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Affymetrix Takes Aim at Illumina with Rollout of New Axiom Exome Array

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By Justin Petrone

Affymetrix this week began shipping its Axiom Exome Genotyping Arrays with the hope that the new chip's content and custom design options can capture what appears to be strong demand in the marketplace for such products.

"We have exceeded our content expectations on the product; it is now available, in inventory, and we are taking orders," Andy Last, executive vice president of Affy's genetic analysis and clinical applications business unit, told BioArray News this week.

Both Affy and rival Illumina introduced exome arrays at the International Congress of Human Genetics in Montreal last year (BAN 10/18/2011).

Illumina has since reported "record orders" for the arrays in the third and fourth quarters of 2011, though it has been unable to fully recognize revenue from those orders due to manufacturing constraints (BAN 2/14/2012).

Last admitted that the firm is later to market than Illumina, but said that the product's content could give it an edge.

"We launched our product second, we are fully aware of that, but we have more coverage, and I think that's allowed a number of people to talk to us the way they weren't talking to us before," Last said. "I think the intriguing component is that there is a high interest in rare SNP variants," he said. "Missing a few is troubling to folks."

"Our competitor has talked about their array being popular with their customers and we are seeing a parallel phenomenon both with existing customers and customers using competitors' products who are also interested because we have some additional content here," Michael Nemzek, Affy's vice president of strategic marketing, genotyping, told BioArray News.

According to Last, the exome array market is a "consortium-driven story," meaning that high volumes have translated to lower prices for customers. The promotional price for the Axiom Exome Array is $45 and the list price will be $70 per sample including reagents.

"Some of the sample sizes we are discussing with [customers] are pretty big," Last said. He and Nemzek declined to name specific customers who are using the chip.

Affy's Axiom Exome Genotyping Arrays contain 318,000 markers, including 35,000 single-base and complex indel markers. Customers also have the option to add 100,000 SNPs of their choice to the array. Affy refers to the arrays that include custom content as Axiom Exome Plus.

At ICHG, the firm introduced an array containing 300,000 markers, with the option to add 50,000 selected SNPs. On its website, Illumina says its exome arrays contain about 250,000 exonic variants and 180 indels.

Affy selected content for the chip from the National Heart, Lung, and Blood Institute's Exome Project, the Genetics of Type 2 Diabetes program, the 1000 Genomes Project, the Cancer Genome Atlas Project, the Sardinia exome study, the Autism Exome Sequencing Study, the UK10K project, and other similar projects, according to the firm.

According to Last, customers who use Affy's menu of population-focused arrays for genome-wide association studies can "fold" the firm's exome content into their studies in a number of ways.

"It doesn't have to be an either/or," said Last. "The interest in the coding regions and variation within them as it is related to missing heritability factors is picking up pace," he said. "The product is available as a standalone and you can run it alongside GWAS arrays … or someone can come back and say that they would like to customize an entire GWAS array and fold this content into that as well," he said.

Exceeding Expectations

While Affy is looking to get a boost from its new exome array product, Illumina has already booked orders for enough chips to process a million samples since it introduced its offering, chief financial officer Marc Stapley said during the San Diego firm's Q4 earnings call.

Illumina launched its 250,000-marker, 12-sample Infinium HumanExome BeadChip in November and Flatley told investors last month that the chip is the "single most successful array we have ever launched" (BAN 1/17/2012).

Illumina actually offers three exome-focused arrays. In November, it also launched its 950,000-marker, nine-sample OmniExpressExome BeadChip; and it launched its 5-million-marker, four-sample HumanOmni5Exome BeadChip this year (BAN 10/18/2011).

The interest in Affy and Illumina's exome arrays aligns with predictions made from two surveys of array users carried out in the past few months.

A survey of genomic researchers conducted by GenomeWeb in partnership with investment firm Mizuho Securities found that most respondents expect exome analysis to be the "most relevant" application for arrays over the next two years (BAN 1/17/12).

In addition, investment firm William Blair reported in a December survey a "great deal of optimism" and a "strong positive reaction" by researchers to the availability of Illumina's exome arrays, despite forecasting flat overall array sales for the next two years (BAN12/13/2011).

As for Illumina, Christian Henry, general manager of genomic solutions, said during the firm's Q4 call that it will most likely recognize revenue in the first half of the year as it ships the products in the first and second quarters.


Have topics you'd like to see covered inBioArray News? Contact the editor at jpetrone [at] genomeweb [.]com

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