Affymetrix To Release Axiom Array Plates Optimised for NIH-funded Genotyping Study of 100,000 People
03 Aug 2011

Affymetrix, Inc. (NASDAQ: AFFX) today announced plans to commercialise four Axiom® population-optimised arrays used to analyse 100,000 samples collected from volunteers in one of the nation’s largest and most diverse genomics projects funded by the National Institutes of Health (NIH). Each Axiom genotyping array is optimised for the major populations, including those from European, East Asian, Latino, and African ancestry. Affymetrix tailored the design of the Axiom Array Plates for each population by using rare variants from several sources, including the 1000 Genomes Project, so they will provide a more informative and cost-effective solution for genome-wide scan and replication studies of previously identified disease risk factors and genetic traits.

In the study’s first peer-reviewed paper, published in the journal of Genomics, scientists detailed the design and performance metrics of the new arrays, which are the latest addition to the Axiom Solution that runs on the GeneTitan® System. “Preliminary results … demonstrate very high-quality genotypes, with sample success rates above 94 percent and over 98 percent of successful samples having [single nucleotide polymorphisms] SNP call rates exceeding 98 percent,” wrote researchers. “At steady state, we have produced 462 million genotypes per week for each Axiom system. The new array provides a valuable addition to the repertoire of tools for large scale genome-wide association studies.” (Hoffmann JT, et al)

“This program is a fine example of how our Axiom technology enables rapid design and delivery of high-quality genotyping arrays,” said Andy Last, PhD, Affymetrix Chief Commercial Officer. “Axiom array plates and the GeneTitan Multi-channel (MC) Instrument helped to accelerate this important study and we’re excited to make them available now to all research scientists who are working to improve the quality of health and medical care.”

Affymetrix leveraged validated SNPs and insertion and deletion (in/del) polymorphisms from its Axiom® Genomic Database to maximize genome-wide coverage, especially for rare variants in each of the major U.S. populations, including individuals of single and mixed ancestry. Additionally, SNPs were selected to provide coverage down to one percent minor allele frequency in gene regions or SNPs previously identified as disease associated from prior genome wide association studies (GWAS). Moreover, SNPs of high importance, based on confirmed traits or disease associations, were derived from several sources, including NHGRI GWAS database, Human Genome Epidemiology (HuGE) Navigator, Pharmacogenetics Knowledge Base (PharmaGKB), Pharmacogenetics Membrane Transporter (PMT) database and candidate SNPs from literature. Variants have been selected to target specific diseases such as heart disease, diabetes, cancer, and many other health conditions for which reliable associations have been found with specific variants.

The complete Axiom® Genotyping Solution includes four Axiom® Genome-Wide Array Plates, the European (EUR), East Asian (EAS), Latino (LAT), and African American (AFR). The Axiom EUR Array Plate will be commercially available in August, the remaining plates later in 2011. Each array plate is offered in the 96-well format with the new Axiom® 2.0 Reagent Kits, an automated target preparation station, along with the GeneTitan MC Instrument and the new Genotyping Console™ 4.1 for automated allele calling and quality control.

The Axiom arrays were developed with scientists at the University of California, San Francisco, to support the large-scale genotyping project with funding from the NIH.

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