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Influence of UKBB Deal at Play in Affymetrix's New 100K-Sample MVP Genotyping Contract


Affymetrix executives in recent weeks have predicted that the firm's agreement with the UK Biobank to genotype its 500,000-sample collection on its Axiom platform could sway other biorepositories to choose its arrays for similar projects.

That appears to have been the case in the decision of BioProcessing Solutions Alliance to use the Santa Clara, Calif.-based microarray vendor's chips to genotype 100,000 samples on behalf of the US Department of Veterans Affairs as part of the VA's Million Veteran Program.

The BioProcessing Solutions Alliance and the VA announced the project last week.

Andrew Brooks, the principal investigator on the project, confirmed with BioArray News that Affymetrix's work with the UKBB was a factor in the decision to work with the company, stating that the design and format of the arrays used to genotype the UKBB samples are "both big advantages for these types of activities."

Brooks added that the BioProcessing Solutions Alliance together with VA researchers will likely use the principles and features of both the custom UKBB arrays as well as Affymetrix's catalog Biobank Array to "create the latest generation of custom arrays geared at MVPs specific disease-related interests."

Both Affymetrix and Illumina last year introduced lower-cost, higher-throughput array formats targeted to biorepositories (BAN 10/16/2012). Though Illumina is perceived in general as being the dominant vendor in the genotyping array market, Affymetrix has tried to use its large genotyping deal with UKBB as a springboard to similar agreements with other biobanks.

Affymetrix announced the agreement with the UKBB in March. Last month, researchers involved in the project said that they had finalized the design of the array, which is focused heavily on the British population, and that Affymetrix had commenced genotyping of the samples (BAN 10/29/2013).

Mike Nemzek, Affymetrix's vice president of strategic marketing for genotyping, told BioArray News at the time that there has been "significant" demand for the UKBB chip design or variations of it, as customers use the chip as a template for their own focused arrays. This week, he acknowledged the impact that the UKBB project had on the BioProcession Solution Alliance's choice.

"I would think so," Nemzek said when asked if the UKBB deal had led to the new agreement. "Certainly, the PIs of the MVP project were aware of the project we're doing with UKBB."


The VA last week awarded a five-year contract for genotyping in support of the Million Veterans Program to the BioProcessing Solutions Alliance. The alliance is a private-public partnership between BioStorage Technologies, a provider of sample management solutions for the bioscience industry, and RUDCR Infinite Biologics, a publicly-funded biorepository based within Rutgers University.

According to the statement, the VA will provide $7.5 million to support the genotyping for the first year, with the balance to be determined. The BioProcessing Solutions Alliance will genotype and analyze 100,000 DNA samples from US military veterans who have elected to participate. Ultimately, the genetic data will be deposited in a database that also contains information about the participants' military exposure, lifestyle, and health.

Researchers and physicians are currently developing the chip that will be used to genotype the samples. Nemzek said that the design of the MVP array has not yet been finalized, but that once the project concludes SNP selection, it will take Affymetrix about five weeks to deliver the arrays to RUCDR.

According to Brooks, who is chief operating officer at RUCDR, the custom content for MVP will be focused on specific disease targets that will help to identify and determine risk assessment for health issues that are of particular interest to VA investigators. "The VA's ability to integrate detailed clinical information with molecular profiling will be a huge asset for this program," he added.

Brooks noted that BioProcessing Solutions Alliance has been contracted to genotype 107,000 subjects in the first year of the agreement. He said that the alliance will carry out the genotyping at BSA East, which is part of the RUCDR main analytical facility at Rutgers' Busch Campus in Piscataway, NJ.

BioArray News interviewed Brooks earlier this year, discussing RUCDR's activities, its alliance with BioStorage, and the demand for Affymetrix and Illumina's biobank arrays (BAN 4/23/2013).