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Agilent Launches Human 1B Chip, Software, and an RNAi Partnership

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Agilent this week introduced the second in its human microarray slides, and rolled out new software that allows automated scanning and data extraction of third-party 1x3 microarrays. Additionally, the company opened the curtain for a small peek at its array sales, and announced a partnership with Lafayette, Colo.-based Dharmacon in the red-hot RNAi sector.

So, as the summer began, and perhaps not coincidentally in time for the massive BIO conference in Washington, DC, Agilent introduced its sixth oligonucleotide array since the Chips to Hits Conference in October.

The company , generally regarded as the No. 2 manufacturer of microarray technology, also said that it has sold some 20,000 microarrays in the second quarter, an announcement significant to industry observers who try to measure array manufacturing numbers to track industry but usually are stymied in
their efforts as up until now, only industry leader Affymetrix released such granular data.

Barney Saunders, vice president and general manager for Agilent’s BioResearch Solutions unit, told BioArray News that the company’s manufacturing facility was operating on normal shifts.


“That’s just part of our capacity, we have a lot left,” he said. “If we need more, we just add more [chip] writers to build up new capacity. Business is robust and holding up very well for us.”

The Palo Alto, Calif.-based company on Monday rolled out its Human 1B 60-mer oligonucleotide array, as a partner to the Human 1A array introduced earlier this year, creating a set of arrays that contains probes for 36,000 genes, as well as open areas for the inclusion of additional custom content. The 1B chip, with 19,000 probes, contains content that focuses on rare human genes, and includes some genes from the Incyte LifeSeq Foundation sequence database. The 1A probes are based on genes from publicly available databases. Both are manufactured in situ, using the company’s ink-jet production process.

The 60-mer probe length follows a developing trend among microarray researchers who are exploring longer-length oligonucleotides as a replacement for cDNA-based probes for higher sensitivity and markedly lower development costs.

The Agilent arrays will be sold separately, with each packaged in a five-array kit containing a hybridization protocol and a CD with design files and annotation information.

New software

The company also introduced version 7.1 of feature extraction software. Agilent is highlighting the speed of the application and its interoperability with third-party 1x3 arrays. According to a statement, the software extracts microarray data in less than 10 minutes per array and introduces new statistical models and algorithms to screen out false positives and false negatives.

The software will be offered with Agilent’s 48-slide automated carousel as a combination scanning system that will include a full day of on-site training.

The software was designed to read as many third-party array formats as possible: “I would hesitate to say everyone, there may be one out there that we didn’t get,” Saunders said.

RNAi and Microarrays

Agilent and Dharmacon, which offers a custom small-interfering RNA design service based on its computing platform, will collaborate on research on the broader cellular effects of RNAi and its application in drug discovery research, the companies said in a joint statement. Dharmacon researchers will silence select genes in a variety of cell systems and then measure the systemic effects by Agilent microarrays. Agilent will follow with additional data analysis to assess global effects on gene expression.

The research will also help Agilent tune its array systems for this application.

Financial details were not disclosed.

“Dharmacon is a clear leader in RNA synthesis for gene silencing,” Saunders said. “They have done a lot of work on their algorithm. We think we can make a distinct contribution.”

Looking Forward

While Agilent now has significant portions of the Human genome on two chips, how far away is that content from being put onto one chip?

Saunders would not say. “If the customers see it as a need to be met, I’m sure industry will respond in due course of time,” he said.

He was also noncommittal as what new organisms might be selected for catalog arrays and any peek at possible automated high-throughput systems.

He was optimistic about the future of gene expression analysis.

“In the long term, gene expression analysis will be a critical technology in the whole life sciences field for many years to come, he said.

“In the future, there will be better validation of data, easier workflows, cost reductions, higher throughput, and automation.

Agilent’s vision is producing a robust end-to-end solution and automation is going to be a key part of the future.”

–MOK

 

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