NEW YORK (GenomeWeb) – Fluidigm over the weekend unveiled a new automated library preparation application for targeted sequencing on its Juno genomic analysis sample prep system.
The new application expands Juno's capabilities beyond SNP genotyping and appears to enable Fluidigm to better compete in the targeted sequencing market — an area it has not focused on much in recent years as it trained its attention on single-cell genomics.
Fluidigm introduced the new application at the European Human Genetics Conference currently being held in Glasgow, Scotland. The company said that it is currently in the hands of some Juno users under an early-access program, and that the full commercial launch is scheduled to occur before the fourth quarter of this year.
The company launched an early-access program for the Juno platform in September with SNP genotyping as the first application. The system uses the company's patented integrated fluidic circuits to perform pre-amplification and genotyping from as little as 5.5 nanograms of input DNA.
Juno accommodates Fluidigm's 96.96 Dynamic Array IFCs, one of which enables pre-amplification and genotyping of up to 96 samples and 96 assays for up to 9,216 data points. The system is also compatible with Fluidigm's other Dynamic Array chip architectures: 48.48, 192.24, and Flex Six. All sample prep and thermal cycling is conducted on these chips, which must then be transferred to a Fluidigm BioMark or EP1 genotyping system for real-time or end-point readouts.
Company spokesperson Howard High told GenomeWeb in September that potential applications for the platform would include sample identification; quality control; DNA fingerprinting by biobanking and cell culture facilities; and integrated genotyping analysis in ag-bio.
Now, with the introduction of the automated library preparation application, Fluidigm will target a different type of customer — one that it already serves to some extent with its Access Array platform, now several years old.
Nancy Ngo, product manager for NGS library preparation at Fluidigm, told GenomeWeb in an email before the ESHG meeting that Access Array also supports targeted sequencing library preparation, but only on the 48.48 IFC. "If the customer has lower to medium sample throughput needs, and/or higher target density needs (e.g. to build large, comprehensive screening panels), the expanded capability coupled with the 48.48 IFC will work perfectly fine on our Access Array system," Ngo said. "However, if the customer needs the flexibility to run either 192 or 48 samples in parallel using the new chemistries, they will have to run these chips using the Juno system."
But, Ngo added, the real selling point of Juno is that it allows users to maximize their productivity in other areas of the lab due its automated workflow.
"Customers have the option of programming the loading and amplification to run overnight, and set the harvesting to finish by the time they arrive in morning," she said. "So they get productivity out of the instrument even during the 'off hours' of the lab."
Libraries prepped on Juno can be sequenced on any Illumina sequencer, and the application supports both bulk DNA and whole-genome amplified single-cell DNA inputs, according to Fluidigm.
Ngo also noted that Juno is capable of more than just targeted library prep. When coupled with, for instance, Fluidigm's Biomark HD, it can provide high-throughput real-time PCR, quantitative digital PCR, and genotyping of even low-input, challenging samples.
The new application will primarily compete with automated, high-throughput target enrichment products from the likes of RainDance Technologies, as well as with manual process sampling solutions from sequencing providers themselves.
However, Fluidigm claims that its new application on Juno will save users time and money compared to the competition. For instance, RainDance's ThunderStorm system can process up to 96 samples in parallel, while researchers can also manually process samples in 96-well plates using TruSeq or AmpliSeq chemistries from Illumina and Thermo Fisher Scientific, respectively.
Running the 192.24 chip on Juno, on the other hand, allows users to essentially double that throughput. Furthermore, "if we compare Fluidigm's 192.24 IFC using our new automated targeted library preparation chemistry to someone using a TruSeq Custom Amplicon project for the same number of samples and targets, the cost of preparing samples using this Fluidigm solution is approximately 80 percent lower," Ngo said.
This kind of time and cost savings is expected to be especially attractive to production genomics laboratories, which "specifically look for low cost per test, automation … and rapid turnaround time," Steve McPhail, Fluidigm's general manager for production genomics, noted in a statement.
Fluidigm said in its recently reported first quarter earnings that it recorded its first sales for the Juno platform in Q1, though it did not provide any dollar figures. During Q1, Fluidigm also announced the Access Array library workflow prep using Juno, which is designed to enable users to validate up to 5,000 known and novel mutations per sample, and is expected to launch in the second half of this year.