Affymetrix, Inc. (NASDAQ:AFFX) today announced the release and immediate shipment of its Axiom Exome Genotyping Arrays, which provide the highest coverage of novel, putatively functional coding variants available.
Affymetrix Axiom(R) Exome Genotyping Arrays (Photo: Business Wire)
The exome, comprising the protein coding regions of the human genome, is the site of over 85% of causal mutations in single gene disorders. In genetic studies of common, complex disorders, the exome is implicated in approximately 60% of disease susceptibility regions discovered to date. By genotyping a large number of exonic variants, researchers will have much greater access to biologically relevant markers with which to identify the most disease-relevant variants for downstream functional validation. These functional studies are expected to be time-consuming and costly but are essential. The Axiom Exome Genotyping Arrays enable a rapid and cost-effective prioritization of candidate causal variants and give researchers the confidence that they are investing their time and budget in the most disease-relevant putatively functional variants.
“The Axiom Exome Genotyping Arrays are the most powerful, innovative, and informative exome genotyping arrays in the marketplace,” said Andy Last, PhD, Executive Vice President of Genetic Analysis and Clinical Applications Business Unit at Affymetrix. “We worked very closely with key opinion leaders to develop the most comprehensive, functionally relevant content and deliver a very cost-effective solution that allows researchers to run large sample sizes to achieve greater statistical power.”
The Axiom Exome Genotyping Arrays exceed the coverage for high-value coding variants compared to currently available arrays on the market. These variants are very rare and cannot be efficiently imputed or tagged. Therefore, it is crucial that as many variants as possible are physically interrogated on the array to maximize important disease variants being screened, identified, and prioritized for functional validation. More than 35,000 single-base and complex insertion and deletion markers (indels) previously not utilized in complex trait genetic studies are included in the more than 318,000 markers on the Axiom Exome Genotyping Arrays. Indels are now at the cutting edge of genetics and recognized by thought-leaders as a class of variants that is likely to be a key factor underlying inherited human traits and diseases. Further, the Axiom Exome Genotyping Arrays include a set of highly informative markers that can enrich previous genome-wide association studies (GWAS), including Ancestry Informative Markers (AIMs), previous GWAS hits, markers for analyzing identity by descent, HLA profiling, and many others. By including a wider selection of AIMs, stratification in admixed populations is possible. These AIMs haven been selected from previous commercial arrays and a novel panel developed by the National Cancer Institute’s Latino Ancestry Cancer Epidemiology (LACE) study.
The Axiom Exome Genotyping Arrays not only offer greater content but also ensure content consistency over time. It is important that the content on a given array is highly reproducible over time among different manufacturing batches when genotyping rare variants in cohort and case-control studies. Unlike array manufacturing approaches where variation of array content can be observed between manufacturing batches, Affymetrix’ array production technology assures that each Axiom Exome Genotyping Array produced in the future has exactly the same content as an array produced today.
The Axiom Exome Genotyping Arrays are available as a standard catalog item and as a customizable version where customers can choose to include up to 100,000 additional markers specific to candidate genes and regions within their area of research. Researchers can submit their own de novo SNPs of interest from NGS or prior GWAS studies and also select variants from more than 11 million genotype-tested markers contained in Affymetrix’ Axiom® Genomic Database to create their own personalized exome array.
Affymetrix worked in close collaboration with leading geneticists to identify the most informative coding SNPs, indels, and other markers to define the Axiom Exome Genotyping Arrays. The marker panels on the Axiom Exome Genotyping Arrays were derived from novel variants discovered in 16 major exome sequencing initiatives by sequencing 12,000 ethnically diverse genomes of European, African, Asian, and Latino ancestry from several disease cohorts including cancer, type 2 diabetes, neurological disorders, and other phenotypic traits.
Leveraging the advanced Axiom® Genotyping Solution platform, the Axiom Exome Genotyping Arrays’ genotyping performance was proven by genotyping approximately 1,200 ethnically diverse samples from International HapMap Project and 1000 Genomes Project sample collections with the Axiom Exome Genotyping Arrays. The resulting genotype data set has been shared with the 1000 Genomes Project and is downloadable for the broader scientific community from the Affymetrix website.
The Axiom Exome Genotyping Arrays are part of the complete Axiom® Genotyping Solution which includes the Axiom® Exome Genotyping Array Plate in the 96-sample format with the Axiom® 2.0 Reagent Kits, an automated target preparation station, the GeneTitan® MC Instrument, and the new Genotyping Console™ Software 4.1 for automated allele calling and quality control.
Affymetrix technology is used by the world's top pharmaceutical, diagnostic, and biotechnology companies, as well as leading academic, government, and nonprofit research institutes. More than 25,000 peer-reviewed papers have been published using the technology. Affymetrix is headquartered in Santa Clara, Calif., and has manufacturing facilities in Santa Clara, Cleveland, Ohio, and Singapore. The company has about 900 employees worldwide and maintains sales and distribution operations across Europe, Asia, and Latin America. For more information about Affymetrix, please visit http://www.affymetrix.com.
All statements in this press release that are not historical are "forward-looking statements" within the meaning of Section 21E of the Securities Exchange Act as amended, including statements regarding Affymetrix' "expectations," "beliefs," "hopes," "intentions," "strategies" or the like. Such statements are subject to risks and uncertainties that could cause actual results to differ materially for Affymetrix from those projected. These and other risk factors are discussed in Affymetrix' Form 10-K for the year ended December 31, 2010, and other SEC reports for subsequent quarterly periods.
NOTE: Affymetrix, the Affymetrix logo, Axiom, GeneChip, GeneTitan, and Genotyping Console are trademarks or registered trademarks of Affymetrix, Inc.
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