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Encouraged by C1 System Adoption, Fluidigm Plans New Single-Cell Genomics Applications


Fluidigm has placed three dozen of its C1 Single-Cell Auto Prep Systems since launching the instrument last year, and hopes to build on its momentum in the fledgling single-cell genomics market by expanding the number of applications that the C1 can support, as well as establishing new single-cell genomics research centers with partner institutions, according to CEO Gajus Worthington.

Worthington touched on Fluidigm's prospects in the single-cell genomics market last week during the firm's fourth-quarter earnings call and also at the Leerink Swann Global Healthcare Conference in New York. In his presentations, which were webcast, Worthington portrayed South San Francisco, Calif.-based Fluidigm as a "pioneer" and "market leader" in a nascent single-cell genomics market that, "while small, is growing by 50 percent a year."

Worthington did not provide a market size for single-cell genomics, but other life sciences firms have also taken note of increasing demand. NanoString Technologies launched a single-cell gene expression analysis application last year (BAN 9/25/2012). Agilent Technologies has also introduced a method for single-cell analysis on its comparative genomic hybridization arrays (BAN 7/3/2012).

Fluidigm expanded its presence in the market last June, when it launched the C1. The automated single-cell isolation and preparation system isolates, lyses, and preamplifies nucleic acid from single cells. Using Fluidigm's C1 Single-Cell Auto Prep Array Integrated Fluidic Circuits, customers can capture and prepare 96 individual cells for analysis per run. At the time of the C1's launch, Fluidigm customers could then profile expression in 96 wells across 96 mRNA targets on the company's BioMark HD instrument. In December, the company introduced C1 mRNA Seq Kits and IFCs to enable the processing of up to 96 single-cell cDNA libraries for quantitation of mRNA expression on Illumina sequencers. According to Worthington, multiple other applications are in development.

"There is a whole menu of research techniques for cell biology that involve imaging, culturing, and provocation, that are done at a tissue level, and there is a whole menu of genomic analysis techniques," Worthington said at Leerink Swann. "We are just starting to connect those two worlds to one another," he said.

Fluidigm intends to offer applications for single-cell microRNA analysis and targeted DNA sequencing by the end of this year. Worthington said that the company is also working on protein expression, DNA methylation, and "more exotic" applications like chromatin immunoprecipitation. "These are all very important techniques that we are going to enable, one by one, for single-cell analysis," he said.

To support the adoption of its technology, Fluidigm has also embarked on a strategy of opening single-cell genomics research centers. In December, the company, together with the Genome Institute of Singapore, announced the creation of the GIS-Fluidigm Single-Cell 'Omics Center. Hosted in GIS' facilities within Singapore's Biopolis, the center features the C1 and BioMark HD systems, as well as various next-generation sequencing instruments, GIS and Fluidigm said at the time.

Also last year, Fluidigm and the Broad Institute opened a new center at the Broad's headquarters in Cambridge, Mass., aimed at developing new methods and discoveries in mammalian single-cell genomics. At the time, Fluidigm and the Broad described the Single-Cell Genomics Center as a hub for collaboration among researchers doing studies in single-cell genomics in stem cells, cancer biology, and other fields.

On the firm's Q4 earnings call, Worthington said that Fluidigm "expects to set up other centers in 2013."

Fluidigm has served a number Asian single-cell genomics clients for years, such as Keio University's Toshio Suda and Kyoto University's Shinya Tamanaka, both of whom have used the company's BioMark HD system in various stem cell studies (BAN 6/30/2009).

The launch of the C1 has expanded Fluidigm's presence in that regional market and others, Worthington said at Leerink Swann, noting that that C1s have been placed in Japan, China, and Korea, in addition to the US, Europe, and Australia. "The phenomenon of single-cell genomics is common to diverse areas of biology and it's a global phenomenon as well," he said.

Some customers are using the system for stem cell and cancer research. Fluidigm initially envisioned the C1 as a tool for the stem cell research community, referring to it as the "stem cell chip" while it was in development (BAN 8/18/2009).

Worthington said at Leerink Swann that stem cell researchers are interested in using the C1 to "take apart the mechanisms" by which stem cells become other cells, with the eventual hope of being able to control cell differentiation, so that cells could be used therapeutically to treat conditions as disparate as a severed spinal column, heart disease, or Alzheimer's disease.

In cancer research, Worthington noted that tumor samples often contain cancer cells, metastatic cells, and cancer stem cells. "In order to understand what is going on with the disease, its progression, and whether or not you can treat it, you have to look at these individual cell types," he said of the rationale for using the C1.

During Fluidigm's Q4 call, he also said that a minority of the firm's C1 customers are traditional cell biologists. In 2011, Fluidigm co-hosted a series of webinars with BD Biosciences showcasing the use of BD's FacsAria III Cell Sorter and the BioMark HD System for single-cell analysis. Worthington said that the interest from the cell biology community was "catalyzed" by this co-marketing work, and that the series led Fluidigm to "realize that there is a whole community out there quite distinct from genomics that has a need for what the C1 can do." While C1-related sales to cell biologists have not contributed much in terms of revenues so far, Worthington said the company does see the cell biology customer segment as a "substantial opportunity" going forward.

Revenue Driver

About 40 percent of Fluidigm's $15.5 million in Q4 revenues were driven by single-cell genomics customers, Worthington said on the call, including sales of 36 C1 systems, C1 reagent sales, and BioMark HD and reagent sales to single-cell gene expression customers.

About 60 percent of BioMark-related sales were driven by single-cell expression, he added, and a quarter of C1 system sales in Q4 also included a BioMark system.

"We are extremely pleased with this level of demand within just six months of launch and ahead of availability of exciting menu expansion on the C1," said Worthington.

Fluidigm ended 2012 with an installed base of about 670 instruments. Worthington said that analytical systems — consisting of its BioMark, BioMark HD, and EP1 — represented approximately 65 percent of the installed base, while preparatory systems, which include its Access Array and C1, represented the remainder of that base.