QX200™ Droplet Digital™ PCR System

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QX200 Droplet Digital PCR System

Overview

Success Stories: Articles and Videos

Success Stories: Articles

Genomic Variation Analysis: Single Nucleotide Polymorphism: Validation of Allele-Specific Expression Predicted by RNA-Seq in Human Brain Specimens
In the context of human brain development, the QX100™ Droplet Digital™ PCR System yields unambiguous results for genotype identification of low-expression genes and provides absolute quantification of allele-specific expression (ASE) without the use of a standard.
Download the article.

Genomic Variation Analysis: Copy Number Variation: DUF1220 Copy Number Variation across Healthy and Diseased Populations
Studying copy number variation (CNV) with the QX100 Droplet Digital PCR System allows the robust identification of genetic factors such as DUF1220 in neurogenetic diseases between individuals with greater accuracy and precision, while effectively validating array CGH data.
Download the article.

Genomic Variation Analysis: Single Nucleotide Polymorphism: Detection of Single Nucleotide Variation Frequencies by Droplet Digital™ PCR
The QX100 Droplet Digital PCR System validated DNA sequencing results of induced pluripotent stem cells (iPSCs). In addition to confirming the high frequency of single nucleotide variations (SNVs), a de novo type of SNV was identified.
Download the article.

Cancer Mutation Analysis: How Droplet Digital PCR Has Revolutionized Noninvasive Plasma-Based Detection of Mutations
Performing Droplet Digital PCR with the QX100 Instrument effectively detected and accurately quantified the EGFR T790M marker in targeted therapies with limited cancer tumor samples.
Download the article.

Viral Quantification: Adeno-Associated Virus Vector Genome Titer Assay
Determining the adeno-associated virus (AAV) vector genome (vg) titer assay is critical in gene therapy applications. The improved sensitivity observed with Droplet Digital PCR (ddPCR™) technology makes it highly suitable for titration of clinical-grade AAV vector preparations.
Download the article.

Gene Expression: Digital Quantification of Potential Therapeutic Target RNAs
Measuring the exact number of long noncoding RNAs (lncRNAs) in subcellular compartments with Droplet Digital PCR (ddPCR) provides insights into their role and mechanism of action.
Download the article.

Third Generation PCR: A Novel Way to Accurately Measure Copy Number Variations in Human Genome
The McCarroll Lab uses Droplet Digital technology to study the distribution and molecular properties of the genome and its influence on gene expression, as well as the genetics underlying schizophrenia and bipolar disorder.
Download the article.

Success Stories: Videos

Droplet Digital™ PCR opens new perspectives in HIV research. Sangamo BioSciences, Inc. is developing HIV therapeutics toward a functional cure using the company’s proprietary zinc finger DNA-binding protein technology.
Download the article.


Professor Alec Morley, a pioneer in digital PCR, and his colleagues in Adelaide have developed tests for detecting acute lymphoblastic leukemia (ALL) and chronic myeloid leukemia (CML) using the unrivaled sensitivity of the QX200 Droplet Digital PCR System.



Droplet Digital™ PCR Publications

Browse the growing list of cited peer-reviewed journal articles in Droplet Digital™ PCR research featuring Bio-Rad products.

The publications appear in journals such as PLOS ONE, Cell, Nucleic Acids Research, and Nature Methods and span the following applications:

Cancer
 
mRNA quantification and expression
Copy number variation
Mutation detection
Droplet Digital PCR methods/ analytical performance
Next-generation sequencing library quantification/validation
Environmental studies
Pathogen detection (microbe/viral)
Epigenetics
Plasma/cell-free DNA
Gene expression  

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QX200™ Droplet Digital™ Brochure

Droplet Digital PCR (ddPCR™) is Bio-Rad's unique digital PCR technology.

  • Unrivaled precision provides absolute quantification of target DNA or RNA molecules without the use of standard curves
  • Addresses the lack of scalable and practical technologies for digital PCR implementation

The QX200 ddPCR system makes this powerful technology accessible to you for unveiling previously unattainable
research levels.

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QX200™ Droplet Digital™ (ddPCR™) Data
Detection of BRAF V600E Mutation

High sensitivity of the QX200 system allows quantification of BRAF V600E mutation in the presence of wild-type DNA using PrimePCR ddPCR assays. A, 2-D fluorescence amplitude plot generated by QuantaSoft™ software shows triplicate wells of a mixed mutant:wild-type sample. The black cluster on the plot represents the negative droplets, the green cluster represents the droplets that are positive for wild-type DNA only, the blue cluster represents the droplets that are positive for mutant DNA only, and the orange cluster represents the droplets that are positive for both mutant and wild-type DNA. B, 2-D fluorescence amplitude plot shows three replicates of a wild-type-only sample. C, fractional abundance plot shows the percentage frequency (orange markers) of the mutant DNA in a wild-type DNA background. The blue markers indicate the concentration of mutant DNA (copies/µl) and the green markers indicate the concentration of wild-type DNA (copies/µl) in each of three replicate samples. All error bars generated by QuantaSoft software represent the 95% confidence interval.



Detection of Herpes Simplex Virus and β2 Microglobulin

ddPCR enables precise and reproducible detection of herpes simplex virus 1 (HSV-1) and ß2 microglobulin (B2M) targets in a duplex assay. A, 2-D fluorescence amplitude plot shows three merged replicate samples of 10,000 copies/well of HSV-1 duplexed with 20,000 copies/well of Β2M. The black cluster on the plot represents the negative droplets, the green cluster represents the droplets that are positive for HSV-1 only, the blue cluster represents the droplets that are positive for B2M only, and the orange cluster represents the droplets that are positive for both HSV-1 and B2M targets. B, concentration plot shows merged triplicate wells across an HSV-1 sample dilution series from 0 to 40,000 copies in a constant background of 20,000 copies (66 ng human genomic DNA) of B2M. The blue markers indicate HSV-1 copies/µl and the green markers indicate B2M copies/µl. All error bars generated by QuantaSoft software represent the 95% confidence interval.



Detection of Copy Number for
Myelocytomatosis Oncogene and β-Globin

The QX200 system provides superior resolution with copy number (CN) calls from CN1 to CN13. A, 2-D fluorescence amplitude plot shows duplicate wells of a CN6 sample duplexed with myelocytomatosis oncogene (MYC) and β-globin (HBB) assays. The black cluster on the plot represents the negative droplets, the green cluster represents the droplets that are positive for MYC only, the blue cluster represents the droplets that are positive for HBB only, and the orange cluster represents the droplets that are positive for both MYC and HBB targets. B, copy number plot shows samples ranging from CN1 to CN13 with precise duplicate well values. All error bars generated by QuantaSoft software represent the 95% confidence interval. NTC, no template control.



Validation for Next-Generation Sequencing

ddPCR provides nearly 1,000-fold greater sensitivity and an amplification bias–free approach compared to RNA-Seq for validation. A, concentration plot shows a twofold dilution of cDNA generated using Bio-Rad’s iScript™ advanced cDNA synthesis kit for RT-qPCR. Two independent measurement sets were made: one at a high concentration range and one at a lower range, with four points overlapping. B, table shows comparative results between ddPCR and MiSeq. ddPCR detected thousands of copies per well with low-abundance transcripts (TBP and GUSB genes) using an input of 100 ng total RNA, which demonstrates enhanced sensitivity. The MiSeq sequencer detected only single-digit reads per kilobase per million reads (RPKM) for these transcripts. ddPCR, Droplet Digital PCR.



Gene Expression Analysis of Stem Cell Markers

High sensitivity and precision of the QX200 system allow reliable detection of small fold changes with rare transcripts. The TGFβ signaling pathway plays a role in ovarian stem cell regulation, and the addition of TGFβ will increase the number of stem cells in the population, increase the expression of putative stem cell markers, and decrease terminal differentiation markers like E-cadherin (ECAD). Data show expression levels of cKIT, CD133, OCT3/OCT4, and ECAD genes across ten samples with and without TGFβ treatment, normalized to PPIA in this study. Reproducible detection of cDNA copies as low as 0.5–1 target/µl in a 20 µl reaction was achieved. S, sample.


The QX200 Droplet Digital PCR (ddPCR™) System provides absolute quantification of target DNA or RNA molecules for EvaGreen or probe-based digital PCR applications.

Benefits of the QX200 Droplet Digital PCR System

  • Most precise and sensitive digital PCR solution for a wide variety of applications
  • Flexible digital PCR chemistry — optimized for TaqMan Hydrolysis Probe and EvaGreen Assays
  • Flexible assay setup — scalable for high sensitivity or high throughput
  • Simple and easy-to-use workflow with 96-sample throughput
  • Droplet partitioning by the QX200 Droplet Digital technology reduces bias from amplification efficiency and PCR inhibitors
  • Convenient assay design — standard curves are not required

See Performance Data for the QX200 Droplet Digital PCR System.

Watch our Success Stories videos to learn more about the applications of the Droplet Digital System in diverse research fields.

View our Droplet Digital PCR reference library with links to scientific journals articles, conference posters, BioRadiations articles and Bio-Rad technical reports.

Applications of the QX200 Droplet Digital PCR System

  • Cancer biomarker studies and copy number variation
    Measure varying degrees of cancer mutations, detect rare DNA target copies, and resolve copy number variation states with superior sensitivity and resolution. PrimePCR™ ddPCR Assays are now available for mutation and copy number detection. These are predesigned, wet-lab validated assays.

  • Pathogen detection
    Employ the extreme precision of the QX200 System to quantify small fold changes in target DNA or RNA molecules in pathogen detection and monitoring.

  • Next generation sequencing
    Perform accurate quantification and qualification of NGS libraries without the use of a standard curve.

  • Gene expression analysis
    Achieve reliable and reproducible measurements of small fold changes for low abundance of mRNA and miRNA.

  • Environmental monitoring
    Test a wide variety of environmental samples like soil and water using the QX200 System.

  • Food testing
    Perform routine evaluation of genetically modified organisms (GMO) using validated ddPCR methods.
Droplet Digital PCR applications guide Download the Droplet Digital PCR applications guide for in-depth information about setting up experiments for applications including:
  • Copy number variation analysis
  • Rare mutation and sequence detection
  • Gene expression
  • Next-generation sequencing library analysis

Droplet Digital PCR Technology and Workflow

The QX200 Droplet Digital PCR System consists of two instruments, the QX200 Droplet Generator and the QX200 Droplet Reader, and their associated consumables.

The QX200 Droplet Generator is used to partition ddPCR reaction mix into 20,000 nanoliter-sized droplets. After PCR on a thermal cycler, droplets from each sample are analyzed individually on the QX200 Droplet Reader. Droplets are sipped and the singulator unpacks the emulsified droplets and streams them in single file past a two-color optical detection system in a serial manner. Up to 96 samples can be processed per run. The PCR-positive and PCR-negative droplets are counted to provide absolute quantification of target DNA in digital form. Alternatively, amplified products can be extracted from droplets following PCR for downstream applications, such as sequencing or cloning.

QX200 Droplet Digital PCR system workflow

Additional Instruments

The QX200 Droplet Digital PCR System requires the use of the C1000 Touch™ Thermal Cycler with 96–Deep Well Reaction Module and the PX1™ PCR Plate Sealer.

Required Accessories

ddPCR Reagents for EvaGreen or TaqMan Hydrolysis Probe-Based Applications

More Information

Explore the features of the QX200 System in more depth in the QX200™ Droplet Digital™ PCR System Brochure (bulletin 6311) or contact your Bio-Rad sales representative for more information.

Starting sample size, µl 20
QX200 droplet generator capacity 1–8 samples/cartridge
Droplets per 20 µl sample 20,000
QX200 droplet reader capacity 1–96 samples
Sample illumination Light-emitting diodes
Sample detection Multi-pixel photon counter
Detection channels FAM (EvaGreen), HEX (VIC)
Linear dynamic range 5 orders of magnitude
Precision ±10%
Droplets per 96-well plate, million ~1.5
QX200 droplet generator dimensions (W x D x H) 28 x 36 x 13 cm (11 x 14 x 5")
QX200 droplet reader dimensions (W x D x H) 66 x 52 x 29 cm (26 x 20 x 11")
QX200™ Droplet Digital™ PCR System

186-4001
Droplet Digital™ PCR System, includes droplet generator, droplet reader, laptop computer, software, associated component consumables, for EvaGreen or probe-based digital PCR applications

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Quantity:   Add to Quote
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QX200™ Droplet Generator

186-4002
Droplet generator for EvaGreen or probe-based digital PCR applications, for use with QX200™ Droplet Digital™ PCR System

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QX200™ Droplet Reader

186-4003
Droplet reader for EvaGreen or probe-based digital PCR applications, for use with the QX200™ Droplet Digital™ System

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Quantity:   Add to Quote
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PX1™ PCR Plate Sealer

181-4000
PCR plate sealer, includes heat sealing instrument, plate support block that holds 96-well and 384-well plates, sealing frame, power cord

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Quantity:   Add to Quote
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C1000 Touch™ Thermal Cycler with 96–Deep Well Reaction Module

185-1197
Modular thermal cycler platform, includes C1000 Touch Thermal Cycler chassis, 96–deep well reaction module, USB flash drive

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Number Description Options
6554 Droplet Digital™ PCR: Detection of DNA Methylation Application Note, Rev A Click to download [ Add to Cart (Free) ]
10040717 QX200 Droplet Generation Oil for EvaGreen Product Insert, Rev B Click to download
10040718 Droplet Generation Oil for Probes Product Insert, Rev B Click to download
6407 Droplet Digital PCR Applications Guide, Rev A Click to download
6541 Droplet Digital™ PCR: TRAPing Telomerase Activity Using Droplet Digital PCR Application Note, Rev A Click to download
6338 Droplet Digital™ PCR (ddPCR™) Supermixes Flier, Rev A Click to download
6311 QX200 Droplet Digital PCR System Brochure, Rev B Click to download
6290 PrimePCR Assays and Panels Brochure, Rev D Click to download
6450 Droplet Digital PCR Publications List, Rev F Click to download
10031907 Instruction Manual, QX200 Droplet Generator, Rev A Click to download
10031906 Instruction Manual, QX200 Droplet Reader and QuantaSoft Software, Rev A Click to download
6512 PrimePCR Assays for Droplet Digital PCR Brochure. Rev A Click to download
6444 PrimePCR Probe Assays for Droplet Digital PCR, Product Information Sheet, Rev B Click to download
10028376 QX200 EvaGreen ddPCR Supermix Product Insert, Rev A Click to download
10026868 ddPCR Supermix for Probes (no dUTP) Product Insert, Rev C Click to download
10026235 ddPCR Supermix for Probes Product Insert, Rev B Click to download
10028782 One-Step RT-ddPCR Kit for Probes Product Insert, Rev B Click to download
10033630 ddPCR Library Quantification Kit for Ion Torrent Product Insert, Rev B Click to download
6473 QX200 ddPCR EvaGreen Supermix Flier, Rev A Click to download
6250 One-Step RT-ddPCR Kit for Probes Flier, Rev A Click to download
6490 ddPCR Library Quantification Kit for Ion Torrent Flier, Rev A Click to download
6495 Bio-Rad’s ddPCR™ Library Quantification Kit for Ion Torrent Enables Accurate Library Quantification and Excellent Balancing of Pooled Libraries, Rev A Click to download
6402 ddPCR Library Quantification Kit for Illumina TruSeq Flier, Rev B Click to download
10031986 ddPCR Library Quantification Kit for Illumina TruSeq Product Insert, Rev C Click to download
6343 QX100 Droplet Digital PCR System for Accurate Quantification of Illumina TruSeq Libraries, Rev B Click to download
6451 Droplet Digital PCR: Guidelines for Multiplexing Using Bio-Rad’s QX100 Droplet Digital PCR System Application Note, Rev A Click to download
6497 Droplet Digital PCR: Linking Microbial Physiology and Phylogeny Using Bio-Rad’s QX100 Droplet Digital PCR System Application Note, Rev A Click to download
6277 Probing Copy Number Variations Using Bio-Rad's QX100 Droplet Digital PCR System, Rev A Click to download [ Add to Cart (Free) ]
6475 Droplet Digital PCR: High-Resolution Copy Number Variation Analysis Application Note, Rev A Click to download
6319 Third Generation PCR: A Novel Way to Accurately Measure Copy Number Variations in Human Genome [Harvard laboratory interview]. BioRadiations, Featured Stories, February 9, 2012 Click to download
6423 Droplet Digital PCR: Ultra-Sensitive Validation Technology for RNA-Seq Application Note, Rev A Click to download [ Add to Cart (Free) ]
6424 Droplet Digital™ PCR: Ultra-Sensitive Rare Event Detection Using Bio-Rad’s QX100™ Droplet Digital PCR System Application Note, Rev B Click to download
6318 Droplet Digital PCR Opens New Perspectives in HIV Research [Sangamo BioSciences, Inc. laboratory interview]. BioRadiations, Solutions, June 15, 2012 Click to download
10023997 Instruction Manual, PX1 PCR Plate Sealer, Rev A Click to download
6257 PX1 PCR Plate Sealer and Heat Sealing Consumables Brochure, Rev A Click to download
6314 Droplet Digital PCR detection of HER2 expression in FFPE breast tissue samples (Poster), Rev A Click to download
6315 Droplet Digital PCR: 3rd generation PCR provides improved detection, quantification, identification, and characterization of microbial targets. (Poster), Rev A Click to download
6316 Droplet Digital RT-ddPCR: Ultra-high sensitivity validation technology for RNA-Seq. (Poster), Rev A Click to download
6317 Detection of rare mutations in blood samples by Droplet Digital PCR (ddPCR). (Poster), Rev A Click to download