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Agilent Rounds Out G3 Upgrade with High-Density Gene-Expression Chips

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By Justin Petrone

Agilent Technologies last week launched its SurePrint G3 gene-expression microarrays. The chips provide up to a million features per standard 1-by-3-inch slide, and are the latest of the array vendor's product lines to be updated to its new G3 format.

According to Agilent, users can use the chip to run up to eight samples on subarrays containing 60,000 probes each. In addition to offering whole-genome content on the array, Agilent's SurePrint G3 arrays now contain coding and non-coding RNAs, including long intergenic non-coding RNAs based on content from a partnership with John Rinn's lab at the Broad Institute, the firm said.

Agilent's density upgrade comes at a time when all other major array companies have made similar improvements to their platforms. Affymetrix, Illumina, and Roche NimbleGen have all launched 2-million-feature plus array products and have continued to add products to their menus in the new formats. Illumina, for instance, has pledged to deliver a 5-million-feature chip for whole-genome genotyping studies to the market by the end of this year (BAN 5/4/2010).

Sharoni Jacobs, Agilent's gene expression and miRNA product manager, told BioArray News that the content of the new arrays has been refreshed to include the latest builds of the human, mouse, and rat genomes.

"The arrays are transcriptome-based, meaning they are designed to the various transcriptome databases," including RefSeq, Ensembl, GenBank, Unigene, and RIKEN for mouse, Jacobs said. "Then the probes are aligned to the genome for annotation," she said. "For design, we used updated transcriptome databases, and our alignments are to the most current genome builds."

For the human and mouse arrays, Agilent added probes for lincRNAs in addition to the traditional mRNA targets. Jacobs said there are around 7,500 human lincRNA targets and approximately 4,500 mouse lincRNA targets included on the new arrays.

According to work published by the Rinn lab, lincRNAs share functional associations with cell-cycle regulation, proliferation, RNA binding proteins, and chromatin remodeling complexes, and may be useful targets for cancer and stem cell studies.

Agilent began upgrading its platform to support higher-density chips two years ago. In June 2008, it introduced a new scanner capable of imaging the higher-density chips with 2-micron resolution, and in September that year, it made available a new data analysis platform to support the G3 platform.

Last year, it rolled out a series of G3 arrays for comparative genomic hybridization studies and copy number variation analysis (BAN 3/3/2009). It also launched G3 arrays for chromatin immunoprecipitation (ChIP)-on-chip studies.

According to Jacobs, by releasing G3 chips for expression, the firm has completed upgrading its array products to the new format. "Most applications are now available on the SurePrint G3 arrays," she said. "We don't have firm plans to expand G3 to other applications at the moment."

Jacobs confirmed that users will have to upgrade to the company's new scanner if they want to use the new G3 expression chips. "Customers need access to Agilent’s High Resolution C Scanner when using SurePrint G3 arrays for any application," she said.

It is possible for customers to upgrade an existing B scanner, which allows 5-micron resolution, to gain the higher resolution needed to image the new chips, or to purchase a C scanner, she said.

Agilent said its new chips are available in catalog and custom configurations. Customers can use the firm's eArray online tool to design custom arrays. When combined with Agilent's Low Input Quick Amp Labeling Kit, also new, sample input for the G3 Gene Expression Microarray is as low as 10 nanograms for the 8 array-by-60,000-probe format, the firm added.

The higher density and multiplexed formats should actually provide a decrease in price per sample, Jacobs said, even though customers are able to survey more probes on more arrays per slide. Jacobs said that the 8x60K arrays provide an approximate 10 percent decrease in price per sample as compared to Agilent's 4x44K arrays for customers that purchase arrays only.

"Customers that are purchasing both arrays and reagents, though, will get the benefit of buying arrays at about a third of the cost they were previously paying," Jacobs said. She did not provide pricing information.

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