Following a trend in the array space of introducing ever higher-density chips, Agilent Technologies last week said that it intends to debut a higher density version of its array platform this summer, which at that time will become available for all the applications Agilent offers, excluding microRNA expression.
Agilent currently sells arrays containing 244,000 features per chip, with multiplex array formats of two, four, or eight arrays per 1 inch x 3 inch slide. According to Jay Kaufman, senior marketing director of genomics at Agilent, by the second or third quarter, Agilent will begin selling chips containing 1 million features per array, with the same multiplex formats available.
Kaufman said the main benefit of the chip will be a reduction in cost per data point compared to Agilent’s current arrays. The company also said it believes that higher-density chips are amenable to emerging applications, such as copy number variation measurement.
“It will enable new applications like [copy number variation, and] accelerate our already rapid market share gains in mature applications like gene expression,” Kaufman told BioArray News in an e-mail last week. “By leveraging the multiplex format in conjunction with the higher density we will be able to continue to offer increasing value to our customers.”
Agilent is timing its upgrade with similar density upgrades across the industry. Last week, for instance, Illumina announced that it plans to debut this year two new chips in a new high-density format called HD that enables the production of 2.3-million-feature arrays (see BAN 1/8/2008
Roche NimbleGen, an Agilent rival that similarly sells chips for applications such as comparative genomic hybridization, chromatin immunoprecipitation (ChIP)-on-chip, and DNA methylation studies, is also in the process of upgrading its chips to a new 2.1-million-feature format called HD2.
HD2 arrays are already available from NimbleGen for CGH and ChIP-on-chip analysis of eukaryotic organisms. Last week, NimbleGen spokesperson Joleen Rau said that the firm plans to upgrade its expression array line to HD2 this quarter. Specifically, 12-plex arrays will become available that contain a dozen 135,000-feature arrays per well, Rau told BioArray News
(see BAN 1/8/2008
Luke Dannenburg, NimbleGen’s epigenetics product manager, told BioArray News
in November 2007 that his firm plans to expand its current DNA methylation product offering on 2.1-million-probe HD2 arrays by April in the form of whole-genome tiling and CpG island/promoter targeted arrays (see BAN 11/20/2007
While its rivals roll out new, higher-density arrays over time, Agilent has decided to introduce chips in the new format within a span of a few weeks. That means that 1-million-feature Agilent chips will become available for gene expression, CGH/CNV, DNA methylation, and ChIP-on-chip applications within the next six to eight months.
Kaufman said that Agilent will rolling out the new products over several weeks at the time of commercial launch and the firm is “still in the process of prioritizing which application areas will benefit most from higher density products and those will be the first to be released into the market place.”
Part of the upgrade includes a next-generation scanner that can read the new higher-density signal outputs from the chips. The scanner offers resolution of 40 pixels per feature. Customers with Agilent’s current scanner will be able to upgrade their system to scan the 1-million-feature arrays.
Agilent’s informatics software has also been upgraded to handle larger data files, though the “array formats, workflows, and protocols, including data analysis, will generally be the same as what our customers are using today,” Kaufman said.
According to Kaufman, two tools that will enable Agilent to introduce the higher-density arrays will be the firm’s SurePrint inkjet array fabrication technology and its eArray chip-design web portal, which will allow users to submit designs for custom arrays on the new high-density platform.
“Our manufacturing process and informatics tools give us an advantage here,” he said. “Since we have very reproducible high-quality data and are making changes to the entire system to maintain this data quality, we can easily port designs that we have for existing products to these new formats.
“Alternatively, we can use our existing designs as a foundation for higher feature count arrays and add content from eArray that has been pre-validated,” he said.
To ease the transition to higher-density chips, Agilent has initiated an early-access program that generates copy number data on the 1-million-feature arrays. According to Kaufman, the program will expand to other applications and additional customers in the coming months.
However, as it begins to push its new chips into the marketplace, Agilent will face competition from firms that offer already higher-density chips, including Affymetrix, NimbleGen, and Illumina. But Kaufman insists Agilent’s multiplex formats have helped the company compete in the array marketplace over the past few years, and claims its manufacturing process makes it stronger than higher-density rival chips, he said.
“It’s not simply a matter of number of features on the array as much as it is the quality of information that users obtain,” Kaufman said. “Due to our probe length and in situ ink jet based synthesis process, Agilent microarrays can use far fewer probes per variant, gene or genomic region to generate meaningful data.”
“There is a clear demand from the research community for ever more features in a cost-effective platform.”
According to Kaufman, the “flexibility of the inkjet platform allows users to broadly survey the entire genome or focus on a single chromosome or single gene if that’s what they want to do.”
For certified Agilent service providers, the higher-density chips are a welcome addition to Agilent’s array product line and come at a time when users are demanding higher-density products for applications such as CGH.
Some users welcome the density upgrade. “There is a clear demand from the research community for ever more features in a cost-effective platform,” Jim Woodgett, director of the microarray center at the University Health Network at the University of Toronto, told BioArray News this week. “The increased competition from companies in this space, driven by the promise of high-throughput sequencing technologies, is resulting in products that are changing the types of questions that can be asked.”
Woodgett added that UHN hopes the new products will also help in multiplexing samples for such users, further broadening the base of researchers benefiting from high-density arrays.
Neil Winegarden, head of operations at the UHN microarray center, said that the density upgrade will have other benefits for Agilent’s microarray business, especially because of the multiplex formats offered through Agilent. “While more content has its obvious uses, it is also important to realize that there are still many applications which simply do not require 200,000, 1 million, or 4 million features,” he told BioArray News.
“If Agilent is able to turn the new 1M feature array into an 8x244k array design they are going to have a real winner on their hands as it will again cut the cost of a whole genome gene expression analysis in about half,” said Winegarden.
John Jaskowiak, executive vice president of business and marketing at ExonHit Therapeutics, another Agilent certified service provider, agreed that the combination of 1-million-feature capabilities with the multiplex formats available through Agilent would benefit the platform.
“If one were to look retrospectively at Agilent’s product plan with the 244K format, they divided up the real estate on the glass slide so that customers could process more samples and drive their per price per microarray study down,” he told BioArray News this week. “When this becomes available ExonHit will be able to directly take advantage of this increase as we have requirements from customers to perform services using microarrays with greater genomic coverage and look forward to this new product.”
Both Winegarden and Jaskowiak predicted that the upgrade will enable Agilent to reach more customers doing CGH and CNV studies, and help the company develop additional new products.
“Having more genomic content on a microarray can be quite beneficial as there are some applications — like copy number variation, transcription-factor binding, chromatin structure determinations, alternative splicing — that can utilize more coverage and reduce the need for running multiple microarrays,” said Jaskowiak.
“I suspect that more features will also allow Agilent the ability to introduce new products, including more detailed products for exon-level analysis, perhaps resequencing, CNV, SNPs, et cetera,” said Winegarden. “Overall customers will likely benefit from more cost effective analyses as well as new products and technologies.”