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For WTCCC, Agilent Will Provide Custom Chips

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Agilent Technologies will provide custom, whole-genome copy number variation-focused arrays to the Wellcome Trust Case Control Consortium, which will use them in the second phase of its 19,000-sample study to identify genetic variants influencing disease susceptibility in a variety of rare and common diseases.

Specifically, the consortium will attempt to link genes to tuberculosis, coronary heart disease, types 1 and 2 diabetes, rheumatoid arthritis, Crohn's disease, bipolar disorder, autoimmune thyroid disease, ankylosing spondylitis, multiple sclerosis, breast cancer, and hypertension.

As part of its deal with the group, Agilent will design and fabricate the custom CNV chips, printing two arrays of 105,000 probes each per slide. Oxford Gene Technology, an

Agilent certified service provider, will use Agilent's Velocity 11 Bravo robot to run the samples at OGT's lab.

For Agilent, the high-volume deal will enable it to hone a CNV-focused microarray product line scheduled to launch later this year. It also gives the Santa Clara, Calif.-based company the opportunity to iron out the protocol for high-throughput, automated array processing.

"We expect that enhancements to the comparative genomic hybridization workflow demonstrated in this project, such as the use of the Velocity 11 Bravo System and the use of a plate for purification, will facilitate widespread use of Agilent CGH/CNV microarrays in high-throughput environments," says Yvonne Linney, Agilent's vice president and general manager of genomics.

"Agilent also plans to provide a very high-resolution CNV-focused catalog array with 1 million features using data from public databases and Agilent's own and collaborative CNV research," she says.

Matthew Hurles, a geneticist at Wellcome Trust, said in a statement that the WTCCC "aims to characterize [the] most common structural modifications of DNA that may play a causative role in these diseases."

Justin Petrone

Microarray Notes

DARPA has granted CombiMatrix $250,000 for proof-of-concept research to find new uses for the company's microarray technology, including label-free detection systems for use in diagnostics, chemical measurement, and chemical agent detection.

Asper Biotech, an Estonian biotechnology company, has obtained a license to commercialize  a new method for SNP-genotyping called arrayed primer extension-2 from the Estonian Biocentre.

Iowa-based Integrated DNA Technologies has completed the expansion of its 21,500-square-foot European oligonucleotide production facility in Haasrode Research Park in Leuven, Belgium. The facility will allow it to provide better services for its customers in Europe, the Middle East, and Africa.

Datapoint

$342 million
Illumina raised $342.6 million in proceeds from its public stock offering this August.

Funded Grants

$1,199,769/FY 2008
Microarray Center for Research on the Nervous System
Grantee:  Dietrich Stephan, TGEN
Began:  August 1, 2005; Ends: May 31, 2010

This Affymetrix Center of Excellence offers a platform to conduct research on the nervous system using microarrays. TGEN will provide assistance with experimental design, data generation, data interpretation, and data dissemination. New research goals include having scientists submit tutorials and projects online, review by an expert IRC, and data warehousing with a six-month timed release to the public.

$291,274/FY 2008
Universal, Compact Combinatorial Microarrays for DNA Binding Site Discovery
Grantee:  Martha Bulyk, Brigham and Women's Hospital
Began:  July 26, 2006; Ends: June 30, 2009

In this project, Bulyk will develop the use of compact combinatorial DNA microarrays in protein-binding microarray experiments in order to identify all possible DNA binding sites of sequence-specific transcription factors. She will also determine the binding affinities of all possible DNA binding sites for 15 S. cerevisiae transcription factors, as well as evaluate the utility of binding affinity data for improved prediction of in vivo binding sites.

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