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Array Vendors Tout Customer Support for Complex Genome-Wide Association Studies

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By Justin Petrone

As criticism surrounding a recent genome-wide association study for longevity has underscored the complexity of GWAS and highlighted the repercussions of poor experimental design, array vendors said that they are willing to lend customers a hand when it comes to setting up and running such studies.

Both Illumina and Affymetrix, the two main GWAS platform providers in the market, said they seek to guide customers through the process of setting up and following through on such projects, even though there are by some estimates "hundreds" of the studies being planned or conducted at the moment and the two West Coast array vendors continue to debut new products.

"Coming from the commercial perspective of Illumina, it starts with the sales prospecting process," Daniel Peiffer, senior product manager of genotyping applications at the company, told BioArray News this week.

According to Peiffer, Illumina hires sales managers with "deep knowledge of GWAS studies" to consult with customers about the "best arrays to use, whether their study will be underpowered," and other issues relevant to running a GWAS.

San Diego-based lllumina also hosts user group symposia to discuss the "positives [and] negatives" of chips and reagents, and releases technical notes to assist customers with their studies.

"We try and help where we can," said Peiffer. "There is a wide range of how customers approach us for help on their studies."

An Affymetrix spokesperson declined to comment for this story. However, the firm takes a similar approach to supporting scientists that use its products, by supplying technical and application notes, field support, and by engaging in partner collaborations.

The Santa Clara, Calif.-based company states on its website that more than 21,000 peer-reviewed papers have been written about studies that use its technologies, which the company said could also help to guide customers conducting association studies.

Against this backdrop of careful marketing is the criticism still ringing from an extreme-longevity GWAS that appeared online July 1 in Science.

Critiques of the study, performed by researchers at Boston University, include the fact that the team used two different Illumina chips — the HumanCNV370-Duo and Human 610-Quad BeadChip — to genotype cases, that the sample size was too small, that the group's analytical methods were not very sophisticated, and that the researchers did not perform a replication study to validate its findings (see related story, this issue).

According to Illumina's Peiffer, while some critics of the BU paper cited the researchers' use of different Illumina chips, it is common for the firm's customers to use multiple arrays in a single study.

"I don't think it is much different from what customers are used to getting from Illumina," said Peiffer. "The majority of studies are done across multiple chips with varying amounts of content," he said. "With these new chips, the content should be 99.9 percent the same."

Illumina continues to release new arrays for use in GWAS. Last month, it began shipping the 2.5-million marker Omni2.5, and a 5-million marker chip, the Omni5, is scheduled for a release later this year.

In addition to the new chips, the firm is rolling out supplemental arrays that contain the content absent on previously released arrays to allow customers that began association studies on older arrays to keep abreast of the new content coming onto the market from sources like the 1000 Genomes Project (BAN 6/29/2010).

"We want to provide latest and greatest content to customers," Peiffer said of the firm's approach. At the same time, while he stressed that newer arrays contain most of the content from previous generations of chips, "some content can be lost or gained from iteration to iteration."

In the case of the BU longevity study, some users familiar with the 610-Quad chip have said that it is known to contain defective loci, and have suggested that several of such loci may have been improperly identified as longevity-associated SNPs.

Peiffer said that Illumina "manually edits every loci" on its arrays, but he acknowledged that "some questionable loci sneak through this process" and Illumina customers are informed that if an association study yields such questionable loci of interest, they should take a second look at those findings.

According to a technical note supplied to BioArray News by Illumina, the firm's BeadStudio array analysis tool allows cross-product integrated analysis and streamlined data export to third-party downstream analysis packages to ease analyses of studies that rely on data from more than one chip.

Illumina said the tool is "important for labs that want to ensure they are using a stable assay platform amenable to lengthy longitudinal or replication studies."

The company also recommends that replication studies be performed using a different technology, usually its own. Peiffer said that Illumina customers have replicated their findings using custom iSelect arrays or even the firm's older GoldenGate genotyping assays.

"We are aware that our customers sometimes use other vendors" in replication studies, Peiffer said. "It is certainly something that we do recommend to all our customers to ensure that what they discover truly are hits."

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