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Fluidigm Set to Expand C1 Application Menu to Include Single-Cell DNA Sequencing

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Fluidigm continues to expand the menu of applications that can be run on single cells prepared for analysis on its C1 Single-Cell AutoPrep System.

CEO Gajus Worthington told investors during the firm's third quarter earnings call last week that the company will soon introduce single-cell whole-genome amplification for the C1, enabling customers to perform targeted DNA sequencing of up to 480 regions.

The South San Francisco, Calif.-based company expects to broaden its menu to support whole-exome and whole-genome sequencing of individual, single cells next year, Worthington said.

Fluidigm launched the C1 in 2012. The automated instrument isolates, lyses, and preamplifies nucleic acid from single cells. Using the C1, customers can capture and prepare 96 individual cells for analysis per run.

At the time of the C1's launch last year, Fluidigm customers could profile expression in 96 wells across 96 mRNA targets on the company's BioMark HD instrument. Since the launch, it has also added protocols for single-cell mRNA sequencing and microRNA expression in conjunction with the BioMark HD.

Worthington said that customer interest in the planned single-cell DNA sequencing applications is "high, especially in research fields such as cancer and immunology." Beyond single-cell cancer sequencing and immunological studies, he said that there is interest in other research areas, such as cell lineage.

While the company believes that targeted sequencing is "where the lion's share of the demand is right now," it expects that market need will "evolve into demand for whole-exome sequencing, followed by whole-genome sequencing of individual cells," Worthington said.

Since its launch, the C1 has quickly become Fluidigm's flagship product. In addition to launching new applications, the company has also worked to set up single-cell genomics research centers in a number of international institutes, such as the Broad Institute and the Genome Institute of Singapore (BAN 4/16/2013).

Those activities are paying off for the company. As GenomeWeb Daily News reported, Fluidigm's Q3 revenues jumped 43 percent compared to the same period in 2012, largely attributable to its single-cell genomics-related sales, which doubled in the quarter.

While the company has placed about 100 C1s with first adopters to date, Worthington said that its efforts are now encouraging newer customers to try the technology. "These customers were previously on the sidelines due to the daunting workflow and cost of isolating and preparing single-cell samples for genomics-based analysis," Worthington said. "The C1 changed this."

He noted that the first two publications to describe the use of the C1 were published in Q3. The first was authored by a team at the University of California, San Francisco, and appeared in Stem Cell Reports in August. According to the paper, the UCSF researchers reprogrammed the transcriptional circuitry of human cardiac H9F fibroblasts to produce an induced-cardiomyocyte-like state in the cells, and used the C1 and BioMark HD to optimize their reprogramming efficiency by monitoring cardiac gene expression.

The second paper to feature the C1 was published online in Nature Methods in September. The authors, a team from the European Molecular Biology Laboratory in Heidelberg, Germany, examined statistical methods for analyzing single-cell mRNA sequencing data generated using the C1 and different Illumina platforms. According to the paper, the group established a quantitative statistical method to distinguish true biological variability in single-cell mRNA Seq data from technical noise.

Worthington also mentioned a third C1-related paper that appeared online in Nature Methods last month. Authored by Stanford University researchers, including Fluidigm Founder and consultant Stephen Quake, the study compared the performance of the C1 to different plate-based methods for isolating and preparing single cells for analysis, and, in Worthington's words, "concluded that the C1 results were better in nearly every respect versus plate-based methodologies."

According to Worthington, Fluidigm is aware of several other papers that discuss the use of the C1 and are near publication. He said that these publications will help support broader market adoption.

Fluidigm believes that the single-cell genomics market will continue its current growth trajectory. Worthington reiterated on the call that the firm expects single-cell genomics to become a $200 million market by the end of 2015.

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