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Agilent to Expand Gene Expression Menu with New Exon Array Offering

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This story was originally posted on Nov. 4.

By Justin Petrone

Agilent Technologies last week said it will soon launch arrays for exon analysis.

The new SurePrint G3 exon microarrays, scheduled to launch later this month, will enable researchers to examine alternately expressed exons, and are in line with Agilent's effort to build its portfolio in the gene expression market.

"This was developed to support exon analysis, because we know that one gene can give rise to multiple proteins through alternative splicing, said Stephanie Fulmer-Smentek, array and diagnostics applications manager in Agilent's genomics R&D group.

"We are basically building out our portfolio," she said. Exon arrays were the "one thing that was missing from our gene expression platform."

BioArray News discussed the new offering with Fulmer-Smentek at the American Society of Human Genetics annual meeting, held in Washington, DC, last week.

The exon chips are based on the company's higher-density, million-feature G3 format, which became available last year. In May, the firm introduced SurePrint G3 gene expression arrays, which include coding and non-coding RNA targets (BAN 5/25/2010).

Fulmer-Smentek acknowledged that Agilent "in theory" could have launched exon arrays prior to the launch of the G3 format, but said the higher density enables the company to do it in a "cost-effective manner."

Upon launch, Agilent's new exon arrays will contain catalog content for human, mouse, and rat in formats of four arrays per slide containing 180,000 features each, and two arrays per slide, containing 400,000 features each. Agilent will also provide custom options for the human, mouse, and rat SurePrint G3 exon products, the firm said. Custom formats include 8x60K, 4x180K, 2x400K, and 1x1M arrays.

RNA is prepared for hybridization using Agilent's Low Input Quick Amp WT labeling kit for whole transcript labeling, and data is analyzed using the firm's GeneSpring GX 11.5 bioinformatics system, the company added.

Agilent faces competition in the exon analysis space from other array firms, like Affymetrix, which has sold exon-level analysis products for five years, as well as from companies that offer exon-level analysis on next-generation sequencing platforms, such as San Diego-based Illumina.

Fulmer-Smentek said that the company is targeting both exon array and sequencing customers with the new offering, noting that some users are "dissatisfied" with the performance of other array-based approaches, and could switch to Agilent's new chips.

"There are also customers who are doing discovery with next-generation sequencing, doing exome sequencing, and want to follow up on those studies, or if they are discovering novel transcripts that they want to add onto custom array," Fulmer-Smentek added.

While some firms have positioned digital gene expression as an alternative to array-based expression profiling, Fulmer-Smentek said that arrays have advantages over sequencing-based approaches.

"When it comes to look at something in many samples, arrays are still easier to use," Fulmer-Smentek said. "Our arrays compare very well with sequencing and the data is easier to analyze, so in terms of throughput and cost, there are a lot of advantages to running expression arrays."


Have topics you'd like to see covered in BioArray News? Contact the editor at jpetrone [at] genomeweb [dot] com

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