Affymetrix will underwrite the design fees required to produce the new arrays, putting industry-standard technology within reach of virtually any research community
Affymetrix has announced that it is launching the GeneChip Consortia Design programme, a collaborative initiative that will bring Affymetrix and plant and animal research communities together to create novel whole-genome arrays.
Under the new programme, Affymetrix will underwrite the design fees required to produce the new arrays, putting industry-standard GeneChip technology within reach of virtually any research community. Genomic community groups have already embraced this new initiative and there are currently plans to produce 12 new array designs under the Consortia Design programme this year: wheat, rice, poplar, corn, pig, cow, chicken, grape, soy, tomato, cotton, and citrus.
"We have selected Affymetrix as our microarray platform of choice for the vitis (grape) microarray consortia because Affymetrix GeneChip arrays are robust, reliable, easy to use, highly reproducible, and cost-effective," said John Cushman, professor of biochemistry at the University of Nevada, Reno and a member of the International Grape Genome Consortia.
"Affymetrix arrays use 11 probe pairs of 25 mers per transcript giving multiple independent measurements of hybridisation.
"Multiple probe pairs offer the best specificity without compromising sensitivity, and are more accurate than a single longer oligo measurement.
"Not only will the data quality be extremely high, but a single platform within the vitis community will allow any number of data comparisons to be made within and across laboratories".
Affymetrix has worked closely with genomic community groups worldwide for several years, developing drosophila, pseuodomonas, arabidopsis, barley, xenopus and zebrafish whole-genome arrays via the catalogue and CustomExpress programmes.
By waiving the array design fee and helping these groups with sequence selection and other design issues, the Consortia Design programme will offer genomic community groups an opportunity to consolidate their sequence data on the Affymetrix industry standard array platform.
"The rapidly growing number of sequences for a wide variety of organisms, the increasing popularity of the GeneChip array system and the success of our other collaborative designs contributed to our decision to start the consortia program," said Lianne McLean, director of gene expression marketing at Affymetrix. "Perhaps the biggest factor is the way that our arrays are being embraced by the academic community.
"Over 2000 peer reviewed papers have been published using Affymetrix technology, with over 1000 published just last year alone".
Past consortia designs have shown that Affymetrix collaborative design process helps ensure that the content on the array is as comprehensive as possible and meets the communities' needs. Additionally, engaging the worldwide community in the design effort has prompted researchers to include previously unpublished EST data, increasing the total amount of information available and improving the quality of the final design.
All content and annotations from the Consortia Design Program arrays will be hosted in the NetAffx data analysis centre.
This online resource integrates access to the data generated by Affymetrix's GeneChip arrays with biological information available in a broad range of public and private databases.
Regular annotation updates will be provided by Affymetrix at no cost to these communities.
