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Completing Platform Upgrade, Agilent Launches High-Density CGH and CNV Chips and Promises More

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Agilent Technologies this week rolled out its SurePrint G3 microarray platform, which contains up to one million probes on a standard 1x3 inch glass slide — up from 244,000 probes on the last version of its chips.

Initial applications available in the G3 format are for comparative genomic hybridization and copy number variation, but Agilent has pledged that all of its array-based applications — which include gene expression, microRNA expression, methylation, chromatin immunoprecipitation, and others — will eventually be available on the higher-density chips.

For Agilent, the debut of SurePrint G3 caps a year of upgrading its microarray platform. In June, the Santa Clara, Calif.-based company introduced a new scanner capable of imaging the higher-density chips, and in September, it made available a new data analysis platform to support the G3 platform.

The density upgrade also comes at a time when all other major array companies have made similar improvements with their platforms. Last year, for instance, both Illumina and Roche NimbleGen launched 2-million-feature platforms, and have continued to add products to their menus in the HD formats.

The SurePrint G3 microarrays for CGH/CNV are available in four standard formats: a single million-feature array per slide, a two array by 400,000 feature format, a four array by 180,000 feature format, and an eight array by 60,000 feature format. The company offers a catalog CGH microarray for each format as well as custom formats, and claims that by providing multiple arrays per slide, the platform "greatly reduces cost per experiment, enabling researchers to perform larger sample studies with the same budget."

Dione Bailey, Agilent product manager of CGH and CNV microarrays, told BioArray News this week that the company plans to "introduce SurePrint G3 arrays for all other array applications that we support," though the firm has "not released timelines for other SurePrint G3 array launches." To support the rollout of the new platform, the company has "also added additional microarray writing equipment" to its manufacturing facility in Santa Clara.

The density upgrade is accompanied by an increase in price. Though the density of Agilent's arrays has quadrupled, its average slide price should increase by around 20 percent, Bailey said. Agilent does not disclose the pricing of its arrays on its site, though several core labs are currently offering its 244,000-feature human genome CGH chips for between $600 and $800 per chip, depending on the number of arrays per kit.

For example, Baylor College of Medicine charges $3,250 for a kit of five 244K CGH arrays, a price of $650 per slide. The Sidney Kimmel Comprehensive Cancer Center's DNA Microarray Core Facility at Johns Hopkins University currently charges $700 for a 244K Agilent CGH array.

To support the rollout of the new platform, Agilent has made several upgrades to its array system over the past year. Last June, Agilent released a new version of its DNA Microarray Scanner that allows users to scan array images at up to 2-micron resolution. Jeffrey McMillan, the firm’s workflow product manager, said at the time that Agilent decided to launch the new scanner ahead of the new arrays in order to give customers time to integrate the system into their existing workflows, and so that they would be prepared to handle the G3 chips when they hit the market (see BAN 6/10/2008).

In September, Agilent launched GeneSpring GX 10.0, which can analyze data from gene-expression, microRNA-expression, alternative-splicing, and RT-PCR experiments (see BAN 9/23/2008).

A final piece of Agilent's platform upgrade has been the integration of reagents acquired with its 2007 purchase of Stratagene into its microarray kits. By the end of 2008, Agilent was manufacturing most of its array labeling kits. In the past, it had to rely more on reagents sold by external providers (see BAN 7/8/2008).

According to Bailey, Agilent is not planning any further upgrades to support the G3 platform.

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Catalog CNV Arrays

As part of the launch of SurePrint G3, Agilent has also introduced a 2x400K CNV catalog array, which is designed to cover the known CNV regions from the Center of Applied Genomics-hosted Database of Genomic Variants.

Agilent said its new CNV catalog array provides high-density coverage of coding and non-coding regions, emphasizing known genes, promoters, miRNAs, CNVs, disease regions, pseudoautosomal and telomeric regions.

According to Bailey, the new CNV chip is a redesign of an earlier array that was a two-array set. "The new high-density technology allowed us to generate a more economic alternative in the form of a 2x400K array," Bailey said. "Many customers are interested at cataloging CNVs in healthy populations. This array serves that market."

An interest by customers in studying copy number variation has prompted array vendors to find different ways to tap into that market. One of Illumina's best selling products, for example, is its HumanCNV370-Duo DNA Analysis BeadChip. Affymetrix serves the market with its 1.8-million feature SNP 6.0 array, which contains 946,000 probes for the detection of CNVs. Roche NimbleGen sells 2.1-million probe CGH arrays, which are also available in 3 x 720K and 12 x 135K formats.

While Agilent's chips contain less features than some other platforms, Bailey claimed that Agilent’s microarrays have the "highest response to single-copy losses and gain, lowest false positive/false negative rates, and the best sensitivity/specificity" compared to its rivals. She also touted Agilent’s ability to print "any oligonucleotide sequences onto the array, as new sequences are identified through many of the next-generation sequencing projects," as providing the firm with a competitive edge.

Bailey added that more CNV-focused chips are in the pipeline for Agilent. She cited ongoing endeavors such as the Wellcome Trust Case-Control Consortium and the 1000 Genomes Project as efforts that will help to "update and define CNV content for further catalog CNV arrays."

In August, Agilent said that it would provide custom whole-genome copy number variation-focused arrays to the Wellcome Trust Case Control Consortium, which will use them in the second phase of its 19,000-sample study to identify genetic variants influencing disease susceptibility in a variety of rare and common diseases (see BAN 8/5/2008).

The company has also stated that the data from the 1000 Genomes Project could guide a new round of chip development. Yvonne Linney, vice president and general manager of Agilent’s genomics business, told BioArray News last June that as more sequence information enters the public domain, there will be a need for more focused studies (see BAN 6/17/2008).

“Many of these studies will be done using microarray approaches, primarily due to the need to focus on subsets of the genome, specific regions, or known mutations or biomarkers that are significant or thought to be causative in a given disease state,” Linney said. She added that the “substantial amount of data” generated from the 1000 Genomes Project will “result in more information that can be used to design the next generation of microarrays.”

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