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Fluidigm Debuts Reusable Chip Format to Meet 'Enormous' Ag-Bio Demand


By Justin Petrone

Fluidigm this week introduced a new biochip that it claims can be reused up to five times and offers an attractive price for customers who process high numbers of samples, particularly in the agricultural biotechnology market.

The new integrated fluidic circuit, called the FR48, enables users to run 48 assays on 48 samples on Fluidigm's existing BioMark and EP1 instruments, as well as a new instrument that was specially designed for the new chip. South San Francisco, Calif.-based Fluidigm recommends that the reusable chip be used a maximum of five times for optimal performance.

The idea for the reusable IFC was born out of Fluidigm's desire to serve clients in the seed, livestock, and fisheries industries that are turning to genotyping to improve food quality and quantity. In particular, Fluidigm sought to reduce the cost of genotyping by five-fold — to a penny per datapoint — in order to meet a price level that researchers at the US Department of Agriculture's Agricultural Research Service believe could encourage food producers worldwide to adopt high-throughput genotyping tools.

"I believe reusability will be revolutionary for our industry and the life-science fields we serve," said Fluidigm CEO Gajus Worthington in a statement. "Reusability lowers costs, eliminates waste, and confers flexibility."

Worthington said the new chips will "contribute to improving the food supply and bring the benefits of genetic analysis and testing" to ag-bio scientists and producers.

Worthington told BioArray News this week that the chips can be used with existing Fluidigm instruments, though the protocol for the reusable chips requires the use of the firm's newly introduced FC1 thermal cycler. The initial setup for the chips includes a new controller, the FC1 Cycler, and either the EP1 Reader or BioMark System. The company said that the analysis workflow — from pipetting to read-out — takes an hour and 20 minutes. Then the chips undergo a two-and-a-half hour cleaning step and dry overnight before they are ready for reuse.

The chips are currently being made available to early-access customers and should become more broadly available later this summer. Worthington said that Fluidigm expects to bring additional reusable chip configurations, instruments, and assays to the market place this year.

The chips have not yet reached the penny-per-data-point goal, but Worthington said that they are currently "well below" five cents per data point, and that the company expects to reach the one-cent milestone sometime later this year.

'Moon Shot'

Fluidigm has long courted the ag-bio market, and has publicly discussed the use of its technology by firms like Dutch seed producer Enza Zaden for use in quality control programs (BAN 5/5/2009). It's a market that has also attracted interest from most large array companies, all of whom claim the segment is growing (BAN 1/13/2009, BAN 1/12/2010).

San Diego-based Illumina, for instance, has launched two BeadChips for use in bovine testing this year: the High-Density Bovine BeadChip, which contains data from more than 20 diverse breeds, and the low-density, 3,000-marker Bovine SNP Panel, which is used to select cattle for breeding.

Despite the availability of these new arrays, current biochips are still too expensive for global adoption of high-throughput genotyping, according to USDA-ARS research geneticist Curt Van Tassell, a member of ARS' Bovine Functional Genomics Laboratory in Beltsville, Md.

Van Tassell, who helped design Illumina's bovine products, said this week that while such tools can "significantly improve our ability to predict an animal's or seed's capability to withstand disease, to produce high-quality product, and to enhance a productive life," the "ongoing challenge has been that genotyping simply costs too much to run the large number of experiments required to find the genetic markers that matter."

Once identified, Van Tassell said the cost is "still too prohibitive to implement these genetic quality controls across the millions and millions of seeds, animals and fish that make up our food production system." While the cost of current technologies, including arrays, continues to decline, Van Tassell said that USDA-ARS "decided to set a 'moon shot' type of goal" to decrease the cost per data point down to a penny.

"If we could achieve that type of cost structure, it would allow us to determine parentage and traceability information for under a dollar per animal," Van Tassell said, adding that this low price point would "allow animal evaluations under conditions that were not feasible before — such as in sub-Saharan Africa" and could be adopted by "some of the world’s poorest livestock producers."

According to Worthington, Fluidigm's reusable chips were directly inspired by the USDA-ARS' goal. Still, the idea of making a reusable commercial microfluidic biochip was considered "controversial," Worthington said. While he declined to name specific naysayers, he said that some in both industry and academia thought Fluidigm's ambition was "impossible."

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The company is now advertising the FR48 — the FR stands for "fast and reusable," Worthington said — as the "world's first reusable biochip architecture for the commercial market." While reusable microarrays have been described previously — a PubMed search of the terms "reusable," "biochip," and "microarray" turned up a handful of results, such as a 2009 paper concerning a reusable surface for carbohydrate arrays — none of the array firms serving the ag-bio market today advertise reusable chips.

While Worthington said the FR48 chips would also be applicable to human research and other markets, he noted that such chips are particularly necessary to handle the large number of samples surveyed in ag-bio. "The characteristics are fundamentally different from human research genotyping," Worthington said, noting that the "sample numbers are enormous."

Specifically, he said that ag-bio users expect to process between 100,000 and a million samples per system, at the same time looking at limited numbers of SNPs, in the range of 96 to 384.

"The production environment places significant constraints on workflow, labor, and cost," Worthington said. "That is why a penny per data point is required."

First Users

While the ultimate goal of Fluidigm is to place its systems at the place of seed, livestock, and fish production, first users will likely be larger centers that offer genotyping services.

Expression Analysis CEO Steve McPhail said in a statement that the North Carolina genomic services provider has "done some work" in the ag-bio area, but that Fluidigm's reusable chips will "enable our agriculture-based customers to realize the tremendous benefits of SNP genotyping at significantly reduced costs."

Van Tassell, for his part, plans to integrate the reusable chips into the USDA's program to identify molecular markers to determine how to increase the predictive accuracy of evaluated traits in cattle.