EP1 System Delivers High Data Quality with Best-In-Class Workflow Efficiency

Thursday, January 8, 2009; South San Francisco –Columbia River Inter-Tribal Fish Commission’s (CRITFC) genetic laboratory is incorporating Fluidigm’s integrated fluidic circuit (IFC) technology to conduct genetics research of salmon in the Columbia River. CRITFC has been using Fluidigm’s flagship 96.96 Dynamic Array chip and the new EP1 System for months as part of their advanced testing program.

Using the 96.96 Dynamic Array and EP1 System, CRITFC can process 96 SNP (single nucleotide polymorphism) markers with 96 salmon DNA samples to provide 9,216 simultaneous reactions per chip. A fully configured EP1 System can process more than 200,000 genotypes per day using TaqMan® assays.

“We are using Fluidigm technology to characterize genetic variation in fish populations to better understand their diversity, adaptation and dispersal, said Shawn Narum, CRITFC lead geneticist. “Genotypes from these SNP markers provide a genetic signature for specific populations. That genetic signature may be used to identify unknown origin fish during migration or in fisheries harvest. This provides information with immediate application to fisheries management in the Columbia River basin, including several salmon stocks listed under the Endangered Species Act.”

“Columbia River Inter-Tribal Fish Commission is sophisticated and assertive in its use of technology to comprehend changes in nature and how those changes impact the lives of their members,” said Gajus Worthington, president and chief executive officer. “Balancing ecology, the tribal way of life and conservation is a challenge, and I suspect most people don’t know that CRITFC is employing advanced yet practical genetic analysis tools to understand and maintain their fish population.”

Since 1995, CRITFC and its four member tribes — Yakama, Nez Perce, Umatilla and Warm Springs — approach salmon restoration through plans and strategies that address salmon recovery at every stage of the salmon’s life-cycle. The first-of-its-kind genetics research is an important facet of the conservation and recovery of salmon in the Columbia River basin.

“Good data is essential in Columbia basin resource management. We were using traditional life science equipment that could only process 384 data points at a time. With the Fluidigm EP1 System, we benefit from a 24-fold increase in production,” noted Narum. “We were able to easily integrate the Fluidigm technology into our laboratory procedures and our results have been very similar with our previous data.”

Fluidigm’s EP1 system provides superior data quality, a fast and easy workflow, and significant cost savings for SNP genotyping studies. The system delivers the highest quality SNP genotyping results on the market with better than 99 percent call rates and 99.75 percent or greater accuracy. All of this is achieved with an easy-to-use, high-throughput workflow that can provide up to 9,216 data points per IFC chip with results in just four hours. The EP1 system, which includes the IFC Controller, Stand-Alone Thermal Cycler and EP1 Reader, provides over 27,000 genotypes a day. By adding more IFC controllers and thermal cyclers to be used in conjunction with a single EP1 Reader, laboratories can generate more than 200,000 genotypes in a day.

The EP1 system can also perform digital PCR, such as for copy number variation analysis. Fluidigm is the only company today offering a commercially available digital PCR system. Using a Fluidigm Digital Array — an IFC designed specifically for digital PCR — the EP1 system provides the highest sensitivity and fastest workflow available for researchers studying copy number variation. The system can easily distinguish between four and five copies and provide results in just a few hours, while requiring only minutes of hands-on time.