Affymetrix has stamped three bioinformatics packages with its "GeneChip Compatible" label under a new category created for its Human Exon 1.0 ST Arrays, BioInform's sister publication BioArray News reported last week.
Tarif Awad, a senior scientist and statistician at Affymetrix, said at IBC's Chips to Hits conference in September that the company decided to create an "exon expression category within compatible data packages" under the GeneChip Compatible Applications Program that it launched last month [BioInform 09-19-05].
The three software packages in the new exon expression category are Partek's Genomics Solution, an upgrade for Stratagene's ArrayAssist, and an exon array analysis module for Biotique's Local Integration System (BLIS) called X-ray.
Partek's product is available immediately, while Biotique's X-ray module is scheduled for release by the end of the month. Awad said during his presentation that he expected Stratagene's upgrade to be available some time this month, but representatives from the company declined to comment.
Awad said that the new exon chips, which Affy officially launched on Oct. 3, present a number of data-analysis challenges. The new Human Exon Array has nearly 30 times the amount of information as the company's Human U33 2.0 array, with 1.4 million probe sets compared to around 54,000 probe sets on the U33. In addition, the new exon chips are much more densely packed, with only 5 microns between probes rather than the 11 microns between probes in the U33.
"To even be able to load that kind of data is one thing, but to be able to do statistics and visualization on it is another."
Tom Downey, president of Partek, told BioInform that "it's not just the size of the data, it's the number of variables" that makes the analysis of the exon arrays especially challenging. "To even be able to load that kind of data is one thing, but to be able to do statistics and visualization on it is another," he said.
Downey said that the volume of data from the chips is only the "first level of complexity, and that requires software to be extremely fast, and extremely memory efficient."
The next level of complexity, he said, "is the statistical one in which one sorts out all the complex interactions between the multiple exons and the alternative splicing that's going on."
Because mechanisms of alternative splicing are still largely unknown, "Some of the statistics to analyze the interplay between the exon and the gene have yet to be developed," Downey said.
Nevertheless, noting that the microarray-analysis community needs to "crawl before we walk and walk before we run," he said that Partek is "certainly up and walking with these arrays." He said the company's software can identify exons that are differentially expressed, "but as to how does that puzzle then assemble into what each of the other exons within that same a gene are doing — that's something that we're actively working on."
Downey said that Partek GS can analyze up to around 500 of the exon arrays on a typical desktop PC "without any pre-filtering of the data." The company expects to increase that capacity to around 10,000 unfiltered exon arrays within the next six to eight months.
Stephen Sanders, chairman and CEO of Biotique Systems, said his company is currently putting the final touches on its X-ray software module, which will enable users of its core BLIS offering to analyze and visualize exon array-expression data.
Sanders told BioInform that that the company is aiming for a late-October release of the software, but cautioned that it could be later because it is still being tested.
Biotique launched BLIS in 2001 as a data-integration platform and developed its first gene-expression module, called BEAM (Biotique Expression Analysis Module) in 2002 in a collaboration with Affymetrix [BioInform 09-09-2002].
Sanders told BioInform that although the firm initially opted not to address the gene-expression analysis market, Biotique co-founder John Burke has been developing a tool for alternative splicing analysis for the last four years. Sanders said that the company considered commercializing the software earlier, "but there was no market for it. Nobody was making the arrays."
Sanders said that X-ray will initially be targeted at existing BLIS customers, but the company is considering making the tool available to academic customers through an ASP model — a bit of déjà vu for the two former DoubleTwist execs. While admitting that he and Burke "still have burnt fingers" from the failure of the ASP model at DoubleTwist, Sanders said that the two have given the idea quite a bit of thought and think that the X-ray application "can be well served" in that format.
"I think it's a great way to serve the application in a lighter manner that will be more affordable for academic users," Sanders said.