Affymetrix Delivers First Custom Axiom Array for Kaiser Permanente/UCSF Genotyping Project
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The array, optimized for European populations, was developed in conjunction with researchers from the Kaiser Permanente Division of Research and University of California, San Francisco (UCSF) as part of an NIH-funded project to create a new resource for studying disease, health, and aging.
“Our collaboration with the Kaiser Permanente/UCSF teams has resulted in these milestones, which demonstrate the overall power of the Axiom Genotyping Solution and our database of validated SNPs.”
The custom array will be used to genotype a significant portion of 100,000 samples collected by the Kaiser Permanente Research Program on Genes, Environment, and Health (RPGEH), which aims to enroll and collect DNA samples for research from 500,000 Kaiser Permanente members in Northern California by 2013.
The array leverages the Axiom database of approximately 6 million validated SNPs and demonstrates their extremely high conversion rate. With content from more than 30 sources, including the 1000 Genomes Project, the array has excellent genetic coverage of low-frequency SNPs relative to other commercially available genome-wide genotyping arrays. Affymetrix will make this array available to any researcher.
Based on initial quality control results, the array’s performance exceeds typical genotyping performance metrics with call rates greater than 99.6 percent and HapMap concordance in excess of 99.7 percent.
To prepare for the large genotyping project, the UCSF/Kaiser Permanente team has completed two pilot projects comprising more than 6,000 samples using the Axiom Genome-Wide Human Array Plate, the CEU-optimized catalog array launched in October 2009.
“This project will generate unprecedented data that will provide the basis for many new studies in the areas of disease outcomes, response to treatment, and factors influencing healthy aging and longevity,” said Cathy Schaefer, PhD, Executive Director of the Kaiser Permanente RPGEH. “We are grateful to Kaiser Permanente members, whose participation in the research program makes this genotyping project possible.”
The complete Axiom Genotyping Solution consists of Axiom Array Plates, complete Axiom Reagent Kits, an automated target preparation protocol developed jointly by Affymetrix and Beckman Coulter, and the GeneTitan® Instrument. Scientists can run more than 760 samples per week with considerably less user intervention relative to competing products.
“Our collaboration with the Kaiser Permanente/UCSF teams has resulted in these milestones, which demonstrate the overall power of the Axiom Genotyping Solution and our database of validated SNPs,” said Kevin King, President and CEO of Affymetrix. “This approach not only leverages Affymetrix’ expanding capabilities in custom genotyping arrays, but also illustrates the need for flexibility and the desire to precisely tailor custom arrays.”
The Kaiser Permanente/UCSF genotyping project of 100,000 samples is made possible by a $24.8 million grant from the National Institutes of Health awarded jointly to the Kaiser Permanente Division of Research and the UCSF Institute for Human Genetics to create a new resource for studying disease, health, and aging.