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Affy Inks Deal with Beckman for Custom Tools

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Affymetrix and Beckman Coulter have partnered to create an automated tool and protocol for genomic research that will pair Beckman's liquid-handling instrumentation with Affy's menu of array-based assays.

Under the terms of the deal, Affy and Beckman will co-develop Affy-specific configurations for Beckman's Biomek FX Dual Arm Multichannel-Span 8 Liquid Handler. The companies claim that the combination of the Biomek with Affy's existing array cartridge platform as well its newer GeneTitan instrument will provide a standardized system containing all of the components necessary to run Affy genotyping and gene-expression assays.

According to Affy, the deal with Beckman will help fill a gap for customers performing higher-throughput studies.

It also comes at a time when other array vendors are looking to provide standardized target--preparation options for their customers as the size of projects increases. Agilent Technologies, for example, said recently that it plans to launch an automated liquid-handling workflow in coming months.

Launched last year, the GeneTitan enables users to run expression-profiling assays in array plates designed to process 16, 24, or 96 samples. Now, the chip maker plans to launch next-generation genotyping assays for use on the system this fall. Unlike the gene-expression assays which contained legacy content, Affy will enable users to survey newly generated catalog and customizable content using its genotyping assays as part of what both Affy and its rivals predict will be a second round of large genome-wide association studies.

Being able to streamline the front end of its assay workflow is therefore "very important" for Affy, according to President and CEO Kevin King.

"With automated target prep robotics in front of our GeneTitan System, our customers will benefit from walk-away automation from prepared samples all the way through array processing and data generation," King said in a statement.

– Justin Petrone

Microarray Notes

Exiqon plans to outsource the manufacturing of all of its research-related products, including its microRNA arrays, by the beginning of next year. The move is part of restructuring to cut costs and reach profitability.

Kinexus, a 10-year-old proteomics company based in Vancouver, BC, will begin offering customers the ability to screen kinases using its internally developed protein kinase chip. The microarray will include at least 200 different human protein kinases.

Researchers at the University of Dublin's Smurfit Institute of Genetics compared chimp and human protein and DNA sequences to identify three human genes that lack orthologues in other species. The work, published in Genome Research, suggests that the human genes evolved from non-coding DNA.

Datapoint

$6.2 million
New funding raised by WaferGen Biosystems, maker of gene expression and genotyping systems.

Funded Grants

$370,800/FY 2009
Development of RIP-Chip methods and tiled arrays to identify functional elements
Grantee: Michael Whitfield, Dartmouth College
Began: May 1, 2008; Ends: Apr. 30, 2011

Whitfield will use recombinant RIP-chip to study how RNA-binding proteins mediate gene expression on a genome-wide scale. He will identify the cis-acting regulatory sequences in mRNAs bound by specific RNA-binding proteins by using limited nuclease digestion and tiled mRNA arrays, and then will determine which miRNAs associate with the argonaute family of proteins.

$181,024/FY 2009
Nonparametric Analysis of Reverse-Phase
Protein Lysate Array Data
Grantee: Jianhua Hu, University of Texas MD Anderson Cancer Center
Began: Aug. 1, 2009; Ends: Jul. 31, 2011

To enable more reliable analysis of protein lysate arrays, Hu will use a "monotone nonparametric response curve to all samples on the same array," according to the abstract. This includes "modern shrinkage ideas in statistics" to improve quantification and using "wild-bootstrap" to assess uncertainties in protein concentrations.

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