A recent agreement between ExonHit Therapeutics and Agilent Technologies that will enable ExonHit's splice variant arrays to be marketed through Agilent's worldwide distribution channels reveals that the array industry's biggest players are taking the splice array market more seriously.
The deal moves the splice arrays from a service offering to a catalog offering and puts Agilent up against a line of whole-genome exon arrays that Affymetrix plans to release later this year, in what may become a battle to provide access to the human transcriptome.
"Scanning the full transcriptome ... will enhance our understanding of disease alterations for therapeutic target identification or increase the scope of discovery for potential biomarkers," Laurent Bracco, ExonHit's chief operating officer, told BioArray News last week.
ExonHit launched its SpliceArray service in February, pledging to make splice variant arrays available for several distinct gene families, including the ion channel, G-protein coupled receptor, and nuclear receptor and co-regulator gene families (see BAN 2/9/2005).
The service provides chips that can monitor the expression of alternatively spliced exons at levels previously unattainable by standard microarrays, according to the company. While the chips are manufactured by Agilent Technologies, ExonHit provides the content. Each family of genes is available on one microarray.
"Our technology lets us put everything on one chip; why would we want to limit a researcher's chance of discovering the complete answer?"
ExonHit claims that the technology will produce a more thorough understanding of how splice variants in an RNA sample can affect data, and has recommended its service to pharmaceutical companies (see BAN 5/25/2005).
To date, the Paris-based company has only been able to offer the SpliceArray service out of its American office in Gaithersburg, Md., however.
The new agreement, announced last week, will now allow researchers worldwide access to ExonHit's SpliceArray chips through Agilent's distribution network, and, according to representatives from both Agilent and ExonHit, reflects a growing demand for the arrays.
"We collaborated with ExonHit to develop the platform and a service model made sense when we were unsure of demand," Agilent spokesperson Stuart Matlow wrote in an e-mail to BioArray News last week. "It turned out that customers developed the capability to do their own alternative splicing experiments, prompting the switch to a product-based model."
Matlow said that while Agilent could not release sales data, "demand is strengthening for alternative splicing arrays and other microarray applications."
ExonHit's Bracco said that demand had been growing, as evidenced by ExonHit's "increased number of customers and by the scientific reports in the past month regarding alternative splicing microarrays."
He added that ExonHit's chips "are manufactured on standard 22K or 44K Agilent formats and are compatible with today's scanner and feature extraction software.
"Traditional data analysis software can also be used downstream of expression data extraction. We have also developed a specific analysis tool that can basically consolidate expression data at the splice event level or at the gene level. This tool will be distributed with the purchased microarrays," Bracco said.
Agilent's Matlow said that the company would make sure that "as ExonHit's application evolves, [Agilent] will make sure that the rest of the platform evolves with it."
Agilent will also play a larger role in marketing ExonHit's arrays now that they will be part of its catalog, according to Matlow.
"We will play an active role in co-marketing the ExonHit arrays," Matlow said. "This includes gathering feedback from customers and conveying it to ExonHit for consideration in future designs."
Bracco said that ExonHit would continue to control all of the content that goes on its arrays but that Agilent's sales force will play an active role in promoting SpliceArrays.
"Specific training has been initiated [and] SpliceArrays are also promoted through Agilent specialized workshops," Bracco said.
Bracco said that the company will continue to offer SpliceArray-based services through its Gaithersburg, Md., office, and that the company plans to increase the number of gene families available and add other arrays as well.
"We plan on expanding the product line with additional thematic SpliceArrays. We also believe that custom SpliceArrays will interest many scientists," said Bracco. A whole-genome mouse splice array is being planned for release later this year (see BAN 6/8/2005).
With Agilent's sales and marketing muscle behind ExonHit's SpliceArrays, the duo should be able to handle increasing demand for chips that enable researchers to study the transcriptome.
However, can Agilent's sales and marketing and ExonHit's content compete with the impending release of Affymetrix's own line of exon arrays?
According to John Blume, vice president of RNA products at Affy, the company will "commercially release [its] GeneChip Human Exon 1.0 ST array within the next few weeks."
Affy's human exon array can "detect over 1 million predicted and empirically identified exons with over 6.5 million probes" according to Blume, and "comparable mouse and rat GeneChip exon arrays" will be released before the end of the year.
"All of these arrays will be available worldwide. We are developing a whole family of products for analysis of transcript diversity and will extend the exon array product line to include other species in 2006 and beyond," Blume told BioArray News.
Like Agilent and ExonHit's chips, Affy's exon arrays will also run on existing equipment, in this case the Affymetrix GCS3000 7G system.
When it comes to the budding competition between the two companies, Affy claims that the sheer volume of the exon probes will "provide the best possible tool for researchers studying the complexity of mRNA transcript expression," Blume said.
The methods of interrogating the transcriptome differ as well between the two companies. On one hand, Affy claims that providing all the exons on one array will be the most beneficial to customers.
"Our technology lets us put everything on one chip; why would we want to limit a researcher's chance of discovering the complete answer?" Blume said.
Yet ExonHit is confident that the specificity of its arrays will make it more attractive to customers looking at the transcriptome than Affy's exon arrays, according to Bracco.
"Without knowing what will be the final features of a yet-to-be-marketed array, I [can] only comment that exon body probes will not be specific for a large number of splice variants such as the ones displaying exon skipping events," Bracco said.
"Junction probes will be required to provide a direct measurement of the expression level for these variants. Such junction probes are present on SpliceArrays."
Justin Petrone ([email protected])