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Affy Rolls Out Axiom Genotyping Platform, Inks 100K-Sample GWAS Deal with Kaiser, UCSF


By Justin Petrone

Affymetrix last week launched its Axiom Genotyping Solution, a high-throughput, automated platform designed to give researchers access to genetic content generated by government and privately funded sequencing projects.

Affy also announced an agreement with the Kaiser Permanente Research Program on Genes, Environment, and Health and the University of California, San Francisco. Terms of that deal call for Kaiser and UCSF to use the Axiom platform to conduct genome-wide analysis of DNA samples from 100,000 Kaiser volunteers in Northern California.

The Axiom platform is Affy’s first major new genotyping offering since the firm launched its 1.8-million-marker SNP Array 6.0 two years ago. The firm believes that Axiom's customizable format will give it an advantage in the highly competitive genome-wide association studies market.

Earlier this year, Illumina, Affy's main rival in the GWAS market, introduced a new array platform for future studies called Omni; and in May debuted the 4-million-feature, four-sample HumanOmni1-Quad BeadChip. The company said at the time that the array was the first of a "beginning of a family of arrays that we will put out there that will contain rare variant content" (see BAN 5/19/2009).

Affy President and CEO Kevin King in a statement likened the custom options available to Axiom users to those available in the digital media industry. "Pre-selected, store-bought music and video content have given way to powerful online digital databases that offer customers maximum flexibility," King said. "Researchers can now create their own 'playlist' in the form of custom arrays that deliver maximum scientific value to their research."

The first catalog product to run on the platform is an Axiom Genome-Wide Human Array Plate optimized to study Caucasian populations. In addition to content selected from public databases of human variations and historical HapMap data, the arrays on the plate include more than 81,000 SNPs from the 1,000 Genomes Project and more than 30,000 coding and non-synonymous SNPs, the firm said.

Jay Kaufman, Affy's vice president of product marketing, told BioArray News in an e-mail last week that the firm plans to introduce a "growing family of catalog arrays." While the first Axiom Array Plate is "optimized for the Caucasian population" with "coverage of Asian and Yoruban ethnicities," Affy expects to produce Axiom Array Plates optimized for "Asian and African populations in the next few months," he said.

The Axiom offering consists of Axiom Array Plates, reagent kits, an automated target-preparation station developed jointly with Beckman Coulter, and the company's GeneTitan Multi-Channel instrument, which integrates a hybridization oven, fluidics processing, CCD imaging device, and analysis software, Affy said.

According to Affy, each Array Plate consists of 24 or 96 microarrays. The 24-Array Plate provides three columns of eight identical microarrays. The 96-Array Plate offers 12 columns of eight identical microarrays. Each array on an Array Plate enables the genotyping of 550,000 to 575,000 SNPs and 18,000 simple indels, Affy said. The oligonucleotide probes on the Array Plates are synthesized in situ using Affy’s photolithographic process.

Kaufman said that all reagents used with Array Plates — "with the exception of one very common laboratory reagent that the customer provides" — are manufactured internally at the firm's Ohio facility, formerly USB. Affy paid $75 million to acquire USB nearly two years ago (see BAN 1/8/2008).

According to Affy, its Axiom platform will support both whole-genome association and candidate-gene association studies, and the company will offer users the ability to customize their arrays. The first Array Plates will support genome-wide association studies and are expected to be delivered to customers this month. The company will also offer Axiom genotyping services through its research services laboratory.

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Custom Content

Though it is introducing catalog products, Affy said in a statement that a "major strength" of its platform is that researchers will "no longer be constrained by the content of fixed-panel arrays."

Instead, some Affy customers will be able to design their arrays using Affy's internally validated database of human genomic variation. In June, Keith Jones, Affy's vice president of product development, said that the company had taken 8 million SNPs from the dbSNP database and, using its automated genotyping assay, generated genotypes for over 1,300 individuals to create its own database of content to be used for designing future catalog and custom arrays (see BAN 6/9/2009).

Jones said at the time that a "select number of customers" would be able to access the database and come up with a customer-defined list of SNPs for their research purposes by year end.

Kaufman said last week that Affy is "already engaged with customers who are interested in designing custom arrays using content from our database." At this point, though, Affy interacts "very closely" in the design process. Kaufman anticipated that as Affy's "infrastructure evolves this process will become more streamlined."

He said that, for now, Affy will "work closely with customers to create a limited number of custom designs." He added that "simultaneously, we will create new and leverage existing infrastructure to allow customers full access to the database, via Affymetrix, in the future."

Kaiser and UCSF

Two customers that have access to Affy's database are Kaiser Permanente and the University of California, San Francisco. The firm said last week that researchers associated with the Kaiser Permanente Research Program on Genes, Environment, and Health and UCSF will use Axiom platform to conduct genome-wide analysis of DNA samples from 100,000 Kaiser volunteers in Northern California.

The research efforts are supported by a two-year, $24.8 million stimulus grant from the National Institutes of Health to use information and biospecimens from 100,000 of Kaiser Permanente's members in a large-scale study of how genetic and environmental interactions affect human health. Funded through the National Institute on Aging, the average age of the participants in the study will be age 65.

According to a statement, UCSF's Institute for Human Genetics will perform the genotyping on the project, which also will make use of Kaiser's historical clinical data and other health-related patient information and its electronic health records.

Affy's Kaufman confirmed that Kaiser and UCSF's "study design will leverage our database of validated SNPs."

The partners said they aim to study genetic and environmental influences over time on a wide range of health conditions, across diverse populations, including data about drug metabolism and drug response that researchers may use to find links between genetic factors and individual drug responses.

RPGEH was launched in 2005, when it began enrolling volunteers from Kaiser's three million members in Northern California. It has now received biospecimens for more than 110,000 volunteers for its biobank, and eventually will store samples and health surveys for 500,000 members from the region, it said. A year ago the RPGEH received an $8.6 million award from the Robert Wood Johnson Foundation's Pioneer Portfolio to fund collection and storage for the first 200,000 samples.