96-16, which uses the firm’s quantitative Nucleic Protection Assay, or qNPA, to measure gene expression. The core attribute of qNPA is its use of a lysis buffer to release the RNA from the sample, thereby removing from the protocol the RNA extraction, amplification, and labeling steps.
 
Additionally, the Tuscan, Ariz.-based company claims that qNPA can be used on most samples, including cultured cell lines, fresh tissue, and formalin-fixed, paraffin-embedded archival material. ArrayPlates are read either by HTG’s Capella Imager, which can read 10 ArrayPlates per day, or its higher-throughput Omix II Imager.
 
According to Seligmann, the impending mid-density format will enable users to survey between 200 and 4,000 genes that they can select from HTG’s catalog. The whole-genome arrays, penciled in for a Q4 ’09 release, will allow customers to query the human genome, while rat- and mouse-theme arrays are planned for subsequent launches.
 
While the mid-density and whole-genome arrays will use the same qNPA approach, Seligmann said that the rat- and mouse-theme arrays will be made available on slides in the footprint of a microtiter plate. Also, though the current assay uses luminescence-based detection, the slide-based assays will use fluorescence detection, thereby allowing customers to scan the arrays using regular microarray scanners.  
 
‘Nuts-to-Bolts Approach’
 
HTG’s impending product launches will follow a number of other recent releases from the company. In September, HTG launched M3 Series, a multiplexed mini-microarray set-up for biomarker discovery and gene profiling (see BAN 9/9/2008).
 

“This makes it a consistent platform. The same assay will be done to identify genes as is performed in downstream applications.”

Over the past year, HTG has also launched a line of qFix arrays that target “genes of interest” such as human and mouse cytokines, and a panel for drug-metabolism studies. The company has also launched an miRNA assay on the ArrayPlate format, and sells custom arrays.
 
So far, though, HTG, which was founded in 1997, has focused on higher-throughput, low-plex applications that have made it a competitor of PCR products such as Applied Biosystem’s catalog of TaqMan assays for target validation and other applications. The expansion to mid-density and whole-genome formats, therefore, is a departure for the firm, one that will bring it into competition with larger array vendors like Affymetrix, Agilent Technologies, and Illumina.
 
However, according to Seligmann the extension to higher-density formats makes sense for the company as it looks to make qNPA available for both upstream and downstream experiments.
 
“Right now you have this concordance issue where you go from a high-density array to PCR, which is a totally different methodology, and you don’t get the same results,” said Seligmann. In terms of HTG’s offering, the “only difference is the array — not the assay, protocol, or the reagents.
 
“It becomes a nuts-to-bolts kind of approach from discovery to the final application assay with the same level of precision at each stage,” he added. “This way, the exact same detection probe is used in a high-density array as is used in a microplate assay.”
 
‘Very Friendly’ with Pharma
 
According to Seligmann, HTG’s main customer base to date has been pharmaceutical and biotech companies. “We are very friendly with the pharma industry,” he said. He cited relationships with Merck, Takeda, Schering-Plough, Sanofi, and Eli Lilly.
 
Merck Capital Ventures holds a stake in privately held HTG, along with Solstice Capital and Valley Ventures. During his presentation at D2D, Seligmann also showed data from Takeda and Schering-Plough studies.
 
HTG’s new objective is to move beyond its pharma base, and Seligmann said that the mid-to-high-density array formats that will be launched next year may help the firm win converts. 
 
“We started off marketing this to the pharmaceutical industry and we are now working into the academic community,” Seligmann said. He said that HTG’s assay has been successful in pharma because qNPA was “directed to high sample throughput, precision, things that were really needed by the drug discovery industry and perhaps were less appreciated in the academic market at the time.”

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