ddPCR Assay Design Service Assays

ddPCR Assay Design Service Assays


QX200™ Droplet Digital™ PCR System 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.

Download PDF

QX200™ Droplet Digital™ (ddPCR™) System 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.

Digital PCR using QX200™ and AutoDG™ ddPCR Systems
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.

Scroll upScroll down

Droplet Digital PCR Publications

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

Browse Publications

Need assistance with ddPCR assay design for your specific application? Contact your Genomics Sales Specialist for more information about the ddPCR Assay Design Service. Availability may vary by region.

A Bio-Rad representative will work with you to design ddPCR Assay Design Service assays. ddPCR ADS assays can be obtained for a wide variety of assays (for example, translocations, mutation detection, multiplex mutation screening, etc.). An assay design may require a combination of multiple catalog numbers and unique Assay IDs. Information required to formulate an assay for a particular design request can be obtained from the assay information pages available at [bio-rad.com/digital-assays] Sequence information can be purchased if desired.

ddPCR ADS assays should be validated prior to use by the end user.

Packaging Options

Based on the design complexity and manufacturing requirements, Expert Design Assays are assigned to one of the catalog numbers listed below.

Catalog# Product Name Reaction Size
12008226 ddPCR ADS FAM Assay 1000
12008227 ddPCR ADS HEX Assay 1000
12008230 ddPCR ADS 450uM Primer 50ul
12008231 ddPCR ADS 125uM FAM Probe 50ul
12008232 ddPCR ADS 125uM HEX Probe 50ul
12008235 ddPCR ADS 375uM Dark Probe with 3' Iowa Black®FQ 50ul

Related Products


Number Description Options
10000095075 ddPCR Assay Design Service Assays Click to download

This product contains electrical or electronic material. Learn more about Bio-Rad's EU Recycle Program

Get Help
Sign Up for Bio-Rad Updates!
Enter your email address below to receive your choice of the latest news, promotions, and more.
PG9AP4SCUMB7 [x-forwarded-proto] = [http] [accept-language] = [en-US,en;q=0.5] [x-forwarded-port] = [80] [x-forwarded-for] = [,] [accept] = [text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8] [seourl] = [/en-us/product/ddpcr-assay-design-service-assays] [x-amzn-trace-id] = [Root=1-5d077b11-2c739a40b8c6528cdaea8390] [x-forwarded-server] = [lsds-prod-s.br.aws-livesite.io] [x-forwarded-host] = [www.bio-rad.com] [x-query-string] = [ID=PG9AP4SCUMB7] [host] = [] [x-request-uri] = [/en-us/product/ddpcr-assay-design-service-assays] [connection] = [Keep-Alive] [accept-encoding] = [gzip] [user-agent] = [CCBot/2.0 (https://commoncrawl.org/faq/)] Catalog/ProductDetail pageStyleKey ddpcr-assay-design-service-assays LSR 03/26/14 02:17 PM en_US true internet/generic 2018-12-28 22:30:28 /default/main/bio-rad/STAGING 1385504243813 US templatedata/internet/generic/data/en_US/GNL/page_generic_footer_b2c_1385505294_US.xml page_generic_footer_b2c /default/main/bio-rad/WORKAREA/default jc7v8okm 2017-10-27 13:13:40 true Done jc7v8okm templatedata/internet/generic/data/en_US/GNL/page_generic_footer_b2c_1385505294_US.xml GNL N /default/main/bio-rad en_US 11/27/23 02:18 PM 1539210190090 2018-12-28 22:30:28 /default/main/bio-rad/WORKAREA/default/templatedata/internet/generic/data/en_US/GNL/page_generic_footer_b2c_1385505294_US.xml footer-page 1 1385504243813 page_generic_footer_b2c <div class="links"> <h4>Support</h4> <ul> <li><a class="msdsLink wtclass linkgeneration" href="/_locale/literature-library">MSDS</a></li> <li><a class="cofaLink wtclass linkgeneration" href="/_locale/_defaultVerticalUrl/support/certificate-of-analysis">Certificate of Analysis</a></li> <li><a class="qcinsertsLink wtclass" href="http://myeinserts.qcnet.com/" target="_blank" rel="noopener noreferrer">QC Inserts</a></li> <li><a class="technicalsupportLink wtclass linkgeneration" href="/_locale/life-science-research/support">Technical Support<br />For Life Science</a></li> <li><a class="expertCSLink wtclass linkgeneration" href="/_locale/_defaultVerticalUrl/purchase-service-programs/expert-care-service?ID=1383780912356">Expert Care Service</a></li> <li><a class="feedBackLink wtclass linkgeneration" id="feedbackID" href="javascript:void(0)">Feedback</a></li> <li><a class="contactUSLink wtclass linkgeneration" href="/_locale/contact-us">Contact Us</a></li> </ul> </div> <div class="links"> <h4>Ordering</h4> <ul> <li><a id="quickOrderLink" class="quickOrderLink wtclass" name="quickOrderLink" href="javascript:openAjaxOverlay('/evportal/portlets/ordering/quickOrderOverlayContent.jsp?quickorder_location=Footer')">Quick Order</a></li> <li><a class="mybioradLink wtclass linkgeneration" href="/_locale/my-bio-rad">My Bio-Rad</a></li> <li><a id="footer_orderLink" class="orderhistoryLink wtclass" href="javascript:void(0);">Order History</a></li> <li><a id="footer_quoteLink" href="javascript:void(0);">Quote History</a></li> <li><a class="supplycentersLink wtclass linkgeneration" href="/_locale/_defaultVerticalUrl/purchase-service-programs/supply-center-program">Supply Centers</a></li> <li><a class="returnpolicyLink wtclass linkgeneration" href="javascript:openAjaxOverlay('/webroot/web/html/returnPolicy-us.html','Return and Refund Policy');">Return and Refund Policy</a></li> </ul> </div> <div class="links"> <h4>Our Products</h4> <ul> <li><a class="lsrLink wtclass linkgeneration" href="/_locale/life-science-research">Life Science Research</a></li> <li><a class="cdLink wtclass linkgeneration" href="/_locale/clinical-diagnostics">Clinical Diagnostics</a></li> <li><a class="infLink wtclass linkgeneration" href="/_locale/spectroscopy">Spectroscopy</a></li> <li><a class="psLink wtclass linkgeneration" href="/_locale/process-separations">Process Separations</a></li> <li><a class="fsLink wtclass linkgeneration" href="/_locale/food-science">Food Science</a></li> <li><a class="lseLink wtclass linkgeneration" href="/_locale/education">Life Science Education</a></li> <li><a class="selectionguideLink wtclass linkgeneration" href="/featured/en/selection-guides.html">Selection Guides</a></li> <li><a class="featuredproductsLink wtclass" href="/featured/en/featured-products.html">Featured Products</a></li> </ul> </div> <div class="links links2"> <h4>Corporate</h4> <ul> <li><a class="aboutbioradLink wtclass linkgeneration" href="/_locale/corporate/about-bio-rad">About Bio-Rad</a></li> <li><a class="careersLink wtclass linkgeneration" href="/_locale/corporate/careers">Careers</a></li> <li><a class="irLink wtclass linkgeneration" href="/_locale/corporate/investor-relations">Investor Relations</a></li> <li><a class="coLink wtclass linkgeneration" href="/_locale/corporate/community-outreach">Community Outreach</a></li> <li><a class="pteLink wtclass linkgeneration" href="/_locale/corporate/protecting-environment">Protecting the Environment</a></li> <li><a class="newsroomLink wtclass linkgeneration" href="/_locale/corporate/newsroom">Newsroom</a></li> </ul> </div> <p> <script type="text/javascript">// <![CDATA[ $(document).ready(function(){ var feedbackOverlayUrl = '/bio-rad/Standalone/FeedbackOverlay.page?standalonePage=true'; $("#feedbackID").click(function(){ openAjaxOverlay(feedbackOverlayUrl,"Feedback"); }); }); // ]]></script> <script type="text/javascript">// <![CDATA[ if($.cookie('evCntryLang')){ (function(){"use strict";var e=null,b="4.0.0", n="10740", additional="", t,r,i;try{t=top.document.referer!==""?encodeURIComponent(top.document.referrer.substring(0,2048)):""}catch(o){t=document.referrer!==null?document.referrer.toString().substring(0,2048):""}try{r=window&&window.top&&document.location&&window.top.location===document.location?document.location:window&&window.top&&window.top.location&&""!==window.top.location?window.top.location:document.location}catch(u){r=document.location}try{i=parent.location.href!==""?encodeURIComponent(parent.location.href.toString().substring(0,2048)):""}catch(a){try{i=r!==null?encodeURIComponent(r.toString().substring(0,2048)):""}catch(f){i=""}}var l,c=document.createElement("script"),h=null,p=document.getElementsByTagName("script"),d=Number(p.length)-1,v=document.getElementsByTagName("script")[d];if(typeof l==="undefined"){l=Math.floor(Math.random()*1e17)}h="dx.steelhousemedia.com/spx?"+"dxver="+b+"&shaid="+n+"&tdr="+t+"&plh="+i+"&cb="+l+additional;c.type="text/javascript";c.src=("https:"===document.location.protocol?"https://":"http://")+h;v.parentNode.insertBefore(c,v)})() } // ]]></script> </p> /webroot/web/html footer_page_b2c_en_US.html /webroot/web/html/footer_page_b2c_en_US.html Karen Moss Footer page Footer 03/26/14 02:17 PM 11/27/23 02:18 PM US en GNL /GNL N 0 en-us Home <script type="text/javascript">$(document).ready(function() { $(".footer-nav > a:nth-child(3)").after(" | <a href='javascript:void(0)' id='regionlink'>Web Accessibility</a>"); var region = $("#headlangID .lang strong").html(); $("#regionlink").click(function(){ window.location.replace( "/webroot/web/html/featured/en/web-accessibility.html?Region=" + region );});});</script>Trademarks Site Terms Terms & Conditions Imprint EU Recycle Program Privacy Change Cookie Setting <script type="text/javascript">$(document).ready(function () {$(".links2").append('<style>.social-links-br {float: left;margin-right: 10px;}.social-links-br img {width: 20px;height: 20px;margin-right: 5px}</style><div class="social-links-br"><a class="no-target-style" href="https://www.linkedin.com/company/bio-rad?trk=top_nav_home" target="_blank"><img src="/webroot/web/images/general/icons/linkedin_round_40x40.png" alt="Bio-Rad LinkedIn"></a><a class="no-target-style" href="https://www.youtube.com/user/BioRadLifeScience" target="_blank"><img src="/webroot/web/images/general/icons/youtube-icon-rnd-40x40.png" alt="Bio-Rad YouTube"></a><a class="no-target-style" href="https://twitter.com/BioRadLifeSci" target="_blank"><img src="/webroot/web/images/general/icons/twitter_round_40x40.png" alt="Bio-Rad Twitter"></a><a class="no-target-style" href="https://www.facebook.com/biorad/" target="_blank"><img src="/webroot/web/images/general/icons/facebook-icon-rnd-40x40.png" alt="Bio-Rad Facebook"></a><a class="no-target-style" href="https://www.instagram.com/bioradlabs/" target="_blank"><img src="/webroot/web/images/general/icons/instagram-icon-rnd-40x40.png" alt="Bio-Rad Instagram"></a></div>');});</script>Copyright &copy; {0} Bio-Rad Laboratories, Inc. All rights reserved. This page was last edited on {0} true True GTM-MJ2DN2S us US en LSR life-science-research life-science-research /prd/en/US/direct/biorad?ts=1&cmd=OrdersWorkspaceDisplay /prd/en/US/direct/biorad?ts=1&cmd=QuotesWorkspaceDisplay /prd/en/US/direct/biorad?ts=1&cmd=InvoiceWorkspaceDisplay&_Tab=Invoice false false true false true true 1040988879 LHsYCOu_wQMQz_Ww8AM window.google_tag_params true 272-THL-329 username CartID_ WT_FPC <script type="text/javascript">$.ajax({url: document.location.protocol + '//munchkin.marketo.net/munchkin.js',dataType: 'script',cache: true,success: function() {Munchkin.init('044-CBN-599');}});</script> <script type="text/javascript" src="/evportal/framework/skins/evolution/js/proxyMunchkin.js"></script> 2019