Droplet Digital PCR

Droplet Digital™ PCR Systems,
Assays, and Kits

Visit bio-rad.com/ddPCR-QXFamily for more information.

Table of Contents
What Is Digital PCR?
Introduction
How Does Droplet Digital PCR (ddPCR™) Work?
Why Droplets?

3
3
4
5

Applications and Assays
Translational Research
Biopharma
Infectious Disease and Wastewater Surveillance
Custom Assay Services

7
7
11
14
16

ddPCR Systems
Platform Selector
QX600™ ddPCR System
QX200™ ddPCR System
QX ONE™ ddPCR System
Automated Droplet Generator
QX200 Droplet Generator

17
17
19
20
21
22
22

Software
QX Manager and QX ONE Software
QX Designer Software

23
23
24

Sustainability

25

Service and Support

26

2 | BIO-RAD LABORATORIES, INC.

What Is Digital PCR?

Welcome to the third generation of PCR technology. Building on conventional andquantitative PCR (qPCR) technologies, digital PCR overcomes common hurdles andoffers new features.
Benefits of Digital PCR
Absolute quantification — digital PCR measures countsof the input target DNA molecules without relying on
standard curves■■■

 recision and sensitivity — digital PCR partitions thePsample into thousands of individual microreactions. Eachmicroreaction is amplified and read individually, enabling
improved precision, sensitivity, and accuracy compared
to qPCR
Inhibitor tolerance — PCR microreactions mitigate
the impact of inhibitors, such as SDS and heparin,better than qPCR

The Droplet Difference
Since 2011, Bio-Rad’s unique Droplet Digital PCR (ddPCR)
technology has established itself as a world-leading, highly
trusted digital PCR format, with thousands of ddPCR
systems in use. Droplet Digital PCR has supported over
8,000 peer-reviewed publications in diverse fields, including
cancer biomarker discovery, infectious disease, and cell andgene therapy.
Benefits of Droplet Digital PCR
In addition to all the benefits of digital PCR, Droplet Digital
PCR offers:■■

 uperior precision and sensitivity — our ddPCR
S
instruments include built-in quality control systems tofurther improve precision and sensitivity
 emoval of PCR efficiency bias — error rates areR
reduced relative to qPCR by removing the reliance on
amplification efficiency

Explore absolute quantification with Droplet Digital PCR.
Download our article, Counting DNA Molecule by Molecule(bulletin 7374).

3 | BIO-RAD LABORATORIES, INC.

How Does Droplet Digital PCR Work?
One PCR Reaction, 20,000 Microreactions

Reaction Mechanics

DNA sample with target sequence is partitioned into droplets

Target and background DNA are randomly distributed among 20,000 droplets

Target sequence is amplified by endpoint PCR in each droplet

Positive droplets are counted to precisely quantify target sequences in the sample

What Does the Workflow Look Like?
Droplet Digital PCR uses a familiar format to provide a simple way to get high-quality
quantitative digital PCR data — no special plates are needed.

1

2

3

4

Step

Step

Step

Step

Sample Preparation
ddPCR reactions areprepared similarly to
traditional PCR orqPCR reactions thatuse hydrolysis probes or
EvaGreen® chemistry.

Droplet Generation
The droplet generator
distributes template
molecules randomly into
approximately 20,000
uniform droplets.

PCR Amplification
Each droplet behaves
as an individual PCR
reaction, as template
molecules inside each
droplet are amplified
by endpoint PCR ina thermal cycler.

Droplet Reading andData Analysis
The droplet reader counts
droplets as positive or
negative based on theirfluorescence. These data
are then used to calculate
absolute template quantityand perform further analysis.

4 | BIO-RAD LABORATORIES, INC.

Why Droplets?
Not All Digital PCR Is Created Equal

Individually read droplets enable a high degree of discrimination between positives andnegatives. This format also allows the creation of 20,000 partitions without expensive,
specialized plates. Accuracy and quality rules are transferable with QX Manager Software
between different instruments and sites for comparable data.

Good Digital PCR Data
From a Bio-Rad QX200 ddPCR System

Bad Digital PCR Data
From “Instrument X”
Positive partition

Positive partition

60
60

4,000
4000

Amplitude

Amplitude

3,000
3000
2,000
2000
1,000
1000

00
–1,000-1000■

 mplitude separationA
between Data
positive and negative
Good dPCR
partitions
providesconfidence
in™results™
from Bio-Rad
QX200
DropletDigitalPCR (ddPCR™) System

5 | BIO-RAD LABORATORIES, INC.

40
40
30
30

20
20
10
10

Negative partition

 ight and consistent amplitudes for positive and negativeTpartitions enable easy threshold setting

■

50
50
Fluorescence intensity (RFU)

Fluorescence intensity [RFU]

5,000
5000

00

■

■

Negative partitionInconsistent amplitudes within partition types make it
difficult to confidently set thresholds
 ack of separation between partitions means that slightL
Bad dPCR
changes in day-to-day
sampleData
prep and reaction setup
from"Instrument
X" quantification
can alter results, preventing accurateWhy Droplets?

Advantages of Droplet Digital PCR:

Fewer instances of:Random Positive Partitions

Unlike well-based PCR, droplets are isolated when reading fluorescence,
preventing bleed through from neighboring reactions. Better consistency
and reproducibility ultimately result in better specificity and sensitivity,
lower noise, and a lower limit of detection.

Fluorescence intensity
Fluorescenceintensity[RFU](RFU)Consistency and Reproducibility
120
120
100
100
80
80
60
60
40
40
20
20

00

Cross-Contamination

Reduced Cross-Contamination and Better Contaminant Mitigation
140
140
Fluorescence intensity
Fluorescenceintensity[RFU](RFU)

Thermal cycling is performed in easily available PCR tubes or strips,
making the transition to ddPCR simple and reducing cross-contamination.
Contaminants in digital PCR reactions such as solids or bubbles cancontribute to poor signal. Droplet partitioning isolates contaminants ina subset of the 20,000 droplets, reducing their effects on the dataset.

120
120

100
RandomPositive Partitions
100
80
80
60
60
40
40
20
20

00

Noise

High Signal-to-Noise Ratio
60
60
Fluorescence intensity
Fluorescenceintensity[RFU](RFU)

The generation of 20,000 partitions per 20 µl reaction increases sensitivity
and signal-to-noise ratio, as compared to methods requiring serial dilution.

50
50

Cross Contamination

40
40
30
30
20
20

10
10
00

Hardware Instability

Stable Optics and Hardware for Analysis
80

Fluorescence intensity
Fluorescenceintensity[RFU]
(RFU)

60

70

50

60

Noise

40

50

30
40
30
20
20

10

10

0

0

Optical Instability
Fluorescence intensity
Fluorescenceintensity[RFU](RFU)

The droplet reader scans one droplet at a time using the same optics foreach droplet, reducing instrument variability. This also eliminates signal drift
and other hardware issues seen in non-droplet systems.

60
60
50
50
40
40

Hardware Instability

30
30
20
20
10
10

00

Optical Instability
6 | BIO-RAD LABORATORIES, INC.

Translational ResearchPrecise Quantification across Applications

Droplet Digital PCR can enhance translational researchby providing critical sensitivity and absolute quantification.
Research applications include gene expression andcopy number variation assays, cancer mutation screening,
quality control for next-generation sequencing (NGS),
and more. Whether seeking proven performance with
the QX200 ddPCR System, higher multiplexing with the
QX600 ddPCR System, or maximum throughput andaccuracy with the QX ONE ddPCR System, there is a
ddPCR solution in our portfolio to fit your needs.
Translational Research: From Bench to Bedside
Applying discoveries from lab and preclinical research to human clinical trials while ensuring quality is labor-intensive. Droplet
Digital PCR can provide confidence when validating biomarkers, optimizing therapeutics for safety and efficacy, testing purification
processes and formulations, and more.

7 | BIO-RAD LABORATORIES, INC.

Translational Research Applications

Cancer Mutation Detection and Screening
Droplet Digital PCR is an ideal solution for detecting mutant DNA, even at concentrations as low as 0.005%
of the total. Sample partitioning limits the number of DNA molecules in each droplet, effectively increasing therelative concentration of mutant DNA in positive droplets.

Gene Expression
In contrast to other techniques, Droplet Digital PCR can accurately quantify small changes (less than two-fold),even for low-abundance targets and in samples that contain PCR inhibitors. The ddPCR format also works
well with multiplexing, as partitioning reduces the competition for resources in each microreaction, ensuringthat multiple targets can be efficiently amplified without bias.

Copy Number Variation
Droplet Digital PCR is a highly effective quantitative method for detecting even small changes. For example,
it can distinguish between five and six copies of a target (a 1.2-fold change). Using ddPCR technology, one
can discriminate, with statistical confidence, between consecutive copy number states with fewer sample
replicates. Droplet Digital PCR offers absolute quantification with the level of precision and resolution needed
for accurate and straightforward copy number variation analysis.

C

A

G

T

G

T

C

A

NGS Validation
When preparing samples for NGS, Droplet Digital PCR can provide precise quantification of DNA to avoid
unnecessary amplification and preserve resource integrity. Absolute quantification allows Droplet Digital PCR
to be easily integrated into the NGS library preparation workflow — balancing pooled library samples andproviding insights into library quality parameters, such as by detecting adapter dimers and measuring libraryinsert size.

Genome Editing
Droplet Digital PCR offers an ultrasensitive, rapid, and low-cost method for absolute quantification of genome
editing events, even from very small amounts of starting material. Clones harboring homozygous andheterozygous edits can be easily distinguished for any target of interest. Droplet Digital PCR enables a rapid
and efficient workflow with the ability to quickly identify and focus on desired clones.

8 | BIO-RAD LABORATORIES, INC.

Translational Research Assays

Multiplex Mutation Screening Kits
Our ddPCR Multiplex Mutation Screening Kits are wet lab–validated and have been designed for rapid
screening of several key cancer mutations in a single reaction. These kits are compatible with traditional
tissue samples, including formalin-fixed paraffin-embedded (FFPE) samples, and liquid biopsies — where theexceptional sensitivity of Droplet Digital PCR enables detection of rare circulating tumor DNA. ddPCR Multiplex
Mutation Screening Kits are available for actionable mutations in common targets such as BRAF, KRAS,
NRAS, and EGFR, or visit our Digital Assay site to easily design assays for over 4 million mutations listed in the
COSMIC database.

Microsatellite Instability (MSI) Kit
The ddPCR Microsatellite Instability (MSI) Kit enables rapid testing of FFPE and plasma samples to assess
MSI marker status in colorectal and other relevant cancers with superior sensitivity and specificity.

Mutation Detection Assays
ddPCR Mutation Detection Assays can be used to detect rare single nucleotide polymorphisms (SNPs) andallelic variants. Our assays are available for >200 targets and have been wet lab–validated, so you can haveconfidence in your results. For other targets of interest, you can design your own custom assays through our
Digital Assay portal.

Gene Expression Assays
ddPCR Gene Expression Assays enable accurate quantification of small fold changes in gene expression, as
small as 2-fold or lower, for low-abundance targets and in samples that contain PCR inhibitors. Choose fromover 60,000 gene expression assays for human, rat, and mouse, with the option of using labeled probes for
multiplexing or EvaGreen® for cost-effective detection of single targets per well.

For Research Use Only. Not for use in diagnostic procedures.

9 | BIO-RAD LABORATORIES, INC.

Translational Research Assays

SMN

SMN1 and SMN2 Copy Number Determination Kits
These kits are designed to accurately and reproducibly determine copy number calls for the SMN1 and SMN2
genes, and can help determine the spinal muscular atrophy (SMA) phenotype.

Copy Number Variation Assays
With wet lab–validated assays readily available for >700 targets and the ability to quickly design assays for
additional targets, you can be confident in your results, even when detecting small changes in copy number.

Library Quantification Kits
Digital PCR Library Quantification Kits can be easily incorporated into the NGS library preparation workflow to
precisely quantify and balance sequencing libraries on Illumina® platforms. These kits provide both accuratequantification and rich qualitative information about your DNA libraries prior to sequencing.

Genome Editing
Droplet Digital PCR Genome Edit Detection Assays offer a fast, precise, simple, and cost-effective methodfor detection of genome editing events created using nucleases that cause double-stranded breaks, such as
CRISPR-Cas9. Assays to detect homology-directed repair (HDR) and non-homologous end joining (NHEJ)
events can be designed and obtained for any target with our easy-to use, intuitive Digital Assay site.

Visit bio-rad.com/digital-assays to browse our premade assays or order custom assays for your targets of interest.

For Research Use Only. Not for use in diagnostic procedures.

10 | BIO-RAD LABORATORIES, INC.

Biopharma
Support for the Entire Pipeline

The sensitivity to detect rare events and variants makes
ddPCR technology ideal for a variety of applications intherapeutic research and development, from candidate
identification to manufacturing quality control. All QX
Systems are compatible with 96-well plates, facilitating
higher throughput. The QX600 System’s ability to multiplex
up to six targets per well enables detailed and sensitive
analysis that can be combined with reverse transcription
for gene expression and pathway analysis. The QX ONE
System’s ability to process up to five 96-well plates per run
and measure four concurrent channels makes it ideal forhigh-throughput applications. Droplet Digital PCR platforms
are available to support the entire biopharma R&D andmanufacturing workflow.
Identify, Characterize, and Validate Target Molecules for Drug Development
Consistency, reproducibility, and reliability are critical to accelerating your drug discovery and development journey, from target
identification through scale-up and manufacturing. To maintain the highest quality standards and productivity, choose products that
automate your workflow and reduce hands-on time so you can focus on your most critical tasks.

TargetDiscovery

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Lead
Discovery

PreclinicalResearch

ClinicalResearch

Process
Development

Manufacturing
and TestingBiopharma Applications

Drug Discovery
Pathway-specific drug discovery is facilitated by parallel analysis of disease- and pathway-specific genes.
Because Droplet Digital PCR partitions samples into droplets, the effects of competition in PCR reactions are
reduced and optical bleedthrough from neighboring wells is eliminated, facilitating accurate multiplexing. The
absolute quantification of Droplet Digital PCR without the need for a standard curve also reduces the numberof reactions needed and enables reliable comparisons without worrying about plate-to-plate variation.

Cell and Gene Therapy
The absolute quantification of Droplet Digital PCR does not require the use of standard curves, granting
it higher precision and reducing the chance for errors in measurement. By delivering an absolute count of
nucleic acids in a therapeutic sample, ddPCR technology can give you more confidence in standard dose
determinations and quality control measurements.

RNA

RNA Therapeutics
Droplet Digital PCR provides the precision and accuracy necessary for the entire RNA therapeutic
development workflow, without sacrificing efficiency. Use ddPCR technology to quantify RNAs and gene
expression when identifying new therapeutic targets, helping you get foundational data you can rely on. For
testing and quality control of multivalent therapeutics, Droplet Digital PCR can precisely determine the ratio
between drug RNA species. In later stages of development, take advantage of absolute quantification toprovide confidence when analyzing biodistribution and establishing safe and effective dosing.

Contaminant Testing
By counting nucleic acids in samples, Droplet Digital PCR eliminates reliance on standard curves. The
concentration of target nucleic acid sequences and contaminants, such as host cell DNA and Mycoplasma,can be accurately measured, enabling stringent quality control. Unlike qPCR, Droplet Digital PCR also does not
require amplification to reach a certain threshold, meaning that the effects of secondary structure and inhibitory
host cell contaminants are minimized.

Cell Line Development
With the exceptional sensitivity of Droplet Digital PCR, you can find quality clones earlier in the cell line
development process, speeding up your workflow. By partitioning samples into droplets, competition
from high-copy templates is reduced, enabling accurate quantification even of low-abundance targets.
Droplet Digital PCR also does not require a standard curve, meaning that you can reliably measure copy
number with fewer reactions, and by extension, fewer cells.

12 | BIO-RAD LABORATORIES, INC.

Biopharma Assays
Vericheck ddPCR Kits
Vericheck ddPCR Detection and Residual DNA Quantification Kits
Vericheck ddPCR Kits enable sensitive and specific quantification of contaminants and impurities during thedevelopment and manufacturing of cell and gene therapies.

Vericheck ddPCR CHO Residual DNA Quantification Kit

Vericheck ddPCR Mycoplasma Detection Kit

For easy quantification of residual CHO DNA.

For sensitive detection of up to 112 speciesof Mycoplasma.

Vericheck ddPCR E. coli Residual DNA Quantification Kit

For accurate quantification of residual E. coli DNA.

Vericheck ddPCR HEK293 Residual DNA Quantification Kit

For specific quantification of HEK293 residual DNA.
Vericheck ddPCR HEK293 Residual DNA Size Kit

For measuring HEK293 residual DNA size without
reference curves.
Vericheck ddPCR Replication Competent Virus Testing Kits

For sensitive detection of replication competent
lentiviruses (RCL) or adeno-associated virus (RCAAV).

Workflows and Tools
Whole Cell DNA Workflow
The ddPCR Whole Cell DNA Workflow is a sensitive, reproducible, and easy workflow to measure thepercentage of modified cells at the DNA level with minimal input cells. It can be applied at multiple steps
during the cell therapy manufacturing process using any of our QX Systems.

Cell and Gene Therapy Assays
The design engine on our Digital Assay site provides a menu of ready-to-order ddPCR Expert Design Assays
targeting common viral vector and plasmid elements (Vector Backbone Assays), enabling robust viral titer andvector copy number measurements. For target genes not yet available as ddPCR Expert Design Assays, theengine can also help you design custom assays.

Genome Edit Detection Assays
The design engine on our Digital Assay site helps you design custom assays for your ddPCR platform of
choice, offering a fast, precise, simple, and cost-effective method for detection of genome editing events
generated by CRISPR-Cas9 or other genome editing tools. Precise detection of such editing events is vital forcell line development and other applications.

13 | BIO-RAD LABORATORIES, INC.

Infectious Disease and Wastewater Surveillance
Sensitivity Where You Need It Most

Pathogen detection and quantification are critical for
identifying, monitoring, and mitigating the impact of
diseases. Whether predicting outbreaks or surveying
seasonal ebb and flow, sensitivity and specificity areparamount. This is especially true for applications suchas wastewater surveillance, where inhibitors and nontarget
sequences are abundant. Droplet Digital PCR excels at
low-level quantification, is highly resistant to inhibitors, andprovides reproducible results with high confidence.
Wastewater Surveillance
Analyzing a diverse range of pathogens and contaminants, drawing on a variety of methods and techniques, and managing a large
volume of samples — these are the demands and challenges of wastewater surveillance. Public health scientists and wastewater
surveillance researchers must maintain high throughput and low instrument downtime while producing reliable results. Explore ourresources and technologies that can take your wastewater testing workflow to the next level.

Infectious Disease and Wastewater Surveillance Applications
Wastewater-Based Epidemiology (WBE)
Targeted nucleic acid sequences, such as those from viruses or bacteria, can be quantified to gain insights into
the prevalence and landscape of pathogens present in a community. Assays using Droplet Digital PCR were able
to detect the SARS-CoV-2 virus in a population 6 days earlier than clinical testing,* with a sensitivity capable ofdetecting one infected individual in 10,000.** Testing wastewater for the presence and diversity of antimicrobial
resistance genes against different drugs could indicate where — and to what extent — resistant bacteria arereleased into the environment.

Infectious Disease Research
Beyond SARS-CoV-2, assays to detect viral and other pathogens using the exceptional sensitivity of ddPCR
technology have been used in wastewater-based epidemiology and other applications. Our expertise andpartnerships have been used to track outbreaks of influenza variants, human monkeypox virus, and respiratorysyncytial virus, among others.

*	Medema G et al. (2020). Presence of SARS-coronavirus-2 RNA in sewage and correlation with reported COVID-19 prevalence in the early stage of the epidemic in the Netherlands.
Environ Sci Technol Lett 7, 511–516.
**	Hart OE and Halden RU (2020). Computational analysis of SARS-CoV-2/COVID-19 surveillance by wastewater-based epidemiology locally and globally: Feasibility, economy,
opportunities and challenges. Sci Total Environ 730, 138875.

14 | BIO-RAD LABORATORIES, INC.

Infectious Disease and Wastewater Surveillance Assays

Wastewater Surveillance Kits
Monitoring wastewater provides an early warning system and a community-wide surveillance method for
disease outbreaks. The PREvalence ddPCR SARS-CoV-2 Wastewater Quantification Kit is a highly sensitiveand cost-effective tool for detection of SARS-CoV-2 in wastewater with reproducible and quantitative results.

Infectious Disease and Wastewater Surveillance Assays
Browse our curated lists of infectious disease and wastewater assays. These ddPCR Expert Design Assays havebeen created by our application specialists to test for a growing range of diseases including influenza A and B,
human monkeypox virus, RSV, and many others. Visit bio-rad.com/digital-assays to see the complete list of targets
available, or request new ones using one of our custom assay services.
Featured infectious disease and wastewater assays.
Assay Name
Wastewater 6-Plex 1 (Adenovirus/Norovirus/MPXV/Enterovirus/Legionella)
Wastewater 6-Plex 2 (Adenovirus/Norovirus/MPXV/Influenza)
SARS-CoV-2 Influenza Multiplex
ddPCR Monkeypox_CongoddPCR Monkeypox_West Africa
Influenza A/B Triplex Assay
Zika NS5
Ebola VP24
Enterococcus spp.
Norovirus
Legionella
Adenovirus A-F
RSV A & RSV B

Don’t see a target you want? Talk to your representative
about one of our custom assay services.

For Research Use Only. Not for use in diagnostic procedures.

15 | BIO-RAD LABORATORIES, INC.

Custom Assay Services
Droplet Digital PCR at Your Fingertips
Find and Customize

DesignBrowseIn addition to validated kits and assays, we offer an online database of assays and design engines made specifically for
Droplet Digital PCR, to help you get the most out of your experiments. Take advantage of 24/7 service at your fingertips: searchor browse our curated lists of predesigned assays or design an assay on demand for your application — mutation detection, copy
number determination, gene expression, genome edit detection, or viral vector copy number for cell and gene therapy applications.
We offer a menu of select Expert Design Assays, designed by experts in Droplet Digital PCR for advanced applications.
Visit bio-rad.com/digital-assays to get started.

Assay Design Engines
Through the Digital Assay web portal, our design engines create assays based on simple genomic coordinates or sequencesthat you provide. The design engines are powered by the same design rules and algorithms as our validated assays.
Our in silico validation engine ensures robust performance of the assay designed.

Want to Multiplex?
Combine assays into a single multiplex design with our Assay Multiplexing Check tool.
Need Help with a Special Assay Request?
Ask your local field application scientist or account specialist about our ddPCR Assay Design Service.
Already Know What You Need?
Order directly through the Bio-Rad website for assays that are formulated and ready to use for Droplet Digital PCR.

For Research Use Only. Not for use in diagnostic procedures.

16 | BIO-RAD LABORATORIES, INC.

ddPCR Systems
Platform Selector
Bio-Rad’s ddPCR systems provide ultrasensitive, absolute nucleic acid quantification.
Use this overview to find the right system for your application.
Key Features*
Detection
Channels

Platesper Run

6

1

6

1

2

1

2

1

4

5

Basic and Translational Research Applications

Automation

Mutation
Detection

Gene
Expression

Copy Number
Variation

NGS
Validation

QX600 AutoDG™ ddPCR System

QX600 ddPCR System

QX200 AutoDG ddPCR System**

QX200 ddPCR System

QX ONE ddPCR System****	Additional features of all systems: capable of generating ~20,000 droplet partitions per sample using 96-well plates; capacity to generate
96 results in ≤6.5 hr.
**	Also available as the U.S. Food and Drug Administration (FDA)-cleared QXDx Automated Droplet Generator and QXDx Droplet Reader
for use with the QXDx BCR-ABL %IS Kit.
***	Features integration of thermal cycling, droplet generation, and droplet reading.
, fully manual; , partially automated; , fully automated.
, good;17 | BIO-RAD LABORATORIES, INC.

, better;, best.

ddPCR Systems
Platform Selector
Bio-Rad’s ddPCR systems provide ultrasensitive, absolute nucleic acid quantification.
Use this overview to find the right system for your application.
Biopharma Applications
Drug
Discovery

Cell and
Gene Therapy

RNA
Therapeutics

Infectious Disease Applications
ContaminantTesting

Cell Line
Development

Wastewater
Surveillance

QX600 AutoDG™ ddPCR System

QX600 ddPCR System

QX200 AutoDG ddPCR System**

QX200 ddPCR System

QX ONE ddPCR System****	Additional features of all systems: capable of generating ~20,000 droplet partitions per sample using 96-well plates; capacity to generate
96 results in ≤6.5 hr.
**	Also available as the U.S. Food and Drug Administration (FDA)-cleared QXDx Automated Droplet Generator and QXDx Droplet Reader
for use with the QXDx BCR-ABL %IS Kit.
***	Features integration of thermal cycling, droplet generation, and droplet reading.
, fully manual; , partially automated; , fully automated.
, good;, better;, best.

18 | BIO-RAD LABORATORIES, INC.

QX600 ddPCR System
Multiplexing Simplified

The QX600 System provides absolute quantification
using Droplet Digital PCR and is capable ofsix-channel detection — our highest degree ofmultiplexing. The QX600 System is shown herewith the Automated Droplet Generator, which isused for reliable partitioning at scale. The system isalso available with the QX200 Droplet Generator for
lower-throughput labs.

Key benefits:
Precise and sensitive multiplexing
Accurate and reproducible results
Portfolio compatibility
Powerful QX Manager Software

Visit bio-rad.com/QX600 to learn more.

Key applications:Multiplexing in mutation detection, gene expression
analysis, copy number variation detection​

■

■

■
■

■

Multiple target detection in wastewater​■

Multiple target detection to measure AAV genome integrity​■

Featured Research Application: Multiplex Mutation Detection
A

B

C
8,000

7,000

7,000

6,000

6,000

5,000

5,000

4,000
3,000
2,000
EGFR WT

1,000
0

3,500
KRAS G12C
3,000

4,000
3,000
2,000
EGFR L858R

1,000

2,000

4,000
HEX amplitude

6,000

–500

1,500
1,000

EGFR T790M

0–500–1,000
0

2,000

500

0

–1,000

BRAF V600E

2,500
ROX amplitude

EGFR DE746-A750

Cy5 amplitude

FAM amplitude

8,000

500

1,500
2,500
Cy5.5 amplitude

3,500

0

2,000
4,000
ATTO 590 amplitude

The QX600 System can be used to detect a panel of actionable cancer mutations with high sensitivity in a single reaction. Two-dimensional fluorescence plotsshow clear detection of six alleles in a single reaction. Dark gray clusters represent droplets negative for the two channels detected in each graph. See bulletin 3560 for fullexperimental details.

19 | BIO-RAD LABORATORIES, INC.

6,000

QX200 ddPCR System
Proven Precision

With its track record of proven precision, theQX200 System* provides two-channel detection for
absolute quantification with Droplet Digital PCR.
The QX200 System shown here includes theAutomated Droplet Generator, which is used forreliable partitioning at scale. The system is alsoavailable with the QX200 Droplet Generator for
lower-throughput labs.

Key benefits:
Excellent precision and sensitivity
Simplified absolute quantification without a standard curve
Modularity in droplet generation
Flexible assay setup■■■■

Visit bio-rad.com/QX200 to learn more.

Key applications:
Mutation detection
Gene expression analysis
Copy number variation detection
Wastewater monitoring
AAV titering
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■
■
■
■

Featured Application: Copy Number Quantification
14

13.4

Copy number

12

11.1

10

12.8

11.1

8
6
4.8

4
2
1.04

0
NTC

2.13
1.04

3.03
2.19

5.95
4.93

6.08

3.08

NTC CN1 CN1 CN2 CN2 CN3 CN3 CN5 CN5 CN6 CN6 CN11 CN11 CN13 CN13
SampleThe QX200 System provides superior resolution with copy number (CN) calls from
CN1 to CN13. The copy number plot shows precise duplicate well values across the full CN
range. See bulletin 6311 for more information.

* Also available as the FDA-cleared QXDx Automated Droplet Generator and QXDx Droplet Reader for use with the QXDx BCR-ABL %IS Kit.

20 | BIO-RAD LABORATORIES, INC.

QX ONE ddPCR System
Precision at Scale

The QX ONE System expands on our proven
Droplet Digital PCR technology to offer superior
throughput, precision, and accuracy withintegrated operation. The QX ONE System
handles droplet generation, thermal cycling,
and reading so that you don’t have to.
Visit bio-rad.com/QXONE to learn more.

Key benefits:
Boosted capacity — high-throughput, automated,
walk-away operation

Featured Application: RSM2 Reproducibility

■

■

■

■

■

 implifed workflows — full integration ofS
instrumentation and consumables allows droplet
generation, cycling, and reading in a single plate ultiplexing — 4-color multiplexing and amplitudeM
multiplexing enable detection of up to 8 unique targets
per reaction
 fficient assays —amplitude multiplexing, probe mixing,Eand drop-off assay strategies are supported350

 treamlined compliance — installation qualification (IQ),
S
operational qualification (OQ), performance qualification(PQ), and regulatory edition software are available for
U.S. FDA 21 CFR Part 11–compliant operation■■

Lentiviral vector copy number quantification■

Therapeutic contaminant testing ultiplexed mutation detection, copy number variationM
detection, and gene expression analysis

21 | BIO-RAD LABORATORIES, INC.

300
250
200
150
100
50

 eamless integration — works with existing Bio-Rad
S
ddPCR supermixes, probe chemistry assays, and kits

Key high-throughput applications:A AV titering and integrity testing■400

Concentration, copies/µl■

A

0
AAV ITR-2

hGFP

CMV-Enh
TargetbGH poly(A)NeoR/KanR

SV40 poly(A)B
TargetConcentration, copies/µl%CV

AAV ITR-2

365 ± 3

0.92

hGFP

171 ± 1

0.63

CMV-Enh

182 ± 20.97

bGH poly(A)180 ± 4

2.29

NeoR/KanR

174 ± 3

1.62

SV40 poly(A)171 ± 2

0.92

Reproducibility of RSM2 ddPCR analysis. The concentration of six targets insamples were independently measured on three different days using a multiplex
ddPCR experiment. A, the concentration of each of the six targets as determined
by Poisson analysis. Error bars represent the upper portion of the 95% confidence
interval. Replicate 1 ( ), replicate 2 ( ), replicate 3 ( ). B, the average and standard
deviation for the three concentration measurements (given in copies/µl) and thecorresponding coefficients of variation (%CV). See bulletin 3578 for experimental
details. CMV-Enh, CMV enhancer.

Automated Droplet Generator
Performance at Scale

The AutoDG instrument partitions each sample
in a 96-well PCR plate into ~20,000 uniform
nanoliter-sized droplets in which nucleic acidmolecules are randomly distributed. After
partitioning, the user can seal the plate and run
PCR to endpoint in a thermal cycler. The droplets
in each sample can then be analyzed using a
QX600 or QX200 Droplet Reader.

Visit bio-rad.com/AutoDG to learn more.

Key features and benefits:
The Automated Droplet Generator simplifies ddPCR workflows and makes digital PCR more scalable and flexible, thanks to its:■■■

 uided setup and loading with large, color touchscreenGinterface and LED lighting
 peed — generates droplets for 96 ddPCR reactions inSunder 45 minutes
Throughput — generates sufficient droplets to keep 4–5
droplet readers running continuously

■

■

■

 perational flexibility — walkaway operation allows
Ousers to work on other tasks while droplets are being
generated
User-definable plate layout with increments of 8 wells
 EPA-filtered enclosure — reduces the possibility ofH
contamination and allows the system to be placed in any
lab environment

QX200 Droplet Generator
Proven Precision

Use the QX200 Droplet Generator to complete the first step of theddPCR workflow, partitioning the ddPCR reaction mix into 20,000
nanoliter-sized droplets for up to eight samples per run. The QX200
Droplet Generator is designed for use with the QX200 or QX600
Droplet Reader for EvaGreen® or probe-based ddPCR applications.

Key feature and benefit:Create consistent droplet counts across users and plates, enabling you to make the most of your QX System when
workflows call for smaller run sizes■

22 | BIO-RAD LABORATORIES, INC.

QX Software
Powerful Software for ddPCR Analysis

The QX Software family is a powerful suite of applications for theacquisition and analysis of your ddPCR data. When connected toa ddPCR system, QX Software provides all necessary functionality
to set up, run, and analyze experiments.

The customized dashboard in QX Software helps streamline and simplify ddPCR analysis to fit your laboratory workflow.

The QX Software Family
The QX Software Family is comprised of QX Manager
Software, supporting QX200 and QX600 Systems, and
QX ONE Software, supporting the QX ONE System.
Visit bio-rad.com/QXManager to learn more.
Key Features

Benefits

User and permission
management

Track and control user access and privileges

Plate setup templates

Streamline your workflow with easy plate andrun configuration

Data visualization charts

Easily review data and eliminate time-consuming
offline analysis

Customizable dashboard

Prioritize the most critical information for yourunique workflow

Clustering tools

Manually determine cluster populations incomplex datasets

Autothresholding

Eliminate the guesswork of setting boundaries
between clusters

PDF reports

Download reports in a read-only, secure format

23 | BIO-RAD LABORATORIES, INC.

Need Tools to Support a Regulated or Controlled Workflow?
Tools for U.S. FDA 21 CFR Part 11 compliance areavailable with QX Manager Software, Premium Edition for
the QX600 and QX200 Systems, or QX ONE Software,
Regulatory Edition for the QX ONE System.
Need Greater Control over Data Analysis Parameters
and Quality Rules?
Implement ddPCR assays with application protocol files(APFs) using QX Manager Software, Premium Editionand design your own APFs from the ground up using
QX Designer Software.

QX Designer Software
Custom, Automated ddPCR Analysis

QX Designer Software offers advanced control for running
experiments with QX Manager Software, Premium Edition on
QX200 or QX600 Droplet Readers. It is a standalone application
allowing you to design, secure, and deploy locked Assay Protocol
Files (APFs) to one or more ddPCR systems.

What Is an APF?
APFs are configuration files that describe the rules for how a ddPCR experiment isconfigured, processed, and analyzed within QX Manager Software, Premium Edition.
APFs offer fine-tuned control over every facet of your run, ensuring consistency andreducing user bias during data analysis.

Key features■ Group wells together by sample■ Quality control rules■ Define custom calculations■ Create custom result elements■ Create custom reports

Visit bio-rad.com/QXDesigner to learn more.

Customized Results
APF plate configuration
1

2

A CTRL CTRLB CTRL
C
D
E
F
G
H

3

4

Custom output examples
5

6

7

8

9

10

11

12

Multi-wellanalysis

2D chart view

Targetconcentration

Positivity
rate

Fractional
abundance

Multi-well 2D chart view

Sample information
Quality control rule violations
Lot data

Key benefits of APFs:
Achieve run-to-run consistency by enforcing
experiment parameters
■

■

■

■

■

■

Remove user bias with automated analysis

Key applications:
Biopharma quality control (QC)
Lab-developed tests
Wastewater testing■■■ liminate the need for supplementary tools forEdata analysis
Ensure data quality is sufficient for calculating results implify experiment workflows with custom
S
result elements
Maintain version control across ddPCR systems

24 | BIO-RAD LABORATORIES, INC.

Sustainability

The ddPCR Droplet Reader Oil EcoTank for Probes
provides a sustainable and resource-efficient
alternative to disposing of oil after a single use byrecycling droplet reader oil.
The EcoTank can be used to read up to 40 plates
on the QX600 Droplet Reader and up to 50 plates
on the QX200 Droplet Reader, enabling a lowercost and greener workflow while delivering thesame best-in-class performance on these systems.

Current oil bottle setup

QX200 Droplet ReaderTM

Oil level

Waste

Oil

New QX600/QX200 Droplet Reader EcoTank setup

QX200 Droplet Reader
TM

Aqueouswaste floats

Oil level

Oil recirculates

25 | BIO-RAD LABORATORIES, INC.

Service and Support

We have the experience and dedicated tools to support a wide rangeof ddPCR applications.
Applications Support
Our dedicated field application scientists leverage an incredible
breadth of skills to:■■ rovide training and assistance with data analysis,Ptroubleshooting, and optimization
 ssist customers with experimental design, assay design,Aand reporting of results

Service
With more than 50 years of dependable and experienced service
and support to the scientific community, we are here when you
need us.
Services include:■

Installation qualification (IQ)■

Operational qualification (OQ)■■ reventative maintenance and operational qualificationP(PM/OQ)
Thermal validation

Droplet Digital PCR Applications Guide
Visit bio-rad.com/ddPCRAppsGuide
for in-depth information about setting up
experiments for ddPCR applications.
Visit bio-rad.com/ddPCR-QXFamily to learn more.
BIO-RAD, AUTODG, DDPCR, DROPLET DIGITAL, DROPLET DIGITAL PCR, QX200, QX600, and
QX ONE are trademarks of Bio-Rad Laboratories, Inc. in certain jurisdictions. All trademarks usedherein are the property of their respective owner. © 2024 Bio-Rad Laboratories, Inc.
EvaGreen is a trademark of Biotium, Inc. Bio-Rad Laboratories, Inc. is licensed by Biotium, Inc. tosell reagents containing EvaGreen Dye for use in real-time PCR, for research purposes only.
Purchase of Digital PCR and/or Single-Cell NGS Sample Preparation products (the “Products”)
from Bio-Rad Laboratories is subject to Bio-Rad Laboratories, Inc. Standard Terms andConditions of Sale, which can be accessed at https://www.bio-rad.com/en-us/terms-conditions.
Unless we expressly state otherwise in additional Terms and Conditions, no rights are granted for
you to distribute or resell the Products. Unless we expressly state otherwise in additional Terms
and Conditions, no rights are granted for the development or commercialization of diagnostic
assays for use with the Products without a license from Bio-Rad. It is the user’s obligation to
obtain a commercial license from Bio-Rad for (i) all commercial uses (not just diagnostic uses)and (ii) sale of assays for use on Bio-Rad’s dPCR and ddSEQ instruments. The Products and/or
their use are covered by U.S. and foreign patents and/or pending patent applications owned by orunder license to Bio-Rad Laboratories, Inc. See https://www.bio-rad.com/en-us/trademarks.

Our service contract plans ensure coverage for routine
maintenance and emergency repairs at no additional cost.
Plans include:■

Service and repair coverage■

Replacement parts, travel, and labor■

Prioritized response time

■

■

■

 reventative maintenance for critical components inP
regulatory environments
Equipment qualification
 alidation services environments, equipment qualification,Vand validation services

Bio-RadLaboratories, Inc.
Website bio-rad.com USA 1 800 424 6723 Australia 61 2 9914 2800 Austria 00 800 00 24 67 23 Belgium 00 800 00 24 67 23 Brazil 4003 0399 Canada 1 905 364 3435
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