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Affy Deems Trio of Informatics Packages Exon Expression Compatible in Time for Chip Launch


Affymetrix has stamped three bioinformatics packages with its new "GeneChip Compatible" label under a new category created for the human exon arrays that it launched this month, according to an Affy official.

Tarif Awad, a senior scientist at Affymetrix, said last month that the company was developing a way to let consumers know which bioinformatics packages would be compatible with expression data gathered using its Human Exon 1.0 ST Arrays.

To do this, Awad said at IBC's Chips to Hits conference in Boston in September, the company decided to create an "exon expression category within compatible data packages" under the GeneChip Compatible Applications Program that it launched last month (see BAN 9/14/2005).

Awad made the announcement the same week that Affy endorsed 20 bioinformatics tools through the GeneChip Compatible program, and shows that the company is doing more to partner with firms in the data analysis space.

The three software packages that will be included in the new exon expression category will be Partek's Genomics Solution, an upgrade for Stratagene's ArrayAssist, and an exon array module called X-ray that will be available to users of Biotique's Local Integration System (BLIS).

According to Awad, Stratagene and Biotique's exon expression compatible features should be ready this month, while Partek's analysis software is ready to go.

During his presentation at Chips to Hits, Awad demonstrated the need for such a category by discussing the difference between the new exon chips and Affy's standard Human U33 2.0 plus array.

The new Human Exon Array has 5.3 million probes compared to the U33's 1.3 million probes, Awad explained, as well as 1.4 million probe sets instead of roughly 54,000 probe sets. 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.

However, Awad said that the high-density exon arrays should not be seen as a replacement for the company's "classic 3' arrays" and likened the greater density and feature size to "having another lens on your microscope." At the same time, Awad said that users will need bioinformatics packages that can handle the higher-density data.


Stephen Sanders, chairman and CEO of Biotique Systems, said his company is currently putting the final touches on a new software module called X-ray that will enable users of its core BLIS offering to analyze and visualize exon array expression data.

However, Sanders told BioArray News last week that the company's target launch date of October could be moved forward. "It's still in development and we haven't tested it yet," Sanders said of X-ray. "We're probably in the alpha stage of development. We are still working on a back-end data structure for it. Those are the things that we are pulling together," he said.

"We are still in pretty good shape for a late October release of X-ray," he added.

When it does become available, Biotique's existing customers will be able to plug the X-ray module into their existing BLIS systems, Sanders said.

He said that the new module would fit into similar offerings the company has added to BLIS in the past by allowing "customers to tailor their system to their needs, instead of buying a huge system that may have functionality that they are not using."

He added that the new effort to provide technology that could handle Affy's exon array data will push Biotique into new markets.

"We've talked to Affy about this as well, and they let us know that the first users of these arrays would be government, academic-oriented users."

While the company's core customers have traditionally been "large pharma, biotech, and [agricultural] tech companies," X-ray will now enable government and academic researchers to use BLIS through an ASP model, Sanders said. "We've talked to Affy about this as well, and they let us know that the first users of these arrays would be government, academic-oriented users," said Sanders.

Stratagene and Partek

Awad said during his presentation that he expected Stratagene to upgrade its ArrayAssist to handle exon array data some time this month, but representatives from the company declined to comment.

ArrayAssist is a single-user desktop software package for analyzing microarray data from multiple microarray platforms, which Affy already includes on its GeneChip Compatible website under the "expression" category.

The only software offering that is ready for use with the exon chips, according to Awad, is Partek's Genomics Solution, which he called "the most powerful array data-analysis package out there" that's "ready now."

Partek CEO Tom Downey told BioArray News via e-mail following the Chips to Hits conference that he "didn't expect" Affy to endorse his product "officially" since Partek is just one of the 20 companies in the GeneChip Compatible program, but that Partek could "apply rigorous statistical methods to very large experimental data such as that produced by current, and soon-to-be-released Affymetrix GeneChips."

Downey said that that his company has "very close interactions with the Partek users at Affymetrix who have given us great feedback that have helped us tune Partek GS to work very well for analysis [of] GeneChip studies."

As part of the greater integration in marketing, Downey will host a web seminar on Affymetrix's website next week to demonstrate Partek's Genomics Solution package.

— Justin Petrone ([email protected])

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