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Fluidigm Launches New Chip Format with Core Labs in Mind; Clinical Settings May Also Benefit


NEW YORK (GenomeWeb) — Fluidigm has launched a new architecture for its Dynamic Array integrated fluidic circuit (IFC) chips designed to provide users with maximum flexibility, time savings, and reduced waste for gene expression, genotyping, and single-cell gene expression studies.

According to Fluidigm officials, the new architecture, called FLEXsix, is the "next evolution" of the company's core IFC product portfolio, and will enable customers to more easily transition from low- to high-throughput experiments using a single chip on the company's BioMark HD or EP1 instruments.

Fluidigm is initially targeting the chips at the academic research and production genomics markets, and particularly core labs that need to accommodate several users with a relatively fast turnaround time. In addition, according to at least one early-access user, the new IFC format could be an important "first step" toward Fluidigm's chips gaining a foothold in clinical labs.

Fluidigm originally introduced the concept of the FLEXsix chip in 2012 as part of a rollout of four new consumable IFC chips.

At the time, company officials noted that the FLEXsix chip, originally for gene expression only, featured six different 12-sample-by-12-assay partitions that would allow users to run assays in myriad configurations — small numbers of samples against a large number of assays or vice-versa — and to use the same chip for multiple experiments. This was in contrast to the company's pre-existing 48.48 or 96.96 IFC chips, which allow users to run a fixed number of assays on a fixed number of samples one time only.

Fluidigm began making the FLEXsix chips available through an early-access program at the beginning of last year, and since that time the company has made a few modifications prior to this month's full commercial launch.

Most importantly is that the current configuration is available for end-point genotyping on the EP1 system as well as gene expression studies using the BioMark HD platform, according to spokesperson Howard High.

"Both models have now been thoroughly tested with all gene expression and genotyping chemistries Fluidigm supports," High told PCR Insider in an email, adding that gene expression experiments can be run traditionally or in single-cell format — a market that Fluidigm has recently helped establish with the launch of its C1 single-cell auto prep system.

"Many of the core architectural elements remain the same," High said. "The FLEXsix IFC architecture still consists of six 12-assay-by-12-sample partitions that can each be run separately or together. The customer can run each partition independently as separate experi¬ments, or run multiple partitions simultaneously. So we're further down the learning curve and the product is now available to all customers worldwide. The product has evolved, but not changed at its core."

Further elaborating on the capabilities of FLEXsix, Nico Tuason, a product manager at Fluidigm, told PCR Insider that Fluidigm developed the format in response to feedback from both current and potential IFC chip customers who wanted to be able to do lower-throughput work in combination with higher-throughput work on Fluidigm's existing 48.48, 96.96, or 192.24 chips, the latter being another new format that the company launched in late 2012.

"Those who were doing lower-throughput work had to basically do it on [well] plates ... before the FlexSix, because if they needed only to look at 12 targets or 12 samples, for example, then they would typically run a 384- or 96-well plate," Tuason said.

"A lot of our current customers who developed … routine testing panels wanted to be able to choose their assays using a lower-throughput method, and that's one of the main reasons we developed this," he added. "Now you can basically do your lower-throughput development work on the FLEXsix, and as you scale up to the 96.96 or 192.24 you don't need to do the reoptimization or bridging studies that you would with competitive systems. Now you can run it on a FLEXsix, and if it works on a FLEXsix, it will work on a 96.96 or a 192.24 IFC."

Fluidigm's new offering would appear to make its BioMark HD system more directly competitive with the QuantStudio 12K Flex system from Thermo Fisher's Life Technologies. Launched in 2011, that platform allows users to perform both high-throughput quantitative and digital PCR experiments and low-throughput gene expression assays using the same software interface.

However, while the QuantStudio 12K Flex is promoted as being able to run 96-well plates, 384-well plates, TaqMan array cards, and OpenArray plates, "each time that you want to change to a different format, you have to change PCR blocks, and not all those blocks work in the same fashion," Tuason said. "You get different consistency of data depending on which one you use, and you also have different volumes, so you're going from [microliter] volumes in 96- and 384-well plates … to nanoliter amounts when you go to the OpenArray plate. With the FLEXsix and the 96.96 and 192.24 … you're always in that same microfluidic environment."

High and Tuason noted that the new offering should help Fluidigm score more customers in core labs, where multiple users often don't have 96 samples or 96 assay targets at the ready each time they want to do an experiment.

"In the past [core lab] customers basically used a Fluidigm platform when they had the numbers of samples or assays [needed]," Tuason said. "Now, not only can they run a smaller number of samples and assays, because it's reusable over the course of 90 days, one person can run a 12-by-12 today, and the next person can run a 24-by-24 a month from now, using the same IFC, without extra cost to the core lab or the individual scientist."

This was actually a big stumbling block for Fluidigm in terms of chip sales, High said.

Fluidigm's customers have "always hated to not run [chips] full or as close to full as they can, even though the cost per experiment might still be cheaper than doing it through more traditional means like a microtiter plate … their brain says 'this device is valuable, and if I only run it half full, I've wasted a resource,'" High said.

This perceived benefit may also be a boon for IFC chip use in clinical labs. According to early-access user Ping Fang, co-director of DNA diagnostics in the Medical Genetics Laboratories at Baylor College of Medicine, her lab conducts a lot of clinical genotyping assays for which Fluidigm only previously offered 48-by-48 or 96-by-96 IFC formats.

"We talked with Fluidigm and said this is not working for our clinical lab, because you basically need to accumulate more than 40 samples [for] a 48-by-48 run, or up to 90 samples for a 96-by-96 run. It's not practical. In the clinical lab we could run this assay once every one or two days, [but] when it requires a fast turnaround time, we cannot hold samples for a whole plate. We needed … the chip to handle just a few samples at a time [without] wasting the entire chip."

"Now, with FLEXsix," Fang said, "you only open a portion of the chip, and when you have a few patient samples you run them on that. And it is very flexible, so [if] you have more markers, you can open more of the blocks. This is why we think it has very good potential for a clinical lab setting."

Fang's lab only tested the gene expression version of the FLEXsix format, but doesn't really run gene expression assays. However, "I told [Fluidigm] that once they have the genotyping chip … we have tests ready to switch to that," Fang said. Examples include assays for hemochromatosis, MTHFR mutations, Factor V Leiden, sickle cell anemia, and achondroplasia, she added.

"Those are all targeted-genotyping analyses, but we only have a few samples per week," she said. "It's difficult for us to put them on a large chip. For Fluidigm, the limitation for clinical labs to adopt their chips is the size. I think this is a very good first step to move them forward to the clinical lab."