PHILADELPHIA — Looking to capitalize on the same perceived manufacturing advantage that helped it win gene expression customers, Illumina this week announced plans to launch an assay for microRNA expression profiling next month.
According to Tanya Boyaniwsky, Illumina’s marketing manager for gene expression, the firm has designed miRNA profiling assays for human and mouse based on its existing GoldenGate genotyping and cDNA-mediated Annealing, Selection, Extension, and Ligation, or DASL, expression assays. The company plans to roll out a catalog miRNA product in October that will be manufactured on its 96-sample Universal Array format like its other expression products.
“MiRNAs are very exciting to us,” Boyaniwsky told BioArray News following an Illumina workshop at IBC Life Sciences’ Discovery 2 Diagnostics conference, held here this week. “It’s a part of the gene-expression portfolio and it’s also the part of the market that is growing quickly.”
Boyaniwsky noted that miRNA-related publications in PubMed and miRNA research grants are both growing at a rate of 60 percent to 70 percent per year, “but if you look at gene expression as a whole it’s a much slower market, so [miRNA] is the niche that we want to get into.”
By entering the miRNA market, Illumina will have to catch up with a host of companies. Invitrogen and Exiqon, a Danish firm that specializes in miRNA, both began selling miRNA arrays in the second half of 2005. This year, four new players joined them: Agilent, which launched an miRNA array in April; Febit, which began offering its Geniom miRNA Biochip in May; Applied Biosystems, which sells both array and RT-PCR-based miRNA products; and Asuragen, which offers its miRNA DiscovArray through a service.
Boyaniwsky acknowledged that there are some effective technologies in the marketplace, but Illumina sees its strength in throughput, assay performance, and a lower price made possible by the company’s manufacturing capabilities.
“We will take the same philosophy that we have had in the expression market into the miRNA expression market,” said Boyaniwsky. “We are going to be the low-cost provider while at the same time allowing as many samples to be run as possible.”
Boyaniwsky declined to disclose specific pricing plans, but touted the throughput of the system, which offers a 96-sample format to enable customers to look at multiple samples and multiple conditions simultaneously. In addition, the company claims its arrays are sensitive enough to work with total RNA from formalin-fixed, paraffin-embedded samples, which could make it attractive to large sample-volume cancer studies.
“A lot of groups are interested in the 96-sample format because they’ve got a lot of samples that have been sitting around for awhile,” she said. “Especially with FFPE samples, people would also like to look at their samples using these arrays because miRNAs are so small [that] they are less subject to degradation. Now they will be able to look at messenger RNA at the same time that they look at miRNA.”
According to Jian-Bing Fan, director of scientific research at Illumina, the company could eventually make its miRNA content available in a lower-sample format. “As a rule, researchers need a sample size of 50 in order to draw any meaningful biological conclusion,” he said. “But we will provide the BeadChip with other sample formats so people will have the option to do that, too.”
Fan told BioArray News at the conference this week that the company also believes its next-gen Solexa sequencing technology could help generate novel miRNA array content. Illumina’s debut product will be based on the Wellcome Trust Sanger Institute’s mirBASE database of known and predicted microRNAs. However, future products may use new miRNAs discovered using the digital expression application on the firm’s Genome Analyzer system.
“We are going to be the low-cost provider while at the same time allowing as many samples to be run as possible.”
“Digital gene expression can be used to globally validate arrays,” said Boyaniwsky. “It is also great for discovery and for rare transcripts. And in fact it can be used to discover new microRNAs,” she said. “If it is in the literature and can be substantiated, then why don’t we go and design probes for it with new high-throughput screening system?”
In terms of target customers, Boyaniwsky said that the company will be looking to place its miRNA chips with existing gene expression customers, especially core labs and service providers, who have signaled interest in the content and have the equipment to run the assays.
One customer that already has access to Illumina’s miRNA assay is the Burnham Institute, located in La Jolla, Calif., up the road from Illumina’s San Diego headquarters.. During Illumina’s workshop at D2D, Louise Laurent, a research fellow at Burnham, showed data from stem cell research that was generated using the miRNA assay.
Laurent told BioArray News after her presentation that the Burnham researchers are trying to determine cell fate during differentiation in order to generate cells that could be used in regenerative medicine for conditions such as Alzheimer’s disease, spinal injuries, and diabetes. The Burnham is also involved in projects to generate cardiomyocites and pancreatic beta-cells.
“We want to be able to increase the efficiency of being able to direct differentiation down to what [cell type] you want,” she said. According to Laurent, the institute has been using alpha and beta versions of the miRNA assay for about a year and also had a hand in suggesting some of the content that will appear on the chips when they debut next month.
Boyaniwsky said that the Burnham Institute has been the alpha tester for the assay. She added that Illumina has four beta sites for the miRNA array and is wrapping up testing now.