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EP1™ System
Key Applications: SNP Genotyping, Copy Number Variation, Sample Quantification for Sequencing

The EP1 System offers the most efficient system for high sample throughput SNP genotyping and other applications using end-point reading after PCR. It allows for extremely low running costs and provides the easiest workflow for low- to mid-multiplex SNP genotyping. The EP1 System is also compatible with the world’s first reusable chips for SNP genotyping which will ultimately drive costs to one cent per genotype.

  • Dramatically lower costs with single-use or reusable chips
  • Accelerated workflow for higher sample throughput
  • Outstanding data quality


EP1™ System

The EP1 System offers the most efficient solution for low to mid-multiplex SNP genotyping, at very high-sample throughput. It consists of IFC Controllers, the FC1 Cycler, and the EP1 Reader. Together with Dynamic Array integrated fluidic circuits (IFCs), it can provide dramatically lower costs through the use of microfluidics and reusable chips. A fast and easy workflow enables results to be obtained in hours with only minutes of hands-on time. Outstanding data quality is consistently achieved, even with lower quality samples.

Additional applications can be performed on the EP1 System using Digital Array IFCs for digital PCR. Applications include copy number variation (CNV) and target quantitation for next-generation sequencing. Digital Array IFCs offer the highest resolution CNV analysis and the most accurate sample quanititation for these applications.

EP1 instrumentation consists of an end-point reader, thermal cycler, and IFC Controllers customized for your throughput requirements.


EP1 Reader

The EP1 Reader is designed for imaging Fluidigm Dynamic Array and Digital Array integrated fluidic circuits (IFCs) in end point mode.  Key advantages include:

  • Easy-to-use acquisition software module that allows each chip run to be started within minutes.
  • Multiplex capability for up to five reporter dyes (three standard).
  • A barcode reader that identifies each chip type and tracks results.


EP1 Reader

FC1™ Cycler

The Fluidigm FC1 Cycler is specially designed for thermal cycling of Fluidigm Dynamic Array and Digital Array IFCs.

Key advantages include:

  • Fast thermal cycling for SNP genotyping applications
  • Easily scalable to meet throughput requirements
  • Intuitive, easy to use touch-screen interface.


FC1™ Cycler

IFC Controllers

IFC controllers are used to automatically set up thousands of reactions in Fluidigm Dynamic Array and Digital Array IFCs in a matter of minutes.  Key advantages include:
  • Automated setup of  Dynamic Array IFCs
  • Significantly reduced liquid handling steps
  • Self-contained and fully integrated design
IFC Controller Dynamic Array IFCs Digital Array IFCs
  48.48 96.96 FR48.48 12.765 48.770
MX x     x x
HX   x      
WX     x  


HX Controller

Dynamic Array™ IFCs

Fluidigm Dynamic Array integrated fluidic circuits (IFCs) deliver a new level of efficiency and throughput for real-time PCR and genotyping applications. Dynamic Array IFCs have an on-chip network of microfluidic channels, chambers and valves that automatically assemble individual PCR reactions, decreasing the number of pipetting steps required by up to 100 fold. Reusable chip formats have also been developed to dramatically decrease costs and increase throughput. The available chip formats are:

  • 192.24 - 192 samples x 24 assays (single use)
  • FR48.48 – 48 samples x 48 assays (reusable, SNP Genotyping use only)
  • 48.48 – 48 samples x 48 assays (single use)
  • 96.96 – 96 samples x 96 assays (single use)
  • FLEXsix – Six 12 samples x12 assays single use partitions
    (unused partitions can be used over 3 months from first run)


The 96.96 Dynamic Array IFC

Digital Array™ IFCs

The Fluidigm Digital Array integrated fluidic circuit (IFC) enables users to conduct digital PCR experiments. The digital array partitions a sample, premixed with PCR reagents, into hundreds of individual PCR reactions. This partitioning of the mixture allows the absolute quantification of target sequences. Digital PCR is a novel technique for PCR applications demanding extremely accurate determination of copy number variation.

Using the Fluidigm digital PCR technology, there are just five easy steps from setup to analysis to discovery.  See how it's done.


The 48.770 Digital Array IFC

SNPtype™ Assays

Take full advantage of your EP1™ or BioMark HD Systems with Fluidigm SNPtype Assays. The assays provide a high-throughput, low-cost single nucleotide polymorphism (SNP) genotyping solution which enables rapid assay design and polymorphism screening. They are based on allele-specific PCR SNP detection chemistry. SNPtype Assays combine the advantages of minimum experimental setup time and flexible assay choices.

Benefits include:

  • Cost savings—low startup and running costs
  • Confidence—locus-specific primer sequences provided
  • Flexibility—change targets on demand


Cluster plot for a typical SNPtype Assay

Each software application was designed to be intuitive and easy-to-use, with the industry’s best graphical user interface. The Fluidigm software features include pipetting templates, easy import/export functionality, predefined experiment layouts, and selection of data viewing options.

Genotyping Analysis

The Fluidigm Genotyping Analysis software includes additional features specific to genotyping applications including:

  • Automatic cluster calling -  a highly accurate cluster calling algorithm that ranks among the best in the industry and automatically increases in accuracy as it processes more samples
  • Multiple chip scoring - combines and scores multiple experiments to decrease the analysis time and improve scoring accuracy for rare genotypes
  • Confidence score -  automatically determines the confidence level of cluster calls


Allele Map

Automatic cluster calling.

Digital PCR Analysis

The digital array software enables you to use the digital array for new, exciting and previously unavailable applications.

  • Multiplex capability - up to four reporter dyes can be used per reaction, allowing you to quantitate up to four targets per sample in each reaction
  • Copy number variation - the software will automatically apply statistical correction and determine the ratio of your targets of interest
  • End-point analysis - allows you to use end-point image for analysis, greatly increasing the throughput of the system


Heat Map and Call/No-Call Map

The software automatically counts and reports the number of positives for each reporter dye.


Specification Sheet

Data Sheets

Application Notes


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SNP Genotyping Workflow

  • Prime. Prime the Dynamic Array IFC to close the interface valves, preventing premature mixing of samples and assays.
  • Transfer. Pipette samples, premixed with master mix, into separate sample inlets, and primer-probe sets into separate primer-probe inlets on the chip.
  • Load. Place the Dynamic Array IFC on the IFC Controller to automatically setup reaction chambers.
  • Thermal Cycle. Place the Dynamic Array IFC on the FC1 Cycler and start the PCR protocol.
  • Read. Place the Dynamic Array IFC on the EP1 Reader for fluorescence detection.
  • Analyze. Use SNP Genotyping Analysis Software to view and analyze color-coded allele maps and cluster diagrams for one or more chip runs.
  • Reuse. For reusable IFCs, pipette cleaning solutions into the IFC and use the IFC Controller to prepare for reuse.


Digital PCR Workflow

  • Prime. Prime the Digital Array IFC to prepare it for transferring samples.
  • Transfer. Pipette each of the samples, premixed with master mix and primer-probe sets, into separate inlets on the frame of the chip.
  • Load. Place the Digital Array IFC on the IFC Controller, and use the software interface to pressure load the assay components into separate panels of reactions.
  • Thermal Cycle. Place the Dynamic Array IFC on the FC1 Cycler and start the PCR protocol.
  • Read. Place the Dynamic Array IFC on the EP1 Reader for fluorescence detection.
  • Analyze. View and analyze digital PCR results.


    Instrument Specifications

    Throughput 2,304 reactions per run (using the FR48.48 Dynamic Array IFC)
    2,304 reactions per run (using the 48.48 Dynamic Array IFC)
    9,216 reactions per run (using the 96.96 Dynamic Array IFC)
    9,180 reactions per run (using the 12.765 Digital Array IFC)
    Sensitivity Single copies present in reaction chambers are routinely detected (using TaqMan® chemistry)
    Excitation Filters
    (center, in nm)
    485, 530, 580 (two empty positions)
    Emission Filters
    (center, in nm)
    525, 570, 630 (two empty positions)
    Detection CCD camera
    Illumination 175-watt Xenon arc lamp
    Thermal Control Peltier-based, ranging from 4ºC - 99ºC
    Max Heating ramp rate: >5ºC/sec
    Max Cooling ramp rate: >5ºC/sec
    Chip Compatibility Dynamic Array IFCs (48.48, 96.96, FR48.48)
    Digital Array IFCs (12.765, 48.770)
    Software Real-time PCR Analysis Software
    Genotyping Analysis Software
    Digital PCR Analysis Software
    Data Collection Software
    Computer and Accessories Internal CPU; LCD flat screen monitor; wireless keyboard and mouse
    Data Storage Options 1 GB/sec Ethernet connection; 40+ GB hard disk space; USB port for memory stick
    Startup Support
    Installation Installation kit; On-site installation and training

    TaqMan is a registered trademark of Roche Molecular Systems, Inc

    Integrated Fluidic Circuits (IFC) Specs

    Parameter 96.96 Dynamic Array IFC 48.48 Dynamic Array IFC FR 48.48 Dynamic Array IFC 48.770 Digital Array IFC 12.765 Digital Array IFC
    Sensitivity of detection Single-copy, per 6.75 nL reaction Single-copy, per 10 nL reaction Single-copy,
    per 8 nL reaction
    per 0.85 nL reaction
    per 6 nL reaction
    Sample wells 96 48 48 48 12
    Reagent (primers/probes) wells 96 48 48 Combined with Sample Combined with Sample
    Input volume per well 5 µl (minimum) 5 µl (minimum) 5 µl (minimum) 8 µl (minimum) 4 µl (minimum)
    Liquid-transfer steps 96 96 96 48 12
    Reactions per chip 9,216
    (96 x 96)
    (48 x 48)
    (48 x 48)
    (48 x 770)
    (12 x 765)
    Experiment tracking Chip-specific barcodes Chip-specific barcodes Chip-specific barcodes Chip-specific barcodes Chip-specific barcodes
    Setup and valve control IFC Controller HX IFC Controller MX IFC Controller WX IFC Controller MX IFC Controller MX
    Detection and analysis EP1 Reader EP1 Reader EP1 Reader  EP1 System EP1 System