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TaqMan OpenArray Genotyping System Simplifies Workflows

Applied Biosystems Inc., today announced that it has commercialized a new analysis system to enable researchers to perform high-sample-throughput genotyping studies that are faster, easier and more cost effective than other commercially available methods. The TaqMan® OpenArray(TM) Genotyping System provides life scientists with the ease-of-use, accuracy, and reproducibility of Applied Biosystems' TaqMan® SNP Genotyping Assays and TaqMan® DME Assays in a flexible format. This system expands the potential uses of TaqMan technology across a wide range of genotyping applications, providing an extremely fast, high-sample-throughput validation and screening tool for researchers in agricultural, pharmaceutical, and other commercial industries, as well as academic institutions.

Among the types of studies that should benefit from the use of this system are those that associate genotypes with complex diseases, ethnic ancestry, drug-treatment response, and traits for breeding and quality control in agricultural studies.

This analysis system is based on the collaboration between Applied Biosystems and BioTrove, Inc. to commercialize the OpenArray platform, under which Applied Biosystems has exclusive rights to develop, market and support custom-built OpenArray plates of TaqMan SNP Genotyping Assays. Researchers using this integrated platform can experience an end-to-end genotyping workflow of less than eight hours, enabling them to analyze thousands to tens of thousands of samples in days, in contrast to weeks or months, on alternative genotyping platforms. Single nucleotide polymorphism (SNP) genotyping studies can also be performed in a cost-effective manner on this new platform, as the TaqMan OpenArray Genotyping System delivers a lower cost per genotype, compared to other commercially available platforms, coupled with a workflow requiring a minimal amount of user interaction.

“A faster, easier, more cost effective, high-sample-throughput genotyping solution that uses gold-standard TaqMan genotyping assays will be critical for advancing science in academic research, as well as industries such as health care, food, and agriculture,” said Peter Dansky, president for Applied Biosystems' functional analysis division. “The TaqMan OpenArray Genotyping System will provide researchers and commercial organizations with a validation and screening tool that has the potential to dramatically improve genotyping efficiencies and simplify their workflows.”

The TaqMan OpenArray Genotyping System enables researchers to perform studies that investigate tens to hundreds of SNPs across thousands to tens of thousands of samples. This scale of genotyping study is often performed as part of breeding and quality control processes in the agricultural industry. In these applications, researchers investigate how SNPs from multiple genes contribute to measurable traits. These SNPs are then used as genetic markers for quality control testing, tracking, or selective breeding of crops and livestock.

Alternatively, large-scale population studies can involve tens of thousands of samples and also require high sample throughput technology to ensure efficient genotyping across candidate SNPs. For example, at the University of California, Davis School of Medicine, a team of researchers are using the TaqMan OpenArray Genotyping System for large-scale population studies aimed at assessing the role of ethnic ancestry in complex genetic disease. In collaboration with Applied Biosystems, Michael F. Seldin, M.D., Ph.D., a professor of biological chemistry and medicine has developed a panel of TaqMan® SNP Genotyping Assays for determining continental origin and admixture proportions in common populations in America. During the past year, as an early access user of the system, Dr. Seldin has been able to perform more cost-effective genotyping projects that involve SNPs from these panels—64, 96 or 128—in large numbers of biological samples.

For example, his team is currently genotyping approximately 20,000 samples from participants in the Women's Health Initiative, a long-term national health study that focuses on strategies for preventing heart disease, breast and colorectal cancer and fracture in postmenopausal women, in order to examine ancestry association with various phenotypes in admixed subject groups including African Americans and Hispanic Americans.

“The TaqMan OpenArray Genotyping System enables a cost and labor efficient genotyping method for projects using tens to hundreds of defined SNPs and large numbers of samples,” said Dr. Seldin. “This platform increases the speed, simplicity, and efficiency of our studies. It also enables a high quantity of sample throughput with similar genotyping quality to that achieved by conventional TaqMan SNP Genotyping Assays.”

The flexible format of this new system allows researchers to perform genotyping studies using a range of SNPs and samples in each experiment. For example, at Simon Fraser University in British Columbia, Canada, Willie Davidson, Ph.D., a professor in the department of molecular biology and biochemistry, leads a group of researchers who have been using the TaqMan SNP Genotyping Assays for research projects that involve the genotyping of Atlantic salmon for selective breeding, population dynamics and conservation biology studies. As an early access user of the TaqMan OpenArray Genotyping System, Dr. Davidson plans to use the system for SNP analysis related to identifying quantitative trait loci, and developing genetic linkage maps, both of which are important resources for gaining a greater understanding of genetic variation within different salmon populations.

“The ease of use of the TaqMan OpenArray Genotyping System, and the flexibility of being able to configure a range of SNPs for a range of samples, makes the system ideal for salmon breeding studies,” said Dr. Davidson. “Moreover, the TaqMan SNP Genotyping Assays are very efficient, robust reagents, and the reproducibility of results is excellent.”

The TaqMan® OpenArray™ Genotyping Plates provide researchers with the flexibility to deploy assays in many different configurations. Each TaqMan OpenArray Genotyping plate contains 3,072 through-holes arranged in 48 subarrays of 64 through-holes each. The TaqMan OpenArray Genotyping System validates or screens up to 256 SNPs across more than 1500 samples per day with minimal user interaction. Alternative platforms require more than a day to obtain results from sample analysis and often involve the need for extensive user interaction.

The system includes an instrument platform, reagents, and consumables, with the main components consisting of the TaqMan® OpenArray™ Genotyping Instrument Platform and TaqMan OpenArray Genotyping Plates that are pre-loaded with pre-designed or custom TaqMan SNP Genotyping or Drug Metabolizing Enzyme (DME) Assays. Researchers will be able to select genotyping assays from Applied Biosystems' comprehensive line of more than 4.5 million individual pre-designed TaqMan SNP Genotyping Assays, Custom TaqMan® SNP Genotyping Assays, or TaqMan DME Genotyping Assays for detecting polymorphisms in the drug metabolism enzyme genes. Once customers receive their assays pre-loaded on TaqMan OpenArray plates, they will then use an automated sample loader to introduce their DNA samples in

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