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Fluidigm Provides More Details on Polaris System, New C1 Applications

Fluidigm Polaris

NEW YORK (GenomeWeb) – Fluidigm previewed several new products and future applications at the Advances in Genome Biology and Technology meeting in Marco Island, Fla., last week, including the Polaris system for single-cell assays and sample prep, a new chip to prepare up to 800 cells for RNA-seq with the C1 Single-Cell Auto Prep system, and multiplexed protein detection in single cells using the C1.

The Polaris system, which has a list price of $400,000 and is expected to start shipping commercially midyear, combines functional studies of single cells on a chip with genomic sample prep. Initially, it will enable researchers to select and individually capture 48 single cells on a chip, expose them to different stimuli in a controlled environment, and prepare their genetic material for gene expression analysis.

Researchers can use the system, for example, to conduct dose-response and time course experiments on single live cells, allowing them to study processes such as cell differentiation, immune response, neurogenesis, and cancer development. Fluidigm is about to start early-access testing for the system at a handful of customer sites.

During a company workshop held at AGBT, Marc Unger, Fluidigm's senior vice president of R&D, explained that Polaris uses the same type of microfluidics as the existing C1, combining it with imaging and on-chip cell culture.

The system uses a new integrated fluidic circuit (IFC), Fluidigm's microfluidic chip. The workflow starts with flowing a cell suspension into a chamber, followed by automatic imaging and selection of cells of interest; active steering of single cells into capture sites; the addition of factors, such as drugs; lysing the cells and amplifying their genetic material; and harvesting the material for analysis, initially RNA sequencing.

Unger said that researchers could use Polaris to select specific cell types, and to measure their gene expression in response to a perturbing agent. They could also conduct time course experiments to measure, for example, T-cell response to infectious agents, such as HIV.

Collaborators at the University of California, San Francisco have already used Polaris to study primary human neurons, he said, selecting individual cells based on surface biomarkers and correlating their gene expression profiles with their cell type.

Fluidigm plans to scale up the chips for Polaris over time to enable the analysis of several thousand cells. Future chips could also enable the study of cell-cell interactions, Unger said.

RNA-seq on 800 single cells

In response to customer demand, Fluidigm has developed an IFC for high-throughput mRNA-seq prep on the C1 system that supports transcriptome sequencing of up to 800 single cells. The new chip will allow researchers to discover subpopulations of cells and to profile rare cell types.

The HT RNA-seq chip is in early-access testing right now and will start shipping commercially in the second quarter. It will use a simplified chemistry to prepare the mRNA that involves barcoding, so material from 40 cells can be pooled and a total of 20 samples are processed for sequencing off the chip. The chip's occupancy rate is high – Unger showed an example where it was 94 percent. Each run takes about 10 hours, including a little more than an hour of hands-on time.

The new chip will cut the cost of RNA-seq for a single cell in half, from $21 to $10.50, Unger said. This includes $3.50 for the IFC and reagents and $7 for sequencing, generating a million reads.

"This is our weapon in the throughput battle" of single-cell genomics prep, Unger said, noting that future chips will support larger numbers of single cells.

Other companies have recently said that they, too, plan to enter the single-cell genome analysis market. WaferGen, for example, said last month that it plans to start an early-access program in the second quarter that will test its SmartChip technology for single-cell prep. The company's chip has more than 5,000 wells and deposits single cells into these using a nanoliter dispenser. A company representative told GenomeWeb at AGBT that WaferGen's existing platforms have lists prices between $110,000 and $165,000, and that the price of the single-cell system would likely be in the same range.

Also, Cellular Research said last month that it plans to commercialize an instrument, called the Resolve system, next year that will be able to process 5,000 to 10,000 single cells for transcriptome sequencing.

Protein expression in single cells

In a poster presentation, Fluidigm also previewed a new application for the C1 system: multiplexed protein detection in single cells.

The company has developed an assay to detect up to 24 proteins in up to 96 cells per experiment. The technology relies on Proximity Extension Assay, where two oligonucleotide-labeled antibodies bind to a target protein. When the two oligos come close together, they partially hybridize and are extended by a DNA polymerase. The product can then be detected by real-time PCR.

According to the poster abstract, Fluidigm researchers have tested the assay in three cancer cell lines and found different patterns of protein expression for a number of targets. The company is currently optimizing the method and developing antibodies for a broader range of cancer targets.

Longer term, the approach could be combined with RNA analysis to detect multiple analytes, such as RNA and proteins, in the same cell.

No commercialization timeline for protein expression analysis on C1 is available yet.