Applied Biosystems this week took steps to shake up the budding miRNA-analysis market by launching its TaqMan Array Human MicroRNA Panel, a new format that puts the firm’s TaqMan RT-PCR technology — widely used by drug makers — in an array format to enable greater high-throughput miRNA studies.
ABI already sells a 1 x 3 inch slide format microarray for microRNA profiling called miRvana, which it acquired with its $273 million purchase of Ambion’s research products division in March 2006 (see BAN 3/7/2006
). The company’s new microRNA offering is a multiple-site microfluidic cartridge that will allow it to capitalize on its existing PCR know-how while at the same time reaching a growing market that now includes rival products or services from Exiqon, Agilent Technologies, Invitrogen, Febit, Asuragen, and others.
ABI is marketing the tool as RT-PCR-meets-high-throughput-miRNA analysis. The system is based on the company’s TaqMan assay chemistry for quantitative gene expression and allows researchers to perform 384 simultaneous real-time PCR reactions without liquid-handling robots or multi-channel pipettes, ABI said. The panels are designed to work with ABI’s 7900HT Fast Real-Time PCR System, offering existing owners of the system the opportunity to add miRNA profiling experiments.
Iain Russell, the product manager of TaqMan microRNA assays for Applied Biosystems, told BioArray News in an e-mail this week that the panel is essentially a high-throughput version of the individual TaqMan miRNA assays the firm has been selling since 2005.
“The streamlined workflow delivered by the TaqMan Array Human MicroRNA Panel and Multiplex RT now enables Applied Biosystems customers to easily extend the use of ... TaqMan MicroRNA Assays to miRNA profiling studies,” he wrote.
He also wrote that the human-focused content of the panel, plus its efficient workflow, distinguished it from the miRvana array. “The entire workflow, from total RNA to data for 365 miRNAs, takes less than 3 hours,” he wrote. “Unlike the Ambion bioarray, the TaqMan Human MicroRNA Panel content is specific to human and focuses on the well characterized miRNA content curated by Sanger miRBase database,” he added.
Furthermore, Russell wrote that TaqMan chemistry coupled with low sample input requirements offered researchers more potential in profiling miRNA than microarray tools sold by rivals. “In cases where researchers are looking to detect and quantify genes that are expressed at low levels, such as miRNA genes, the TaqMan arrays offer the sensitivity to detect genes at very low copy numbers that would otherwise be invisible to genome survey technologies, such as microarrays,” he wrote.
“In cases such as disease research, where researchers have limited amounts of starting RNA sample available to analyze, the TaqMan miRNA arrays are the ideal choice of analysis tool because they generate accurate gene expression data while requiring lower volumes of starting sample than do other analysis methods,” wrote Russell.
He also described the miRNA microarrays sold by firms like Exiqon and Agilent as “large-scale gene expression analysis tools” that “require more sample, are less-sensitive, take more time to complete, and [are] incapable of detecting low-expressed genes, compared with TaqMan-based arrays.”
ABI’s expanded miRNA portfolio doesn’t come as a surprise. Most large microarray vendors either have launched off-the-shelf products or have ongoing custom collaborations with miRNA researchers. However, the impact of ABI’s launch may be in its ability to use the perceived sensitivity of its TaqMan technology to outpace competitors selling microarrays in the 1 x 3 inch format.
“We have tested several miRNA array formats ... and felt that there were always specificity issues associated with miRNA arrays. That's why we decided to switch to the miRNA TaqMan assay format,” Peng Jin, an assistant professor of human genetics at the Emory University School of Medicine, wrote in an e-mail to BioArray News this week.
Jin wrote that his lab now uses the ABI panel to do miRNA profiling, “which requires us to screen as many miRNAs as possible” and that ABI’s miRNA card “provides us a convenient way to do this.”
“Whereas an array can theoretically be read on one of many different brands of scanner, this assay is dedicated to the 7900HT – which does not fit in everyone’s budget.”
Neil Winegarden, head of operations of the microarray facility at the Universal Health Network in Toronto, who is familiar with ABI’s other technology but is not using the TaqMan Array Human MicroRNA Panel, wrote in an e-mail to BioArray News this week that ABI’s new product is “intriguing in that it offers a level of sensitivity that will likely be unmatched by miRNA arrays for some time.”
According to Winegarden, “ABI’s solution seems quite elegant in that it removes some of the limitations of traditional qPCR-based assays” because “one of the more attractive reasons for using an array is that each gene is probed using the exact same conditions, whereas a typical q-PCR assay requires that the researcher aliquot the RNA in to each well,” which opens the door to result variability .
ABI’s new panel enables a single sample to be automatically distributed into several wells, which could reduce that variability. Still, Winegarden wrote that ABI’s assay might suffer from scalability issues and that non-ABI users may be required to buy expensive equipment to run it, such as a thermal cycler and the 7900 system.
“Whereas an array can theoretically be read on one of many different brands of scanner, this assay is dedicated to the 7900HT — which does not fit in everyone’s budget,” Winegarden wrote. “That being said, there are several such instruments already in place. For those that already have one and do not need to realize a capital equipment cost, this will be a very attractive solution.”
Exiqon CEO Lars Kongsbak ,isn’t convinced that ABI’s new product will impact Exiqon’s marketing strategy, which is centered on the firm’s locked nucleic acid technology, an approach that the company claims increases the thermal stability, sensitivity, and specificity of its miRcury miRNA microarray products.
Kongsbak wrote in an e-mail to BioArray News this week that ABI’s panel “suffers from the same significant drawback as the Agilent array — that it is based on a looped primer technology that requires a defined length of the miRNA 3’ end.”
According to Kongsbak, the 3’ end often varies due to post-transcriptional editing, “which jeopardizes fixed 3’ assays.” He also wrote that of “all the ABI assays we have looked at, the TaqMan probe is covering a region of the miRNA target that also is targeted by one of the primers, which means that the probes do not add additional specificity than” assays that use SYBR Green staining gels. He added that Exiqon is “capable of defining assays with increased specificity as we can include LNA into primers and probes.”