Last week Affymetrix became the latest microarray company to debut a catalog offering for microRNA expression profiling.
Developed under a partnership with Hatfield, Penn.-based labeling kit maker Genisphere, the firms' new microRNA solution for miRNA expression profiling includes an assay, a GeneChip miRNA array, an miRNA quality-control software tool; and Genisphere's FlashTag Biotin RNA Labeling Kit, which provides enzyme-linked oligosorbant assay-based quality control to monitor labeling efficiency, and does not require sample purification.
Affy is entering an miRNA array market that is marked by competition from a number of players such as Invitrogen, Exiqon, Agilent Technologies, Febit, LC Sciences, Illumina, Phalanx, and others, most of which have been selling miRNA chips for years.
For example, Exiqon and Invitrogen debuted their miRNA expression profiling offerings in November 2005 (see BAN 11/23/2005). Both Agilent and Febit began selling miRNA arrays in April 2007 (see BAN 4/10/2007, BAN 5/1/2007). Illumina joined the fray in September 2007, while, this month, Phalanx Biotech debuted its own miRNA array platform (see BAN 9/18/2007, BAN 3/10/2009).
Despite this competition, an Affy spokesperson claimed this week that the firm's interest in the miRNA array market is an extension of its gene-expression profiling offering, and argued that the market is poised to grow at a compound annual growth rate of 25 percent through 2015, leaving Affy plenty of room to profit on what it believes are several "key advantages" over its rivals.
Lisa English, director of integrated communications, told BioArray News that Affy chose to enter the market based on "market opportunity and customer feedback." She said that cancer researchers who use the company's GeneChip platform are "looking to integrate data generated from gene expression and genotyping studies with their miRNA data.
"Researchers also value the capability of running multiple applications on a single platform and this is another valuable capability for existing Affymetrix customers," English said. "This 'integrated genomics' approach to biomarker discovery is extremely powerful, providing critical new insights into the molecular mechanisms that underlie disease and drug response."
According to English, both academic and industrial customers have voiced their need to "combine data from different approaches," and the company expects that many of its "longtime expression customers will be interested in our miRNA offering, as well as customers who are new to Affymetrix," she said.
English also cited a report that forecasts robust growth for miRNA array sales over the next six years. According to the report, published by Frost & Sullivan last year, the total US miRNA expression-profiling market is expected to grow at a compound annual growth rate of 25 percent through 2015.
"An increased understanding of the role of miRNAs in biological pathways, such as those that underlie disease onset, drug response, and disease progression, is fueling this growth," English said. "MiRNAs have been shown to regulate gene expression by base-pairing with target messenger RNAs, leading to mRNA cleavage or translational repression," she said. "The scientific community is still developing a database of predicted miRNA target genes necessary to better understand gene regulation."
According to English, Affy hopes to pull ahead of competitors based on the performance of its assay, the popularity of its array platform, its quality control feature, and its comprehensive miRNA coverage of 71 organisms on a single array.
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Up to Date?
English said that GeneChip miRNA array content is derived from the Wellcome Trust Sanger Centre and University of Manchester-hosted miRBase version 11, in addition to probe sets targeting human small nucleolar RNAs and small cajal body-specific RNAs derived from the Natural Science Foundations of China-hosted snoRNABase and the Ensembl archive.
One potential issue facing Affy, according to competitors, is that miRBase v. 11 became available in April 2008 and had 6,396 entries. The database has been updated twice since, most recently this month, and now contains 9,539 entries. The quarterly updates of the database have allowed some firms to capitalize on their abilities to quickly synthesize new arrays (see BAN 9/19/2008).
"Every version of miRBase will contain new validated miRNAs and every miRNA in your experiment will increase your chances to find something," said Febit Chief Scientific Officer Peer Stähler last week. Febit announced that it was making miRNA Geniom biochips available with the content from miRBase v. 13 within hours up the database's upgrade.
"The difference between versions 11 and 12 was about 25 percent of all relevant miRNAs," Stähler told BioArray News. "If you start a study you don't know which miRNA will be available as a marker and which will give you a valuable result," he said. "If you want to optimize your chances to find something significant, you should use the most recent content."
According to Stähler, the miRNA profiling field is still developing rapidly with "hot papers" coming out weekly. "It's a fast-moving, relatively young field, but its moving into translational genomics and now there are quite good papers that show that clinical use is not far off," Stähler said. "I don't know who can afford to not access the newest content. If you have a platform where the cost for updating content is almost nothing, then there is no reason why you shouldn't update your platform."
Stähler said that the miRNA market is "quite competitive," and that his Heidelberg, Germany-based firm has to fight for market share with "at least 10 companies" who offer miRNA arrays to a growing number of customers, traditionally in the oncological research community, but increasingly among agricultural biotechnology firms and pharmaceutical companies.
To stay competitive, Febit plans to launch an miRNA expression-profiling assay capable of working with samples from formalin-fixed, paraffin-embedded tissue next month, Stähler said.
Likewise, Lars Kongsbak, CEO of Copenhagen, Denmark-based Exiqon, said that his firm's line miRcury miRNA arrays are kept up to date with the latest content. For miRBase 13, launched this month, "we have 96 percent coverage of the human miRNAs, plus another 435 miRNAs that are not yet in the database that we call miRPlus miRNAs."
According to Kongsbak, the miRNA market trend is "going towards total solutions" with customers requiring sample preparation, arrays, and qPCR from the "same provider to secure that the reagents provide for robust cross platform performance."
Konsbak told BioArray News this week that Exiqon recently upgraded its locked nucleic acid-enhanced qPCR portfolio for miRNA profiling and released new sample-preparation kits for RNA extraction designed to support work on FFPE samples.
While touting the freshness of the content of your platform is one marketing approach, other competitors choose to downplay the importance of staying up to date with the miRBase releases.
Luke Chen, vice president of business development at Phalanx, told BioArray News this month that most of the changes between versions 11 and 12 for miRBase involved an increase in the number of species, while "the increase in human, mouse, and rat miRNAs has actually not been that big." Like Affy, Phalanx's miRNA OneArrays are based on miRBase v. 11.
Affy's English said that though the company's catalog offering covers miRBase v. 11, its customers always have the option to order miRNA arrays featuring the most up-to-date content via Affy's MyGeneChip custom array program.
"To do this, customers simply download sequences from miRBase in a Fasta format and submit them to our bioinformatics services group for a new custom array design that includes the most up-to-date miRNA content," English said. "As genomes of new organisms are sequenced, and new miRNAs are discovered for those genomes already sequenced, the MyGeneChip program can deliver custom miRNA arrays tailored to a customer’s specific content and research needs."