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Affy, NuGen, and Beckman Pact Underscores Growing Interest in Automated Sample Prep

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Agencourt Bioscience, NuGen Technologies, and Affymetrix Clinical Services Laboratory last week launched a product for the automated isolation and target preparation of RNA from whole blood samples stored in blood tubes.
 
The automated sample prep was originally designed for use in Affy's CLIA-approved clinical lab, but is now also available to customers using Affy's GeneChip technology in internal R&D including pharmas and biotechs, according to the firms.
 
While at first sight the bundling deal seems like a springboard to increase pharma sales for the three principal companies, it also comes at a time when interest in sample prep — often eclipsed by interest in upgrades in content or density — grows in the microarray community.
 
The product uses Agencourt's RNAdvance blood chemistry and NuGen’s Ovation whole-blood technology for RNA amplification and labeling, which are carried out with Agencourt's RNAClean kit and its SPRIPlate 96R magnet plate. 
 
Automation of the sample prep process is then performed with Beckman Coulter’s ArrayPLEX application on its Biomek FX liquid-handling workstation. Customized methods for use with Affy's technology were developed by Array Automation, a joint venture of Beckman Coulter and Affymetrix, the companies said.
 
According to a spokesperson for Beckman Coulter, which owns Agencourt, the automated offering is not restricted to Affymetrix and was designed to meet an "increased need” for automated sample preparations “in the future” for clinical research, where customers need to study larger populations in less time and with less manual intervention.  
 
"Others will want to establish their own testing sites and will be able to duplicate this automated solution in their laboratories, “ the spokesperson told BioArray News in an e-mail last week. “Many leading pharmaceutical companies are already using Agencourt and Beckman Coulter solutions for sample prep in their drug discovery research."
 
Cynthia French, vice president and director of ACSL, told BioArray News in an e-mail this week that developing an automated sample-prep workflow was a prerequisite for establishing the labs, which she said were functional at the end of last year.
 
ACSL is "focused on analyzing a high-volume number of clinical samples in an efficient manner," French wrote. "The protocol with Agencourt and NuGEN is one of the methods established in the lab to address this need."
 
French wrote that a "sample-prep solution is a critical component for our standard offering and it is included with all of our test methods."
 
Additionally, she wrote that Affy could spin similar methodologies out of ACSL as they are developed, perhaps partnering with other firms in a similar manner.
 
"The laboratory only recently opened its doors in Q4 2006 and quickly began the validation of the various methods for our menu of molecular diagnostic patient and clinical trial testing services," French wrote. "This is one of the initial offerings of the lab and we expect to add methods based on customer demand."
 
A 'Highly Contentious' Issue
 
As Affy, NuGen, and Agencourt work together to make the automated sample-prep products and methodology available to interested pharma customers, many in the array industry as starting to take note of sample prep as an area for debate on what kinds of methods and protocols should be used. Sample prep has perhaps grown in importance because more and more clinical laboratories are using array-based tests.
 
Stephen Hewitt, the director of the tissue array research program at the National Institutes of Health, told BioArray News this week that sample prep is a "highly contentious issue" and that those that are beginning to offer array-based assays in the clinic are painfully aware that "if there's junk going in, there will be junk coming out of the assay."
 

"This is one of the initial offerings of the lab and we expect to add additional methods based on customer demand."

However, Hewitt said blood samples were probably among the easiest to introduce to an automated format, whereas sample prep for other kinds of samples, such as formalin-fixed, paraffin-embedded biopsy material, would prove difficult to automate and could ultimately provide data for pharmaceutical companies engaged in the biomarker discovery process that the US Food and Drug Administration could, down the line, find highly questionable.
 
Juraj Petrik, the head of microbiology R&D at the Scottish National Blood Transfusion Service, has been involved for several years on a project to develop a protein array-based multiplex assay for blood screening and typing. The array is being designed to replace slower, single-plex tests that are currently employed for screening at SNBTS.
 
Petrik told BioArray News in an e-mail this week that when it comes to using blood sample, there are two opposing trends in the sample-prep arena that are defined by cost and efficiency. "One is to keep assays as simple and cheap as possible, especially for high-throughput applications," Petrik wrote.
 
"Another is to design sophisticated assays that include a sample preparation and concentration step," he wrote.
Petrik wrote that currently, labs might be able to get by with current automated methods, like those offered by Affy, NuGen, and Agencourt.
 
However, he said in the future it might make sense to develop a sample-prep chip that could be more efficient than current tools.
 
"If the microarray-based assays proved robust enough not to require special sample processing and preparation steps that would be a clear advantage for high-throughput assays," Petrik wrote. "In the long term, as testing becomes more and more complex I think there would be a case for a sample-preparation chip," he added.
 
According to Petrik, a sample-prep chip would "ideally separate cells in the first step, subsequently separate red cells, white cells and platelets, and then extract nucleic acid from plasma/serum and white cells, and after albumin removal separate proteins into antibodies and the rest."

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