{"id":19606,"date":"2026-04-01T20:42:44","date_gmt":"2026-04-01T20:42:44","guid":{"rendered":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/?p=19606"},"modified":"2026-04-06T18:45:51","modified_gmt":"2026-04-06T18:45:51","slug":"multiplex-qpcr-optimization-6-plex","status":"publish","type":"post","link":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/multiplex-qpcr-optimization-6-plex\/","title":{"rendered":"Optimizing multiplex qPCR: How to amplify up to 6 targets without compromising analytical sensitivity"},"content":{"rendered":"\n<p>What happens when a multiplex qPCR assay begins to lose performance as additional targets are introduced? An assay that performs reproducibly in singleplex can exhibit Ct shift, reduced sensitivity, or compressed dynamic range when scaled to 5- or 6-plex.<\/p>\n\n\n\n<p>As plex level increases, competition among primers, probes, reporter dyes, and polymerase intensifies, and small imbalances can become amplified under multiplex conditions. Modest \u0394Ct changes may affect quantification accuracy if reaction components are not designed to function together under multiplex conditions. Successfully scaling multiplex qPCR requires more than combining additional assays within the same reaction; it requires coordinated optimization of probe chemistry, dye compatibility, and master mix formulation.<\/p>\n\n\n\n<div class=\"wp-block-tf-blocks-intro-summary\">\n<h2 class=\"wp-block-heading\" id=\"h-what-you-ll-learn-in-this-article\"><strong>What you\u2019ll learn in this article<\/strong><\/h2>\n\n\n\n<p>To scale confidently from 1-plex to 6-plex without compromising sensitivity, it is important to understand where multiplex workflows typically lose performance and how to mitigate those effects.<\/p>\n\n\n\n<p>In this article, we\u2019ll cover:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Why \u0394Ct shift occurs during multiplex scale-up<\/li>\n\n\n\n<li>How probe chemistry influences signal strength and spectral separation<\/li>\n\n\n\n<li>The role of master mix formulation in maintaining amplification efficiency and dynamic range<\/li>\n\n\n\n<li>Considerations for preserving low-copy detection in higher-plex reactions<\/li>\n\n\n\n<li>Practical steps to evaluate and optimize 5- and 6-plex assays<\/li>\n<\/ul>\n\n\n\n<p>Explore additional information including the chemistry and workflow considerations that support reliable high-order multiplex qPCR development.<\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-tf-blocks-definition-block\">\n<h2 class=\"wp-block-heading\" id=\"h-what-is-multiplex-qpcr\"><strong>What is multiplex qPCR?<\/strong><\/h2>\n\n\n\n<p>Multiplex qPCR is defined as the amplification of more than one target in a single reaction, using different reporter dyes to distinguish each target.<\/p>\n\n\n\n<p>In typical workflows:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Each assay\/target pair is labeled with a distinct reporter dye<\/li>\n\n\n\n<li>All assays are combined with a single master mix and template<\/li>\n\n\n\n<li>Amplification is detected across separate optical channels<\/li>\n<\/ul>\n<\/div>\n\n\n\n<figure class=\"wp-block-image aligncenter size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"936\" height=\"344\" src=\"https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/04\/workflow-multiplexing-1.png\" alt=\"Diagram showing four qPCR targets combined into a single reaction with master mix and detected across multiple channels.\" class=\"wp-image-19607\" srcset=\"https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/04\/workflow-multiplexing-1.png 936w, https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/04\/workflow-multiplexing-1-300x110.png 300w, https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/04\/workflow-multiplexing-1-768x282.png 768w\" sizes=\"auto, (max-width: 936px) 100vw, 936px\" \/><\/figure>\n\n\n\n<p>Multiplexing can also involve the amplification of multiple targets with a single channel, depending on assay design.<\/p>\n\n\n\n<figure class=\"wp-block-image aligncenter size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"936\" height=\"295\" src=\"https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/04\/workflow-multiplexing-2.png\" alt=\"Diagram showing grouped qPCR targets combined into fewer assays within a multiplex reaction workflow.\" class=\"wp-image-19608\" srcset=\"https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/04\/workflow-multiplexing-2.png 936w, https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/04\/workflow-multiplexing-2-300x95.png 300w, https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/04\/workflow-multiplexing-2-768x242.png 768w\" sizes=\"auto, (max-width: 936px) 100vw, 936px\" \/><\/figure>\n\n\n\n<p>When properly designed, multiplex qPCR may enable:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Reduced reagent and sample usage<\/li>\n\n\n\n<li>Increased throughput<\/li>\n\n\n\n<li>Shorter workflow time<\/li>\n\n\n\n<li>Precision when comparing targets within the same reaction<\/li>\n<\/ul>\n\n\n\n<p>However, these advantages depend heavily on assay design and reaction optimization. Understanding what multiplex qPCR is only the starting point. Performance at higher plex levels depends on how the assay is designed and how reaction components interact.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\" id=\"h-general-considerations-for-multiplex-assay-design\"><strong>General considerations for multiplex assay design<\/strong><\/h2>\n\n\n\n<p>Successful multiplex qPCR workflows require alignment across several variables:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Application and sample type<\/li>\n\n\n\n<li>Primer and probe design<\/li>\n\n\n\n<li>Master mix compatibility<\/li>\n\n\n\n<li>Thermal cycling conditions<\/li>\n\n\n\n<li>Instrument and dye compatibility<\/li>\n<\/ul>\n\n\n\n<p>Specific assay design considerations include:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Minimizing nonspecific amplification<\/li>\n\n\n\n<li>Selecting dye\/quencher combinations that reduce background and cross-talk<\/li>\n\n\n\n<li>Optimizing annealing temperature and extension time across all targets<\/li>\n\n\n\n<li>Limiting competition or inhibition between assays<\/li>\n\n\n\n<li>Accounting for expression range differences among targets<\/li>\n\n\n\n<li>Optimizing primer and probe concentrations to balance amplification efficiencies and reduce polymerase saturation<\/li>\n<\/ul>\n\n\n\n<p>These parameters become increasingly critical as plex level rises.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\" id=\"h-how-probe-chemistry-influences-multiplex-performance\"><strong>How probe chemistry influences multiplex performance<\/strong><\/h2>\n\n\n\n<p>Probe chemistry directly affects signal clarity, background suppression, dynamic range, and scale-up performance. <a href=\"https:\/\/www.thermofisher.com\/us\/en\/home\/life-science\/oligonucleotides-primers-probes-genes\/applied-biosystems-custom-primers-probes.html\" target=\"_blank\" rel=\"noreferrer noopener\">Applied Biosystems\u2122 QSY\u2122 probe portfolio with TaqMan\u2122 QSY2\u2122 probes<\/a>, supports higher-order multiplexing.<br><br>Key characteristics include:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Increased analytical sensitivity<\/li>\n\n\n\n<li>Wider dynamic range<\/li>\n\n\n\n<li>Performance retention when scaling from 1-plex to 6-plex<\/li>\n\n\n\n<li>Smaller \u0394Ct difference between 1-plex and 6-plex reactions compared to certain alternative probes<\/li>\n<\/ul>\n\n\n\n<p>QSY2 probes support high-throughput 5- and 6-plex reactions using Cyanine 5 and Cyanine 5.5 reporter dyes, helping expand multiplex panel capacity while maintaining signal separation. Probes must be redesigned when switching between MGB and QSY quenchers, reinforcing that dye-quencher pairing is not interchangeable.<br><br>For custom multiplex panel development, <a href=\"https:\/\/www.thermofisher.com\/tools\/oligos\/custom-primer-probe\" target=\"_blank\" rel=\"noreferrer noopener\">Applied Biosystems\u2122 Custom Primers &amp; Probes<\/a> provide configurable dye and quencher options support up to six targets in a single reaction.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\" id=\"h-why-\u03b4ct-retention-matters-in-6-plex-reactions\"><strong>Why \u0394Ct retention matters in 6-plex reactions<\/strong><\/h2>\n\n\n\n<p>A key performance metric is \u0394Ct retention when scaling from singleplex to multiplex. TaqMan QSY2 probes have demonstrated smaller \u0394Ct differences between 1-plex and 6-plex reactions in internal performance evaluations compared to selected alternative probe chemistries.<\/p>\n\n\n\n<p>Maintaining a small \u0394Ct during scale-up helps preserve:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Quantification confidence<\/li>\n\n\n\n<li>Low-copy sensitivity<\/li>\n\n\n\n<li>Dynamic range stability<\/li>\n<\/ul>\n\n\n\n<p>\u0394Ct drift during scale-up often reflects reaction imbalance rather than primer design alone.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\" id=\"h-the-role-of-master-mix-formulation-in-multiplex-stability\"><strong>The role of master mix formulation in multiplex stability<\/strong><\/h2>\n\n\n\n<p>Assay design alone does not determine multiplex success. Master mix formulation is a primary contributor to performance retention under multiplex load. The Applied Biosystems\u2122 TaqPath\u2122 portfolio includes master mixes verified for multiplexing applications including TaqPath\u2122 DuraPlex\u2122 1-Step RT-qPCR Master Mix <a href=\"https:\/\/www.thermofisher.com\/order\/catalog\/product\/A58666\" target=\"_blank\" rel=\"noreferrer noopener\">with Rox<\/a> and <a href=\"https:\/\/www.thermofisher.com\/order\/catalog\/product\/A58669\" target=\"_blank\" rel=\"noreferrer noopener\">no Rox<\/a> designed and optimized for higher-order multiplexing.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\" id=\"h-preserving-performance-in-complex-sample-matrices\"><strong>Preserving performance in complex sample matrices<\/strong><\/h2>\n\n\n\n<p>Multiplex qPCR performance must be maintained across diverse and sometimes inhibitory sample types, including blood-derived matrices, viral transport media, and biologically complex specimens.<\/p>\n\n\n\n<p>Key workflow considerations include:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>High tolerance to inhibitors commonly found in clinical research or biological samples<\/li>\n\n\n\n<li>Stable amplification across varying template inputs<\/li>\n\n\n\n<li>Compatibility with automated liquid handling systems<\/li>\n\n\n\n<li>Benchtop stability of assembled reactions for high-throughput workflows<\/li>\n\n\n\n<li>Consistent lot-to-lot performance to support longitudinal studies<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\" id=\"h-what-is-the-best-way-to-optimize-multiplex-qpcr-for-6-targets\"><strong>What is the best way to optimize multiplex qPCR for 6 targets?<\/strong><\/h2>\n\n\n\n<p>After understanding the chemistry and reaction dynamics, optimization should prioritize analytical reproducibility, low-copy sensitivity, and robustness across sample types. Effective multiplex qPCR optimization generally includes:<\/p>\n\n\n\n<ol class=\"wp-block-list\">\n<li>Establishing baseline singleplex assay efficiency<\/li>\n\n\n\n<li>Comparing \u0394Ct between singleplex and multiplex formats<\/li>\n\n\n\n<li>Confirming slope consistency and dynamic range retention<\/li>\n\n\n\n<li>Evaluating analytical performance across relevant input ranges<\/li>\n\n\n\n<li>Assessing inhibitor tolerance using representative sample matrices<\/li>\n\n\n\n<li>Confirming reproducibility across reagent lots<\/li>\n<\/ol>\n\n\n\n<p>Successful 6-plex performance depends on two major factors:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Assay design (primer\/probe chemistry, dye-quencher pairing)<\/li>\n\n\n\n<li>Master mix formulation optimized for multiplexing<\/li>\n<\/ul>\n\n\n\n<p>Probe chemistries such as <a href=\"https:\/\/www.thermofisher.com\/order\/catalog\/product\/4482777\" target=\"_blank\" rel=\"noreferrer noopener\">TaqMan QSY and QSY2 Probes<\/a> are engineered to support higher-order multiplexing with improved performance retention during scale-up, while master mixes such as <a href=\"https:\/\/www.thermofisher.com\/order\/catalog\/product\/A58669\" target=\"_blank\" rel=\"noreferrer noopener\">TaqPath DuraPlex<\/a> are formulated to support simultaneous multi-target amplification with broad dynamic range.<\/p>\n\n\n\n<p>This combination can help maintain analytical confidence when expanding panels for gene expression profiling, viral detection, or biomarker evaluation.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\" id=\"h-ready-to-optimize-multiplex-qpcr\"><strong>Ready to optimize multiplex qPCR?<\/strong><\/h2>\n\n\n\n<p>For a practical, step-by-step approach to optimizing multiplex reactions, including guidance on assay balancing and scale-up evaluation, read the <a href=\"https:\/\/assets.thermofisher.com\/TFS-Assets\/LSG\/manuals\/taqman_optimization_man.pdf\" target=\"_blank\" rel=\"noreferrer noopener\">TaqMan\u2122 Multiplex PCR Optimization Guide.<\/a><\/p>\n\n\n\n<p><a href=\"https:\/\/documents.thermofisher.com\/TFS-Assets\/LSG\/manuals\/taqman_optimization_man.pdf\" target=\"_blank\" rel=\"noreferrer noopener\">Download the TaqMan Multiplex PCR Optimization Guide to support assay development and scale-up.<\/a><\/p>\n\n\n\n<p>For additional data and assay design insights discussed in this article, watch the <a href=\"https:\/\/players.brightcove.net\/665001591001\/default_default\/index.html?videoId=6369340452112\" target=\"_blank\" rel=\"noreferrer noopener\">Mastering Multiplexing webinar<\/a><\/p>\n\n\n\n<h2 class=\"wp-block-heading\" id=\"h-explore-qpcr-multiplex-ready-assays-and-master-mixes-designed-for-high-order-multiplexing\"><strong>Explore qPCR multiplex-ready assays and master mixes designed for high-order multiplexing:<\/strong><\/h2>\n\n\n\n<p><a href=\"https:\/\/www.thermofisher.com\/us\/en\/home\/life-science\/oligonucleotides-primers-probes-genes\/applied-biosystems-custom-primers-probes.html\" target=\"_blank\" rel=\"noreferrer noopener\">Browse TaqMan Multiplex probes and qPCR primers<\/a><br><a href=\"https:\/\/www.thermofisher.com\/order\/catalog\/product\/4316034\">Shop TaqM<\/a><a href=\"https:\/\/www.thermofisher.com\/order\/catalog\/product\/4316034\" target=\"_blank\" rel=\"noreferrer noopener\">an MGB Probe for 5-plex multiplexing<\/a><br><a href=\"https:\/\/www.thermofisher.com\/us\/en\/home\/life-science\/pcr\/real-time-pcr\/real-time-pcr-assays\/assay-design.html\" target=\"_blank\" rel=\"noreferrer noopener\">Design a custom multiplex assay<\/a><br><a href=\"https:\/\/www.thermofisher.com\/order\/catalog\/product\/A58666\" target=\"_blank\" rel=\"noreferrer noopener\">Shop TaqPath DuraPlex 1-Step RT-qPCR Master Mix<\/a><br><a href=\"https:\/\/www.thermofisher.com\/us\/en\/home\/global\/forms\/life-science\/assay-support.html\" target=\"_blank\" rel=\"noreferrer noopener\">Speak to a multiplexing specialist<\/a><\/p>\n\n\n\n<h2 class=\"wp-block-heading\" id=\"h-build-a-reliable-6-plex-workflow-with-probes-and-master-mixes-designed-for-high-order-qpcr-multiplex-performance\"><strong>Build a reliable 6-plex workflow<\/strong> <strong>with probes and master mixes designed for high-order qPCR multiplex performance.<\/strong><\/h2>\n\n\n\n<p><a href=\"https:\/\/www.thermofisher.com\/taqman\/gene-expression\/assay\/query?keyword=*\" target=\"_blank\" rel=\"noreferrer noopener\">TaqMan Predesigned Gene Expression Assays<\/a><br><a href=\"https:\/\/www.thermofisher.com\/order\/custom-genomic-products\/tools\/cadt\/\" target=\"_blank\" rel=\"noreferrer noopener\">Custom TaqMan Assays<\/a><br><a href=\"https:\/\/www.thermofisher.com\/order\/catalog\/product\/4482777\" target=\"_blank\" rel=\"noreferrer noopener\">TaqMan QSY and QSY2 Probes<\/a><br><a href=\"https:\/\/www.thermofisher.com\/order\/catalog\/product\/A58666\" target=\"_blank\" rel=\"noreferrer noopener\">TaqPath DuraPlex 1-Step RT-qPCR Master Mix<\/a><br><a href=\"https:\/\/www.thermofisher.com\/us\/en\/home\/life-science\/pcr\/real-time-pcr\/real-time-pcr-instruments\/quantstudio-systems.html\" target=\"_blank\" rel=\"noreferrer noopener\">QuantStudio Real-Time PCR Systems<\/a><\/p>\n\n\n<style>.kt-accordion-id19606_709b5a-a8 .kt-accordion-inner-wrap{column-gap:var(--global-kb-gap-md, 2rem);row-gap:10px;}.kt-accordion-id19606_709b5a-a8 .kt-accordion-panel-inner{border-top:0px solid transparent;border-right:1px solid transparent;border-bottom:1px solid transparent;border-left:1px solid transparent;background:#ffffff;padding-top:var(--global-kb-spacing-sm, 1.5rem);padding-right:var(--global-kb-spacing-sm, 1.5rem);padding-bottom:var(--global-kb-spacing-sm, 1.5rem);padding-left:var(--global-kb-spacing-sm, 1.5rem);}.kt-accordion-id19606_709b5a-a8 > .kt-accordion-inner-wrap > .wp-block-kadence-pane > .kt-accordion-header-wrap > .kt-blocks-accordion-header{border-top:1px solid #eeeeee;border-right:1px solid #eeeeee;border-bottom:1px solid #eeeeee;border-left:2px solid #eeeeee;border-top-left-radius:0px;border-top-right-radius:0px;border-bottom-right-radius:0px;border-bottom-left-radius:0px;background:#ffffff;color:#444444;padding-top:14px;padding-right:16px;padding-bottom:14px;padding-left:16px;}.kt-accordion-id19606_709b5a-a8:not( .kt-accodion-icon-style-basiccircle ):not( .kt-accodion-icon-style-xclosecircle ):not( .kt-accodion-icon-style-arrowcircle )  > .kt-accordion-inner-wrap > .wp-block-kadence-pane > .kt-accordion-header-wrap .kt-blocks-accordion-icon-trigger:after, .kt-accordion-id19606_709b5a-a8:not( .kt-accodion-icon-style-basiccircle ):not( .kt-accodion-icon-style-xclosecircle ):not( .kt-accodion-icon-style-arrowcircle )  > .kt-accordion-inner-wrap > .wp-block-kadence-pane > .kt-accordion-header-wrap .kt-blocks-accordion-icon-trigger:before{background:#444444;}.kt-accordion-id19606_709b5a-a8:not( .kt-accodion-icon-style-basic ):not( .kt-accodion-icon-style-xclose ):not( .kt-accodion-icon-style-arrow ) .kt-blocks-accordion-icon-trigger{background:#444444;}.kt-accordion-id19606_709b5a-a8:not( .kt-accodion-icon-style-basic ):not( .kt-accodion-icon-style-xclose ):not( .kt-accodion-icon-style-arrow ) .kt-blocks-accordion-icon-trigger:after, .kt-accordion-id19606_709b5a-a8:not( .kt-accodion-icon-style-basic ):not( .kt-accodion-icon-style-xclose ):not( .kt-accodion-icon-style-arrow ) .kt-blocks-accordion-icon-trigger:before{background:#ffffff;}.kt-accordion-id19606_709b5a-a8 > .kt-accordion-inner-wrap > .wp-block-kadence-pane > .kt-accordion-header-wrap > .kt-blocks-accordion-header:hover, \n\t\t\t\tbody:not(.hide-focus-outline) .kt-accordion-id19606_709b5a-a8 .kt-blocks-accordion-header:focus-visible{color:#444444;background:#ffffff;border-top-color:#878787;border-top-style:solid;border-right-color:#878787;border-right-style:solid;border-bottom-color:#878787;border-bottom-style:solid;border-left-color:#878787;border-left-style:solid;}.kt-accordion-id19606_709b5a-a8:not( .kt-accodion-icon-style-basiccircle ):not( .kt-accodion-icon-style-xclosecircle ):not( .kt-accodion-icon-style-arrowcircle ) .kt-accordion-header-wrap .kt-blocks-accordion-header:hover .kt-blocks-accordion-icon-trigger:after, .kt-accordion-id19606_709b5a-a8:not( .kt-accodion-icon-style-basiccircle ):not( .kt-accodion-icon-style-xclosecircle ):not( .kt-accodion-icon-style-arrowcircle ) .kt-accordion-header-wrap .kt-blocks-accordion-header:hover .kt-blocks-accordion-icon-trigger:before, body:not(.hide-focus-outline) .kt-accordion-id19606_709b5a-a8:not( .kt-accodion-icon-style-basiccircle ):not( .kt-accodion-icon-style-xclosecircle ):not( .kt-accodion-icon-style-arrowcircle ) .kt-blocks-accordion--visible .kt-blocks-accordion-icon-trigger:after, body:not(.hide-focus-outline) .kt-accordion-id19606_709b5a-a8:not( .kt-accodion-icon-style-basiccircle ):not( .kt-accodion-icon-style-xclosecircle ):not( .kt-accodion-icon-style-arrowcircle ) .kt-blocks-accordion-header:focus-visible .kt-blocks-accordion-icon-trigger:before{background:#444444;}.kt-accordion-id19606_709b5a-a8:not( .kt-accodion-icon-style-basic ):not( .kt-accodion-icon-style-xclose ):not( .kt-accodion-icon-style-arrow ) .kt-accordion-header-wrap .kt-blocks-accordion-header:hover .kt-blocks-accordion-icon-trigger, body:not(.hide-focus-outline) .kt-accordion-id19606_709b5a-a8:not( .kt-accodion-icon-style-basic ):not( .kt-accodion-icon-style-xclose ):not( .kt-accodion-icon-style-arrow ) .kt-accordion-header-wrap .kt-blocks-accordion-header:focus-visible .kt-blocks-accordion-icon-trigger{background:#444444;}.kt-accordion-id19606_709b5a-a8:not( .kt-accodion-icon-style-basic ):not( .kt-accodion-icon-style-xclose ):not( .kt-accodion-icon-style-arrow ) .kt-accordion-header-wrap .kt-blocks-accordion-header:hover .kt-blocks-accordion-icon-trigger:after, .kt-accordion-id19606_709b5a-a8:not( .kt-accodion-icon-style-basic ):not( .kt-accodion-icon-style-xclose ):not( .kt-accodion-icon-style-arrow ) .kt-accordion-header-wrap .kt-blocks-accordion-header:hover .kt-blocks-accordion-icon-trigger:before, body:not(.hide-focus-outline) .kt-accordion-id19606_709b5a-a8:not( .kt-accodion-icon-style-basic ):not( .kt-accodion-icon-style-xclose ):not( .kt-accodion-icon-style-arrow ) .kt-accordion-header-wrap .kt-blocks-accordion-header:focus-visible .kt-blocks-accordion-icon-trigger:after, body:not(.hide-focus-outline) .kt-accordion-id19606_709b5a-a8:not( .kt-accodion-icon-style-basic ):not( .kt-accodion-icon-style-xclose ):not( .kt-accodion-icon-style-arrow ) .kt-accordion-header-wrap .kt-blocks-accordion-header:focus-visible .kt-blocks-accordion-icon-trigger:before{background:#ffffff;}.kt-accordion-id19606_709b5a-a8 .kt-accordion-header-wrap .kt-blocks-accordion-header:focus-visible,\n\t\t\t\t.kt-accordion-id19606_709b5a-a8 > .kt-accordion-inner-wrap > .wp-block-kadence-pane > .kt-accordion-header-wrap > .kt-blocks-accordion-header.kt-accordion-panel-active{color:#444444;background:#ffffff;border-top-color:#eeeeee;border-top-style:solid;border-right-color:#eeeeee;border-right-style:solid;border-bottom-color:#eeeeee;border-bottom-style:solid;border-left-color:#0e9cd1;border-left-style:solid;}.kt-accordion-id19606_709b5a-a8:not( .kt-accodion-icon-style-basiccircle ):not( .kt-accodion-icon-style-xclosecircle ):not( .kt-accodion-icon-style-arrowcircle )  > .kt-accordion-inner-wrap > .wp-block-kadence-pane > .kt-accordion-header-wrap > .kt-blocks-accordion-header.kt-accordion-panel-active .kt-blocks-accordion-icon-trigger:after, .kt-accordion-id19606_709b5a-a8:not( .kt-accodion-icon-style-basiccircle ):not( .kt-accodion-icon-style-xclosecircle ):not( .kt-accodion-icon-style-arrowcircle )  > .kt-accordion-inner-wrap > .wp-block-kadence-pane > .kt-accordion-header-wrap > .kt-blocks-accordion-header.kt-accordion-panel-active .kt-blocks-accordion-icon-trigger:before{background:#444444;}.kt-accordion-id19606_709b5a-a8:not( .kt-accodion-icon-style-basic ):not( .kt-accodion-icon-style-xclose ):not( .kt-accodion-icon-style-arrow ) .kt-blocks-accordion-header.kt-accordion-panel-active .kt-blocks-accordion-icon-trigger{background:#444444;}.kt-accordion-id19606_709b5a-a8:not( .kt-accodion-icon-style-basic ):not( .kt-accodion-icon-style-xclose ):not( .kt-accodion-icon-style-arrow ) .kt-blocks-accordion-header.kt-accordion-panel-active .kt-blocks-accordion-icon-trigger:after, .kt-accordion-id19606_709b5a-a8:not( .kt-accodion-icon-style-basic ):not( .kt-accodion-icon-style-xclose ):not( .kt-accodion-icon-style-arrow ) .kt-blocks-accordion-header.kt-accordion-panel-active .kt-blocks-accordion-icon-trigger:before{background:#ffffff;}@media all and (max-width: 1024px){.kt-accordion-id19606_709b5a-a8 .kt-accordion-panel-inner{border-top:0px solid transparent;border-right:1px solid transparent;border-bottom:1px solid transparent;border-left:1px solid transparent;}}@media all and (max-width: 1024px){.kt-accordion-id19606_709b5a-a8 > .kt-accordion-inner-wrap > .wp-block-kadence-pane > .kt-accordion-header-wrap > .kt-blocks-accordion-header{border-top:1px solid #eeeeee;border-right:1px solid #eeeeee;border-bottom:1px solid #eeeeee;border-left:2px solid #eeeeee;}}@media all and (max-width: 1024px){.kt-accordion-id19606_709b5a-a8 > .kt-accordion-inner-wrap > .wp-block-kadence-pane > .kt-accordion-header-wrap > .kt-blocks-accordion-header:hover, \n\t\t\t\tbody:not(.hide-focus-outline) .kt-accordion-id19606_709b5a-a8 .kt-blocks-accordion-header:focus-visible{border-top-color:#878787;border-top-style:solid;border-right-color:#878787;border-right-style:solid;border-bottom-color:#878787;border-bottom-style:solid;border-left-color:#878787;border-left-style:solid;}}@media all and (max-width: 1024px){.kt-accordion-id19606_709b5a-a8 .kt-accordion-header-wrap .kt-blocks-accordion-header:focus-visible,\n\t\t\t\t.kt-accordion-id19606_709b5a-a8 > .kt-accordion-inner-wrap > .wp-block-kadence-pane > .kt-accordion-header-wrap > .kt-blocks-accordion-header.kt-accordion-panel-active{border-top-color:#eeeeee;border-top-style:solid;border-right-color:#eeeeee;border-right-style:solid;border-bottom-color:#eeeeee;border-bottom-style:solid;border-left-color:#0e9cd1;border-left-style:solid;}}@media all and (max-width: 767px){.kt-accordion-id19606_709b5a-a8 .kt-accordion-inner-wrap{display:block;}.kt-accordion-id19606_709b5a-a8 .kt-accordion-inner-wrap .kt-accordion-pane:not(:first-child){margin-top:10px;}.kt-accordion-id19606_709b5a-a8 .kt-accordion-panel-inner{border-top:0px solid transparent;border-right:1px solid transparent;border-bottom:1px solid transparent;border-left:1px solid transparent;}.kt-accordion-id19606_709b5a-a8 > .kt-accordion-inner-wrap > .wp-block-kadence-pane > .kt-accordion-header-wrap > .kt-blocks-accordion-header{border-top:1px solid #eeeeee;border-right:1px solid #eeeeee;border-bottom:1px solid #eeeeee;border-left:2px solid #eeeeee;}.kt-accordion-id19606_709b5a-a8 > .kt-accordion-inner-wrap > .wp-block-kadence-pane > .kt-accordion-header-wrap > .kt-blocks-accordion-header:hover, \n\t\t\t\tbody:not(.hide-focus-outline) .kt-accordion-id19606_709b5a-a8 .kt-blocks-accordion-header:focus-visible{border-top-color:#878787;border-top-style:solid;border-right-color:#878787;border-right-style:solid;border-bottom-color:#878787;border-bottom-style:solid;border-left-color:#878787;border-left-style:solid;}.kt-accordion-id19606_709b5a-a8 .kt-accordion-header-wrap .kt-blocks-accordion-header:focus-visible,\n\t\t\t\t.kt-accordion-id19606_709b5a-a8 > .kt-accordion-inner-wrap > .wp-block-kadence-pane > .kt-accordion-header-wrap > .kt-blocks-accordion-header.kt-accordion-panel-active{border-top-color:#eeeeee;border-top-style:solid;border-right-color:#eeeeee;border-right-style:solid;border-bottom-color:#eeeeee;border-bottom-style:solid;border-left-color:#0e9cd1;border-left-style:solid;}}<\/style>\n<div class=\"wp-block-kadence-accordion alignnone\"><div class=\"kt-accordion-wrap kt-accordion-id19606_709b5a-a8 kt-accordion-has-2-panes kt-active-pane-0 kt-accordion-block kt-pane-header-alignment-left kt-accodion-icon-style-arrow kt-accodion-icon-side-right\" style=\"max-width:none\"><div class=\"kt-accordion-inner-wrap\" data-allow-multiple-open=\"false\" data-start-open=\"0\">\n<div class=\"wp-block-kadence-pane kt-accordion-pane kt-accordion-pane-1 kt-pane19606_cd9805-50\"><h2 class=\"kt-accordion-header-wrap\"><button class=\"kt-blocks-accordion-header kt-acccordion-button-label-show\" type=\"button\"><span class=\"kt-blocks-accordion-title-wrap\"><span class=\"kt-blocks-accordion-title\"><strong>Multiplex qPCR FAQ<\/strong>s<\/span><\/span><span class=\"kt-blocks-accordion-icon-trigger\"><\/span><\/button><\/h2><div class=\"kt-accordion-panel kt-accordion-panel-hidden\"><div class=\"kt-accordion-panel-inner\"><style>.kt-accordion-id19606_190706-3d .kt-accordion-inner-wrap{column-gap:var(--global-kb-gap-md, 2rem);row-gap:10px;}.kt-accordion-id19606_190706-3d .kt-accordion-panel-inner{border-top:0px solid transparent;border-right:1px solid transparent;border-bottom:1px solid transparent;border-left:1px solid transparent;background:#ffffff;padding-top:var(--global-kb-spacing-sm, 1.5rem);padding-right:var(--global-kb-spacing-sm, 1.5rem);padding-bottom:var(--global-kb-spacing-sm, 1.5rem);padding-left:var(--global-kb-spacing-sm, 1.5rem);}.kt-accordion-id19606_190706-3d > .kt-accordion-inner-wrap > .wp-block-kadence-pane > .kt-accordion-header-wrap > .kt-blocks-accordion-header{border-top:1px solid #eeeeee;border-right:1px solid #eeeeee;border-bottom:1px solid #eeeeee;border-left:2px solid #eeeeee;border-top-left-radius:0px;border-top-right-radius:0px;border-bottom-right-radius:0px;border-bottom-left-radius:0px;background:#ffffff;color:#444444;padding-top:14px;padding-right:16px;padding-bottom:14px;padding-left:16px;}.kt-accordion-id19606_190706-3d:not( .kt-accodion-icon-style-basiccircle ):not( .kt-accodion-icon-style-xclosecircle ):not( .kt-accodion-icon-style-arrowcircle )  > .kt-accordion-inner-wrap > .wp-block-kadence-pane > .kt-accordion-header-wrap .kt-blocks-accordion-icon-trigger:after, .kt-accordion-id19606_190706-3d:not( .kt-accodion-icon-style-basiccircle ):not( .kt-accodion-icon-style-xclosecircle ):not( .kt-accodion-icon-style-arrowcircle )  > .kt-accordion-inner-wrap > .wp-block-kadence-pane > .kt-accordion-header-wrap .kt-blocks-accordion-icon-trigger:before{background:#444444;}.kt-accordion-id19606_190706-3d:not( .kt-accodion-icon-style-basic ):not( .kt-accodion-icon-style-xclose ):not( .kt-accodion-icon-style-arrow ) .kt-blocks-accordion-icon-trigger{background:#444444;}.kt-accordion-id19606_190706-3d:not( .kt-accodion-icon-style-basic ):not( .kt-accodion-icon-style-xclose ):not( .kt-accodion-icon-style-arrow ) .kt-blocks-accordion-icon-trigger:after, .kt-accordion-id19606_190706-3d:not( .kt-accodion-icon-style-basic ):not( .kt-accodion-icon-style-xclose ):not( .kt-accodion-icon-style-arrow ) .kt-blocks-accordion-icon-trigger:before{background:#ffffff;}.kt-accordion-id19606_190706-3d > .kt-accordion-inner-wrap > .wp-block-kadence-pane > .kt-accordion-header-wrap > .kt-blocks-accordion-header:hover, \n\t\t\t\tbody:not(.hide-focus-outline) .kt-accordion-id19606_190706-3d .kt-blocks-accordion-header:focus-visible{color:#444444;background:#ffffff;border-top-color:#878787;border-top-style:solid;border-right-color:#878787;border-right-style:solid;border-bottom-color:#878787;border-bottom-style:solid;border-left-color:#878787;border-left-style:solid;}.kt-accordion-id19606_190706-3d:not( .kt-accodion-icon-style-basiccircle ):not( .kt-accodion-icon-style-xclosecircle ):not( .kt-accodion-icon-style-arrowcircle ) .kt-accordion-header-wrap .kt-blocks-accordion-header:hover .kt-blocks-accordion-icon-trigger:after, .kt-accordion-id19606_190706-3d:not( .kt-accodion-icon-style-basiccircle ):not( .kt-accodion-icon-style-xclosecircle ):not( .kt-accodion-icon-style-arrowcircle ) .kt-accordion-header-wrap .kt-blocks-accordion-header:hover .kt-blocks-accordion-icon-trigger:before, body:not(.hide-focus-outline) .kt-accordion-id19606_190706-3d:not( .kt-accodion-icon-style-basiccircle ):not( .kt-accodion-icon-style-xclosecircle ):not( .kt-accodion-icon-style-arrowcircle ) .kt-blocks-accordion--visible .kt-blocks-accordion-icon-trigger:after, body:not(.hide-focus-outline) .kt-accordion-id19606_190706-3d:not( .kt-accodion-icon-style-basiccircle ):not( .kt-accodion-icon-style-xclosecircle ):not( .kt-accodion-icon-style-arrowcircle ) .kt-blocks-accordion-header:focus-visible .kt-blocks-accordion-icon-trigger:before{background:#444444;}.kt-accordion-id19606_190706-3d:not( .kt-accodion-icon-style-basic ):not( .kt-accodion-icon-style-xclose ):not( .kt-accodion-icon-style-arrow ) .kt-accordion-header-wrap .kt-blocks-accordion-header:hover .kt-blocks-accordion-icon-trigger, body:not(.hide-focus-outline) .kt-accordion-id19606_190706-3d:not( .kt-accodion-icon-style-basic ):not( .kt-accodion-icon-style-xclose ):not( .kt-accodion-icon-style-arrow ) .kt-accordion-header-wrap .kt-blocks-accordion-header:focus-visible .kt-blocks-accordion-icon-trigger{background:#444444;}.kt-accordion-id19606_190706-3d:not( .kt-accodion-icon-style-basic ):not( .kt-accodion-icon-style-xclose ):not( .kt-accodion-icon-style-arrow ) .kt-accordion-header-wrap .kt-blocks-accordion-header:hover .kt-blocks-accordion-icon-trigger:after, .kt-accordion-id19606_190706-3d:not( .kt-accodion-icon-style-basic ):not( .kt-accodion-icon-style-xclose ):not( .kt-accodion-icon-style-arrow ) .kt-accordion-header-wrap .kt-blocks-accordion-header:hover .kt-blocks-accordion-icon-trigger:before, body:not(.hide-focus-outline) .kt-accordion-id19606_190706-3d:not( .kt-accodion-icon-style-basic ):not( .kt-accodion-icon-style-xclose ):not( .kt-accodion-icon-style-arrow ) .kt-accordion-header-wrap .kt-blocks-accordion-header:focus-visible .kt-blocks-accordion-icon-trigger:after, body:not(.hide-focus-outline) .kt-accordion-id19606_190706-3d:not( .kt-accodion-icon-style-basic ):not( .kt-accodion-icon-style-xclose ):not( .kt-accodion-icon-style-arrow ) .kt-accordion-header-wrap .kt-blocks-accordion-header:focus-visible .kt-blocks-accordion-icon-trigger:before{background:#ffffff;}.kt-accordion-id19606_190706-3d .kt-accordion-header-wrap .kt-blocks-accordion-header:focus-visible,\n\t\t\t\t.kt-accordion-id19606_190706-3d > .kt-accordion-inner-wrap > .wp-block-kadence-pane > .kt-accordion-header-wrap > .kt-blocks-accordion-header.kt-accordion-panel-active{color:#444444;background:#ffffff;border-top-color:#eeeeee;border-top-style:solid;border-right-color:#eeeeee;border-right-style:solid;border-bottom-color:#eeeeee;border-bottom-style:solid;border-left-color:#0e9cd1;border-left-style:solid;}.kt-accordion-id19606_190706-3d:not( .kt-accodion-icon-style-basiccircle ):not( .kt-accodion-icon-style-xclosecircle ):not( .kt-accodion-icon-style-arrowcircle )  > .kt-accordion-inner-wrap > .wp-block-kadence-pane > .kt-accordion-header-wrap > .kt-blocks-accordion-header.kt-accordion-panel-active .kt-blocks-accordion-icon-trigger:after, .kt-accordion-id19606_190706-3d:not( .kt-accodion-icon-style-basiccircle ):not( .kt-accodion-icon-style-xclosecircle ):not( .kt-accodion-icon-style-arrowcircle )  > .kt-accordion-inner-wrap > .wp-block-kadence-pane > .kt-accordion-header-wrap > .kt-blocks-accordion-header.kt-accordion-panel-active .kt-blocks-accordion-icon-trigger:before{background:#444444;}.kt-accordion-id19606_190706-3d:not( .kt-accodion-icon-style-basic ):not( .kt-accodion-icon-style-xclose ):not( .kt-accodion-icon-style-arrow ) .kt-blocks-accordion-header.kt-accordion-panel-active .kt-blocks-accordion-icon-trigger{background:#444444;}.kt-accordion-id19606_190706-3d:not( .kt-accodion-icon-style-basic ):not( .kt-accodion-icon-style-xclose ):not( .kt-accodion-icon-style-arrow ) .kt-blocks-accordion-header.kt-accordion-panel-active .kt-blocks-accordion-icon-trigger:after, .kt-accordion-id19606_190706-3d:not( .kt-accodion-icon-style-basic ):not( .kt-accodion-icon-style-xclose ):not( .kt-accodion-icon-style-arrow ) .kt-blocks-accordion-header.kt-accordion-panel-active .kt-blocks-accordion-icon-trigger:before{background:#ffffff;}@media all and (max-width: 1024px){.kt-accordion-id19606_190706-3d .kt-accordion-panel-inner{border-top:0px solid transparent;border-right:1px solid transparent;border-bottom:1px solid transparent;border-left:1px solid transparent;}}@media all and (max-width: 1024px){.kt-accordion-id19606_190706-3d > .kt-accordion-inner-wrap > .wp-block-kadence-pane > .kt-accordion-header-wrap > .kt-blocks-accordion-header{border-top:1px solid #eeeeee;border-right:1px solid #eeeeee;border-bottom:1px solid #eeeeee;border-left:2px solid #eeeeee;}}@media all and (max-width: 1024px){.kt-accordion-id19606_190706-3d > .kt-accordion-inner-wrap > .wp-block-kadence-pane > .kt-accordion-header-wrap > .kt-blocks-accordion-header:hover, \n\t\t\t\tbody:not(.hide-focus-outline) .kt-accordion-id19606_190706-3d .kt-blocks-accordion-header:focus-visible{border-top-color:#878787;border-top-style:solid;border-right-color:#878787;border-right-style:solid;border-bottom-color:#878787;border-bottom-style:solid;border-left-color:#878787;border-left-style:solid;}}@media all and (max-width: 1024px){.kt-accordion-id19606_190706-3d .kt-accordion-header-wrap .kt-blocks-accordion-header:focus-visible,\n\t\t\t\t.kt-accordion-id19606_190706-3d > .kt-accordion-inner-wrap > .wp-block-kadence-pane > .kt-accordion-header-wrap > .kt-blocks-accordion-header.kt-accordion-panel-active{border-top-color:#eeeeee;border-top-style:solid;border-right-color:#eeeeee;border-right-style:solid;border-bottom-color:#eeeeee;border-bottom-style:solid;border-left-color:#0e9cd1;border-left-style:solid;}}@media all and (max-width: 767px){.kt-accordion-id19606_190706-3d .kt-accordion-inner-wrap{display:block;}.kt-accordion-id19606_190706-3d .kt-accordion-inner-wrap .kt-accordion-pane:not(:first-child){margin-top:10px;}.kt-accordion-id19606_190706-3d .kt-accordion-panel-inner{border-top:0px solid transparent;border-right:1px solid transparent;border-bottom:1px solid transparent;border-left:1px solid transparent;}.kt-accordion-id19606_190706-3d > .kt-accordion-inner-wrap > .wp-block-kadence-pane > .kt-accordion-header-wrap > .kt-blocks-accordion-header{border-top:1px solid #eeeeee;border-right:1px solid #eeeeee;border-bottom:1px solid #eeeeee;border-left:2px solid #eeeeee;}.kt-accordion-id19606_190706-3d > .kt-accordion-inner-wrap > .wp-block-kadence-pane > .kt-accordion-header-wrap > .kt-blocks-accordion-header:hover, \n\t\t\t\tbody:not(.hide-focus-outline) .kt-accordion-id19606_190706-3d .kt-blocks-accordion-header:focus-visible{border-top-color:#878787;border-top-style:solid;border-right-color:#878787;border-right-style:solid;border-bottom-color:#878787;border-bottom-style:solid;border-left-color:#878787;border-left-style:solid;}.kt-accordion-id19606_190706-3d .kt-accordion-header-wrap .kt-blocks-accordion-header:focus-visible,\n\t\t\t\t.kt-accordion-id19606_190706-3d > .kt-accordion-inner-wrap > .wp-block-kadence-pane > .kt-accordion-header-wrap > .kt-blocks-accordion-header.kt-accordion-panel-active{border-top-color:#eeeeee;border-top-style:solid;border-right-color:#eeeeee;border-right-style:solid;border-bottom-color:#eeeeee;border-bottom-style:solid;border-left-color:#0e9cd1;border-left-style:solid;}}<\/style>\n<div class=\"wp-block-kadence-accordion alignnone\"><div class=\"kt-accordion-wrap kt-accordion-id19606_190706-3d kt-accordion-has-2-panes kt-active-pane-0 kt-accordion-block kt-pane-header-alignment-left kt-accodion-icon-style-arrow kt-accodion-icon-side-right\" style=\"max-width:none\"><div class=\"kt-accordion-inner-wrap\" data-allow-multiple-open=\"false\" data-start-open=\"0\">\n<div class=\"wp-block-kadence-pane kt-accordion-pane kt-accordion-pane-1 kt-pane19606_d444be-e0\"><div class=\"kt-accordion-header-wrap\"><button class=\"kt-blocks-accordion-header kt-acccordion-button-label-show\" type=\"button\"><span class=\"kt-blocks-accordion-title-wrap\"><span class=\"kt-blocks-accordion-title\"><strong>What causes performance loss in high\u2011order multiplex qPCR?<\/strong><\/span><\/span><span class=\"kt-blocks-accordion-icon-trigger\"><\/span><\/button><\/div><div class=\"kt-accordion-panel kt-accordion-panel-hidden\"><div class=\"kt-accordion-panel-inner\">\n<p>Performance loss in high-order multiplex qPCR can result from competition among primers, probes, reporter dyes, and polymerase, leading to Ct shift, reduced efficiency, and compressed dynamic range.<\/p>\n<\/div><\/div><\/div>\n\n\n\n<div class=\"wp-block-kadence-pane kt-accordion-pane kt-accordion-pane-2 kt-pane19606_3189d6-4a\"><div class=\"kt-accordion-header-wrap\"><button class=\"kt-blocks-accordion-header kt-acccordion-button-label-show\" type=\"button\"><span class=\"kt-blocks-accordion-title-wrap\"><span class=\"kt-blocks-accordion-title\"><strong>How can I minimize \u0394Ct when scaling from 1\u2011plex to 6\u2011plex?<\/strong><\/span><\/span><span class=\"kt-blocks-accordion-icon-trigger\"><\/span><\/button><\/div><div class=\"kt-accordion-panel kt-accordion-panel-hidden\"><div class=\"kt-accordion-panel-inner\">\n<p>To minimize \u0394Ct when scaling multiplex qPCR from 1-plex to 6-plex, use probe chemistry and master mix formulations designed specifically for high-order multiplexing. Multiplex-optimized probes such as <a href=\"https:\/\/www.thermofisher.com\/order\/catalog\/product\/4482777\" target=\"_blank\" rel=\"noreferrer noopener\">TaqMan QSY or QSY2 Probes<\/a> are engineered to help retain analytical performance during scale-up, while master mixes <a href=\"https:\/\/www.thermofisher.com\/order\/catalog\/product\/A58669\" target=\"_blank\" rel=\"noreferrer noopener\">like TaqPath DuraPlex 1-Step RT-qPCR Master Mix<\/a> are formulated to support simultaneous multi-target amplification.<\/p>\n<\/div><\/div><\/div>\n<\/div><\/div><\/div>\n\n\n<style>.kt-accordion-id19606_52d7ca-4d .kt-accordion-inner-wrap{column-gap:var(--global-kb-gap-md, 2rem);row-gap:10px;}.kt-accordion-id19606_52d7ca-4d .kt-accordion-panel-inner{border-top:0px solid transparent;border-right:1px solid transparent;border-bottom:1px solid transparent;border-left:1px solid transparent;background:#ffffff;padding-top:var(--global-kb-spacing-sm, 1.5rem);padding-right:var(--global-kb-spacing-sm, 1.5rem);padding-bottom:var(--global-kb-spacing-sm, 1.5rem);padding-left:var(--global-kb-spacing-sm, 1.5rem);}.kt-accordion-id19606_52d7ca-4d > .kt-accordion-inner-wrap > .wp-block-kadence-pane > .kt-accordion-header-wrap > .kt-blocks-accordion-header{border-top:1px solid #eeeeee;border-right:1px solid #eeeeee;border-bottom:1px solid #eeeeee;border-left:2px solid #eeeeee;border-top-left-radius:0px;border-top-right-radius:0px;border-bottom-right-radius:0px;border-bottom-left-radius:0px;background:#ffffff;color:#444444;padding-top:14px;padding-right:16px;padding-bottom:14px;padding-left:16px;}.kt-accordion-id19606_52d7ca-4d:not( .kt-accodion-icon-style-basiccircle ):not( .kt-accodion-icon-style-xclosecircle ):not( .kt-accodion-icon-style-arrowcircle )  > .kt-accordion-inner-wrap > .wp-block-kadence-pane > .kt-accordion-header-wrap .kt-blocks-accordion-icon-trigger:after, .kt-accordion-id19606_52d7ca-4d:not( .kt-accodion-icon-style-basiccircle ):not( .kt-accodion-icon-style-xclosecircle ):not( .kt-accodion-icon-style-arrowcircle )  > .kt-accordion-inner-wrap > .wp-block-kadence-pane > .kt-accordion-header-wrap .kt-blocks-accordion-icon-trigger:before{background:#444444;}.kt-accordion-id19606_52d7ca-4d:not( .kt-accodion-icon-style-basic ):not( .kt-accodion-icon-style-xclose ):not( .kt-accodion-icon-style-arrow ) .kt-blocks-accordion-icon-trigger{background:#444444;}.kt-accordion-id19606_52d7ca-4d:not( .kt-accodion-icon-style-basic ):not( .kt-accodion-icon-style-xclose ):not( .kt-accodion-icon-style-arrow ) .kt-blocks-accordion-icon-trigger:after, .kt-accordion-id19606_52d7ca-4d:not( .kt-accodion-icon-style-basic ):not( .kt-accodion-icon-style-xclose ):not( .kt-accodion-icon-style-arrow ) .kt-blocks-accordion-icon-trigger:before{background:#ffffff;}.kt-accordion-id19606_52d7ca-4d > .kt-accordion-inner-wrap > .wp-block-kadence-pane > .kt-accordion-header-wrap > .kt-blocks-accordion-header:hover, \n\t\t\t\tbody:not(.hide-focus-outline) .kt-accordion-id19606_52d7ca-4d .kt-blocks-accordion-header:focus-visible{color:#444444;background:#ffffff;border-top-color:#878787;border-top-style:solid;border-right-color:#878787;border-right-style:solid;border-bottom-color:#878787;border-bottom-style:solid;border-left-color:#878787;border-left-style:solid;}.kt-accordion-id19606_52d7ca-4d:not( .kt-accodion-icon-style-basiccircle ):not( .kt-accodion-icon-style-xclosecircle ):not( .kt-accodion-icon-style-arrowcircle ) .kt-accordion-header-wrap .kt-blocks-accordion-header:hover .kt-blocks-accordion-icon-trigger:after, .kt-accordion-id19606_52d7ca-4d:not( .kt-accodion-icon-style-basiccircle ):not( .kt-accodion-icon-style-xclosecircle ):not( .kt-accodion-icon-style-arrowcircle ) .kt-accordion-header-wrap .kt-blocks-accordion-header:hover .kt-blocks-accordion-icon-trigger:before, body:not(.hide-focus-outline) .kt-accordion-id19606_52d7ca-4d:not( .kt-accodion-icon-style-basiccircle ):not( .kt-accodion-icon-style-xclosecircle ):not( .kt-accodion-icon-style-arrowcircle ) .kt-blocks-accordion--visible .kt-blocks-accordion-icon-trigger:after, body:not(.hide-focus-outline) .kt-accordion-id19606_52d7ca-4d:not( .kt-accodion-icon-style-basiccircle ):not( .kt-accodion-icon-style-xclosecircle ):not( .kt-accodion-icon-style-arrowcircle ) .kt-blocks-accordion-header:focus-visible .kt-blocks-accordion-icon-trigger:before{background:#444444;}.kt-accordion-id19606_52d7ca-4d:not( .kt-accodion-icon-style-basic ):not( .kt-accodion-icon-style-xclose ):not( .kt-accodion-icon-style-arrow ) .kt-accordion-header-wrap .kt-blocks-accordion-header:hover .kt-blocks-accordion-icon-trigger, body:not(.hide-focus-outline) .kt-accordion-id19606_52d7ca-4d:not( .kt-accodion-icon-style-basic ):not( .kt-accodion-icon-style-xclose ):not( .kt-accodion-icon-style-arrow ) .kt-accordion-header-wrap .kt-blocks-accordion-header:focus-visible .kt-blocks-accordion-icon-trigger{background:#444444;}.kt-accordion-id19606_52d7ca-4d:not( .kt-accodion-icon-style-basic ):not( .kt-accodion-icon-style-xclose ):not( .kt-accodion-icon-style-arrow ) .kt-accordion-header-wrap .kt-blocks-accordion-header:hover .kt-blocks-accordion-icon-trigger:after, .kt-accordion-id19606_52d7ca-4d:not( .kt-accodion-icon-style-basic ):not( .kt-accodion-icon-style-xclose ):not( .kt-accodion-icon-style-arrow ) .kt-accordion-header-wrap .kt-blocks-accordion-header:hover .kt-blocks-accordion-icon-trigger:before, body:not(.hide-focus-outline) .kt-accordion-id19606_52d7ca-4d:not( .kt-accodion-icon-style-basic ):not( .kt-accodion-icon-style-xclose ):not( .kt-accodion-icon-style-arrow ) .kt-accordion-header-wrap .kt-blocks-accordion-header:focus-visible .kt-blocks-accordion-icon-trigger:after, body:not(.hide-focus-outline) .kt-accordion-id19606_52d7ca-4d:not( .kt-accodion-icon-style-basic ):not( .kt-accodion-icon-style-xclose ):not( .kt-accodion-icon-style-arrow ) .kt-accordion-header-wrap .kt-blocks-accordion-header:focus-visible .kt-blocks-accordion-icon-trigger:before{background:#ffffff;}.kt-accordion-id19606_52d7ca-4d .kt-accordion-header-wrap .kt-blocks-accordion-header:focus-visible,\n\t\t\t\t.kt-accordion-id19606_52d7ca-4d > .kt-accordion-inner-wrap > .wp-block-kadence-pane > .kt-accordion-header-wrap > .kt-blocks-accordion-header.kt-accordion-panel-active{color:#444444;background:#ffffff;border-top-color:#eeeeee;border-top-style:solid;border-right-color:#eeeeee;border-right-style:solid;border-bottom-color:#eeeeee;border-bottom-style:solid;border-left-color:#0e9cd1;border-left-style:solid;}.kt-accordion-id19606_52d7ca-4d:not( .kt-accodion-icon-style-basiccircle ):not( .kt-accodion-icon-style-xclosecircle ):not( .kt-accodion-icon-style-arrowcircle )  > .kt-accordion-inner-wrap > .wp-block-kadence-pane > .kt-accordion-header-wrap > .kt-blocks-accordion-header.kt-accordion-panel-active .kt-blocks-accordion-icon-trigger:after, .kt-accordion-id19606_52d7ca-4d:not( .kt-accodion-icon-style-basiccircle ):not( .kt-accodion-icon-style-xclosecircle ):not( .kt-accodion-icon-style-arrowcircle )  > .kt-accordion-inner-wrap > .wp-block-kadence-pane > .kt-accordion-header-wrap > .kt-blocks-accordion-header.kt-accordion-panel-active .kt-blocks-accordion-icon-trigger:before{background:#444444;}.kt-accordion-id19606_52d7ca-4d:not( .kt-accodion-icon-style-basic ):not( .kt-accodion-icon-style-xclose ):not( .kt-accodion-icon-style-arrow ) .kt-blocks-accordion-header.kt-accordion-panel-active .kt-blocks-accordion-icon-trigger{background:#444444;}.kt-accordion-id19606_52d7ca-4d:not( .kt-accodion-icon-style-basic ):not( .kt-accodion-icon-style-xclose ):not( .kt-accodion-icon-style-arrow ) .kt-blocks-accordion-header.kt-accordion-panel-active .kt-blocks-accordion-icon-trigger:after, .kt-accordion-id19606_52d7ca-4d:not( .kt-accodion-icon-style-basic ):not( .kt-accodion-icon-style-xclose ):not( .kt-accodion-icon-style-arrow ) .kt-blocks-accordion-header.kt-accordion-panel-active .kt-blocks-accordion-icon-trigger:before{background:#ffffff;}@media all and (max-width: 1024px){.kt-accordion-id19606_52d7ca-4d .kt-accordion-panel-inner{border-top:0px solid transparent;border-right:1px solid transparent;border-bottom:1px solid transparent;border-left:1px solid transparent;}}@media all and (max-width: 1024px){.kt-accordion-id19606_52d7ca-4d > .kt-accordion-inner-wrap > .wp-block-kadence-pane > .kt-accordion-header-wrap > .kt-blocks-accordion-header{border-top:1px solid #eeeeee;border-right:1px solid #eeeeee;border-bottom:1px solid #eeeeee;border-left:2px solid #eeeeee;}}@media all and (max-width: 1024px){.kt-accordion-id19606_52d7ca-4d > .kt-accordion-inner-wrap > .wp-block-kadence-pane > .kt-accordion-header-wrap > .kt-blocks-accordion-header:hover, \n\t\t\t\tbody:not(.hide-focus-outline) .kt-accordion-id19606_52d7ca-4d .kt-blocks-accordion-header:focus-visible{border-top-color:#878787;border-top-style:solid;border-right-color:#878787;border-right-style:solid;border-bottom-color:#878787;border-bottom-style:solid;border-left-color:#878787;border-left-style:solid;}}@media all and (max-width: 1024px){.kt-accordion-id19606_52d7ca-4d .kt-accordion-header-wrap .kt-blocks-accordion-header:focus-visible,\n\t\t\t\t.kt-accordion-id19606_52d7ca-4d > .kt-accordion-inner-wrap > .wp-block-kadence-pane > .kt-accordion-header-wrap > .kt-blocks-accordion-header.kt-accordion-panel-active{border-top-color:#eeeeee;border-top-style:solid;border-right-color:#eeeeee;border-right-style:solid;border-bottom-color:#eeeeee;border-bottom-style:solid;border-left-color:#0e9cd1;border-left-style:solid;}}@media all and (max-width: 767px){.kt-accordion-id19606_52d7ca-4d .kt-accordion-inner-wrap{display:block;}.kt-accordion-id19606_52d7ca-4d .kt-accordion-inner-wrap .kt-accordion-pane:not(:first-child){margin-top:10px;}.kt-accordion-id19606_52d7ca-4d .kt-accordion-panel-inner{border-top:0px solid transparent;border-right:1px solid transparent;border-bottom:1px solid transparent;border-left:1px solid transparent;}.kt-accordion-id19606_52d7ca-4d > .kt-accordion-inner-wrap > .wp-block-kadence-pane > .kt-accordion-header-wrap > .kt-blocks-accordion-header{border-top:1px solid #eeeeee;border-right:1px solid #eeeeee;border-bottom:1px solid #eeeeee;border-left:2px solid #eeeeee;}.kt-accordion-id19606_52d7ca-4d > .kt-accordion-inner-wrap > .wp-block-kadence-pane > .kt-accordion-header-wrap > .kt-blocks-accordion-header:hover, \n\t\t\t\tbody:not(.hide-focus-outline) .kt-accordion-id19606_52d7ca-4d .kt-blocks-accordion-header:focus-visible{border-top-color:#878787;border-top-style:solid;border-right-color:#878787;border-right-style:solid;border-bottom-color:#878787;border-bottom-style:solid;border-left-color:#878787;border-left-style:solid;}.kt-accordion-id19606_52d7ca-4d .kt-accordion-header-wrap .kt-blocks-accordion-header:focus-visible,\n\t\t\t\t.kt-accordion-id19606_52d7ca-4d > .kt-accordion-inner-wrap > .wp-block-kadence-pane > .kt-accordion-header-wrap > .kt-blocks-accordion-header.kt-accordion-panel-active{border-top-color:#eeeeee;border-top-style:solid;border-right-color:#eeeeee;border-right-style:solid;border-bottom-color:#eeeeee;border-bottom-style:solid;border-left-color:#0e9cd1;border-left-style:solid;}}<\/style>\n<div class=\"wp-block-kadence-accordion alignnone\"><div class=\"kt-accordion-wrap kt-accordion-id19606_52d7ca-4d kt-accordion-has-2-panes kt-active-pane-0 kt-accordion-block kt-pane-header-alignment-left kt-accodion-icon-style-arrow kt-accodion-icon-side-right\" style=\"max-width:none\"><div class=\"kt-accordion-inner-wrap\" data-allow-multiple-open=\"false\" data-start-open=\"0\">\n<div class=\"wp-block-kadence-pane kt-accordion-pane kt-accordion-pane-1 kt-pane19606_82c6e7-5d\"><div class=\"kt-accordion-header-wrap\"><button class=\"kt-blocks-accordion-header kt-acccordion-button-label-show\" type=\"button\"><span class=\"kt-blocks-accordion-title-wrap\"><span class=\"kt-blocks-accordion-title\">&nbsp;<strong>Which reporter dyes are recommended for 5-plex and 6-plex qPCR?<\/strong><\/span><\/span><span class=\"kt-blocks-accordion-icon-trigger\"><\/span><\/button><\/div><div class=\"kt-accordion-panel kt-accordion-panel-hidden\"><div class=\"kt-accordion-panel-inner\">\n<p>For 5-plex and 6-plex multiplex qPCR, reporter dyes such as Cyanine 5 (Cy5) and Cyanine 5.5 (Cy5.5) are commonly used to expand channel capacity while helping reduce spectral overlap. These dyes are supported by <a href=\"https:\/\/www.thermofisher.com\/order\/catalog\/product\/4482777\" target=\"_blank\" rel=\"noreferrer noopener\">TaqMan QSY2 probe chemistry<\/a>, which is designed to maintain signal clarity and performance at higher plex levels.<\/p>\n\n\n\n<p>Dye selection should always be confirmed against your instrument\u2019s optical configuration and the expected abundance of each target to facilitate optimal signal separation and quantitative accuracy.<\/p>\n<\/div><\/div><\/div>\n<\/div><\/div><\/div>\n<\/div><\/div><\/div>\n<\/div><\/div><\/div>\n\n\n\n<p>For Research Use Only. Not for use in diagnostic procedures.<\/p>\n\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"<p>What happens when a multiplex qPCR assay begins to lose performance as additional targets are introduced? An assay that performs reproducibly in singleplex can exhibit Ct shift, reduced sensitivity, or compressed dynamic range when scaled to 5- or 6-plex. As plex level increases, competition among primers, probes, reporter dyes, and polymerase intensifies, and small imbalances<\/p>\n","protected":false},"author":120,"featured_media":19610,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"_kad_blocks_custom_css":"","_kad_blocks_head_custom_js":"","_kad_blocks_body_custom_js":"","_kad_blocks_footer_custom_js":"","_monsterinsights_skip_tracking":false,"_genesis_hide_title":false,"_genesis_hide_breadcrumbs":false,"_genesis_hide_singular_image":false,"_genesis_hide_footer_widgets":false,"_genesis_custom_body_class":"","_genesis_custom_post_class":"","_genesis_layout":"","_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[54],"tags":[1844,273,57,119,2584,2586,2585,2542],"division":[],"class_list":{"0":"post-19606","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-cancer-research","8":"tag-cancer-research","9":"tag-cell-free-dna","10":"tag-digital-pcr","11":"tag-liquid-biopsy","12":"tag-minimal-residual-disease","13":"tag-mutation-monitoring","14":"tag-next-generation-sequencing-2","15":"tag-precision-oncology","16":"entry"},"_selected_authors":[],"_selected_reviewers":[1486],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO Premium plugin v27.8 (Yoast SEO v27.8) - https:\/\/yoast.com\/product\/yoast-seo-premium-wordpress\/ -->\n<title>Multiplex qPCR Optimization for 5 and 6 Plex Assays<\/title>\n<meta name=\"description\" content=\"Learn multiplex qPCR optimization strategies for 5- and 6-plex assays, including \u0394Ct control, probe chemistry, and master mix selection for reliable results.\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.thermofisher.com\/blog\/behindthebench\/multiplex-qpcr-optimization-6-plex\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Optimizing multiplex qPCR: How to amplify up to 6 targets without compromising analytical sensitivity\" \/>\n<meta property=\"og:description\" content=\"Learn multiplex qPCR optimization strategies for 5- and 6-plex assays, including \u0394Ct control, probe chemistry, and master mix selection for reliable results.\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.thermofisher.com\/blog\/behindthebench\/multiplex-qpcr-optimization-6-plex\/\" \/>\n<meta property=\"og:site_name\" content=\"Behind the Bench\" \/>\n<meta property=\"article:publisher\" content=\"https:\/\/www.facebook.com\/thermofisher\" \/>\n<meta property=\"article:published_time\" content=\"2026-04-01T20:42:44+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2026-04-06T18:45:51+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/04\/mulitplexing-image.png\" \/>\n\t<meta property=\"og:image:width\" content=\"936\" \/>\n\t<meta property=\"og:image:height\" content=\"525\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/png\" \/>\n<meta name=\"author\" content=\"Behind The Bench Staff\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:creator\" content=\"@thermofisher\" \/>\n<meta name=\"twitter:site\" content=\"@thermofisher\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Behind The Bench Staff\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"7 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\\\/\\\/schema.org\",\"@graph\":[{\"@type\":\"Article\",\"@id\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/multiplex-qpcr-optimization-6-plex\\\/#article\",\"isPartOf\":{\"@id\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/multiplex-qpcr-optimization-6-plex\\\/\"},\"author\":{\"name\":\"Behind The Bench Staff\",\"@id\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/#\\\/schema\\\/person\\\/9bbb2d67616274d3d4a21a584f7f4a0c\"},\"headline\":\"Optimizing multiplex qPCR: How to amplify up to 6 targets without compromising analytical sensitivity\",\"datePublished\":\"2026-04-01T20:42:44+00:00\",\"dateModified\":\"2026-04-06T18:45:51+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/multiplex-qpcr-optimization-6-plex\\\/\"},\"wordCount\":1285,\"commentCount\":0,\"image\":{\"@id\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/multiplex-qpcr-optimization-6-plex\\\/#primaryimage\"},\"thumbnailUrl\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/wp-content\\\/uploads\\\/sites\\\/9\\\/2026\\\/04\\\/mulitplexing-image.png\",\"keywords\":[\"cancer research\",\"cell-free DNA\",\"digital PCR\",\"liquid biopsy\",\"Minimal residual disease\",\"Mutation monitoring\",\"Next-generation sequencing\",\"precision oncology\"],\"articleSection\":[\"Cancer Research\"],\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"CommentAction\",\"name\":\"Comment\",\"target\":[\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/multiplex-qpcr-optimization-6-plex\\\/#respond\"]}]},{\"@type\":\"WebPage\",\"@id\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/multiplex-qpcr-optimization-6-plex\\\/\",\"url\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/multiplex-qpcr-optimization-6-plex\\\/\",\"name\":\"Multiplex qPCR Optimization for 5 and 6 Plex Assays\",\"isPartOf\":{\"@id\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/#website\"},\"primaryImageOfPage\":{\"@id\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/multiplex-qpcr-optimization-6-plex\\\/#primaryimage\"},\"image\":{\"@id\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/multiplex-qpcr-optimization-6-plex\\\/#primaryimage\"},\"thumbnailUrl\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/wp-content\\\/uploads\\\/sites\\\/9\\\/2026\\\/04\\\/mulitplexing-image.png\",\"datePublished\":\"2026-04-01T20:42:44+00:00\",\"dateModified\":\"2026-04-06T18:45:51+00:00\",\"author\":{\"@id\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/#\\\/schema\\\/person\\\/9bbb2d67616274d3d4a21a584f7f4a0c\"},\"description\":\"Learn multiplex qPCR optimization strategies for 5- and 6-plex assays, including \u0394Ct control, probe chemistry, and master mix selection for reliable results.\",\"breadcrumb\":{\"@id\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/multiplex-qpcr-optimization-6-plex\\\/#breadcrumb\"},\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/multiplex-qpcr-optimization-6-plex\\\/\"]}]},{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/multiplex-qpcr-optimization-6-plex\\\/#primaryimage\",\"url\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/wp-content\\\/uploads\\\/sites\\\/9\\\/2026\\\/04\\\/mulitplexing-image.png\",\"contentUrl\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/wp-content\\\/uploads\\\/sites\\\/9\\\/2026\\\/04\\\/mulitplexing-image.png\",\"width\":936,\"height\":525,\"caption\":\"As multiplex level increases, \u0394Ct shift can impact quantification accuracy if assay components are not optimized.\"},{\"@type\":\"BreadcrumbList\",\"@id\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/multiplex-qpcr-optimization-6-plex\\\/#breadcrumb\",\"itemListElement\":[{\"@type\":\"ListItem\",\"position\":1,\"name\":\"Home\",\"item\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/\"},{\"@type\":\"ListItem\",\"position\":2,\"name\":\"Optimizing multiplex qPCR: How to amplify up to 6 targets without compromising analytical sensitivity\"}]},{\"@type\":\"WebSite\",\"@id\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/#website\",\"url\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/\",\"name\":\"Behind the Bench\",\"description\":\"\",\"potentialAction\":[{\"@type\":\"SearchAction\",\"target\":{\"@type\":\"EntryPoint\",\"urlTemplate\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/?s={search_term_string}\"},\"query-input\":{\"@type\":\"PropertyValueSpecification\",\"valueRequired\":true,\"valueName\":\"search_term_string\"}}],\"inLanguage\":\"en-US\"},{\"@type\":\"Person\",\"@id\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/#\\\/schema\\\/person\\\/9bbb2d67616274d3d4a21a584f7f4a0c\",\"name\":\"Behind The Bench Staff\",\"image\":{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\\\/\\\/secure.gravatar.com\\\/avatar\\\/52d5c16ece4bd1c0a49a63521c2b6a25c54a3f0c33f7afed215ba7e0cdff69e3?s=96&d=mm&r=g\",\"url\":\"https:\\\/\\\/secure.gravatar.com\\\/avatar\\\/52d5c16ece4bd1c0a49a63521c2b6a25c54a3f0c33f7afed215ba7e0cdff69e3?s=96&d=mm&r=g\",\"contentUrl\":\"https:\\\/\\\/secure.gravatar.com\\\/avatar\\\/52d5c16ece4bd1c0a49a63521c2b6a25c54a3f0c33f7afed215ba7e0cdff69e3?s=96&d=mm&r=g\",\"caption\":\"Behind The Bench Staff\"},\"url\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/author\\\/behind-the-bench-staff\\\/\"}]}<\/script>\n<!-- \/ Yoast SEO Premium plugin. -->","yoast_head_json":{"title":"Multiplex qPCR Optimization for 5 and 6 Plex Assays","description":"Learn multiplex qPCR optimization strategies for 5- and 6-plex assays, including \u0394Ct control, probe chemistry, and master mix selection for reliable results.","robots":{"index":"index","follow":"follow","max-snippet":"max-snippet:-1","max-image-preview":"max-image-preview:large","max-video-preview":"max-video-preview:-1"},"canonical":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/multiplex-qpcr-optimization-6-plex\/","og_locale":"en_US","og_type":"article","og_title":"Optimizing multiplex qPCR: How to amplify up to 6 targets without compromising analytical sensitivity","og_description":"Learn multiplex qPCR optimization strategies for 5- and 6-plex assays, including \u0394Ct control, probe chemistry, and master mix selection for reliable results.","og_url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/multiplex-qpcr-optimization-6-plex\/","og_site_name":"Behind the Bench","article_publisher":"https:\/\/www.facebook.com\/thermofisher","article_published_time":"2026-04-01T20:42:44+00:00","article_modified_time":"2026-04-06T18:45:51+00:00","og_image":[{"width":936,"height":525,"url":"http:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/04\/mulitplexing-image.png","type":"image\/png"}],"author":"Behind The Bench Staff","twitter_card":"summary_large_image","twitter_creator":"@thermofisher","twitter_site":"@thermofisher","twitter_misc":{"Written by":"Behind The Bench Staff","Est. reading time":"7 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"Article","@id":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/multiplex-qpcr-optimization-6-plex\/#article","isPartOf":{"@id":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/multiplex-qpcr-optimization-6-plex\/"},"author":{"name":"Behind The Bench Staff","@id":"https:\/\/admin.acceleratingscience.com\/behindthebench\/#\/schema\/person\/9bbb2d67616274d3d4a21a584f7f4a0c"},"headline":"Optimizing multiplex qPCR: How to amplify up to 6 targets without compromising analytical sensitivity","datePublished":"2026-04-01T20:42:44+00:00","dateModified":"2026-04-06T18:45:51+00:00","mainEntityOfPage":{"@id":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/multiplex-qpcr-optimization-6-plex\/"},"wordCount":1285,"commentCount":0,"image":{"@id":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/multiplex-qpcr-optimization-6-plex\/#primaryimage"},"thumbnailUrl":"https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/04\/mulitplexing-image.png","keywords":["cancer research","cell-free DNA","digital PCR","liquid biopsy","Minimal residual disease","Mutation monitoring","Next-generation sequencing","precision oncology"],"articleSection":["Cancer Research"],"inLanguage":"en-US","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/www.thermofisher.com\/blog\/behindthebench\/multiplex-qpcr-optimization-6-plex\/#respond"]}]},{"@type":"WebPage","@id":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/multiplex-qpcr-optimization-6-plex\/","url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/multiplex-qpcr-optimization-6-plex\/","name":"Multiplex qPCR Optimization for 5 and 6 Plex Assays","isPartOf":{"@id":"https:\/\/admin.acceleratingscience.com\/behindthebench\/#website"},"primaryImageOfPage":{"@id":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/multiplex-qpcr-optimization-6-plex\/#primaryimage"},"image":{"@id":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/multiplex-qpcr-optimization-6-plex\/#primaryimage"},"thumbnailUrl":"https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/04\/mulitplexing-image.png","datePublished":"2026-04-01T20:42:44+00:00","dateModified":"2026-04-06T18:45:51+00:00","author":{"@id":"https:\/\/admin.acceleratingscience.com\/behindthebench\/#\/schema\/person\/9bbb2d67616274d3d4a21a584f7f4a0c"},"description":"Learn multiplex qPCR optimization strategies for 5- and 6-plex assays, including \u0394Ct control, probe chemistry, and master mix selection for reliable results.","breadcrumb":{"@id":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/multiplex-qpcr-optimization-6-plex\/#breadcrumb"},"inLanguage":"en-US","potentialAction":[{"@type":"ReadAction","target":["https:\/\/www.thermofisher.com\/blog\/behindthebench\/multiplex-qpcr-optimization-6-plex\/"]}]},{"@type":"ImageObject","inLanguage":"en-US","@id":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/multiplex-qpcr-optimization-6-plex\/#primaryimage","url":"https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/04\/mulitplexing-image.png","contentUrl":"https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/04\/mulitplexing-image.png","width":936,"height":525,"caption":"As multiplex level increases, \u0394Ct shift can impact quantification accuracy if assay components are not optimized."},{"@type":"BreadcrumbList","@id":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/multiplex-qpcr-optimization-6-plex\/#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Home","item":"https:\/\/admin.acceleratingscience.com\/behindthebench\/"},{"@type":"ListItem","position":2,"name":"Optimizing multiplex qPCR: How to amplify up to 6 targets without compromising analytical sensitivity"}]},{"@type":"WebSite","@id":"https:\/\/admin.acceleratingscience.com\/behindthebench\/#website","url":"https:\/\/admin.acceleratingscience.com\/behindthebench\/","name":"Behind the Bench","description":"","potentialAction":[{"@type":"SearchAction","target":{"@type":"EntryPoint","urlTemplate":"https:\/\/admin.acceleratingscience.com\/behindthebench\/?s={search_term_string}"},"query-input":{"@type":"PropertyValueSpecification","valueRequired":true,"valueName":"search_term_string"}}],"inLanguage":"en-US"},{"@type":"Person","@id":"https:\/\/admin.acceleratingscience.com\/behindthebench\/#\/schema\/person\/9bbb2d67616274d3d4a21a584f7f4a0c","name":"Behind The Bench Staff","image":{"@type":"ImageObject","inLanguage":"en-US","@id":"https:\/\/secure.gravatar.com\/avatar\/52d5c16ece4bd1c0a49a63521c2b6a25c54a3f0c33f7afed215ba7e0cdff69e3?s=96&d=mm&r=g","url":"https:\/\/secure.gravatar.com\/avatar\/52d5c16ece4bd1c0a49a63521c2b6a25c54a3f0c33f7afed215ba7e0cdff69e3?s=96&d=mm&r=g","contentUrl":"https:\/\/secure.gravatar.com\/avatar\/52d5c16ece4bd1c0a49a63521c2b6a25c54a3f0c33f7afed215ba7e0cdff69e3?s=96&d=mm&r=g","caption":"Behind The Bench Staff"},"url":"https:\/\/admin.acceleratingscience.com\/author\/behind-the-bench-staff\/"}]}},"taxonomy_info":{"category":[{"value":54,"label":"Cancer Research"}],"post_tag":[{"value":1844,"label":"cancer research"},{"value":273,"label":"cell-free DNA"},{"value":57,"label":"digital PCR"},{"value":119,"label":"liquid biopsy"},{"value":2584,"label":"Minimal residual disease"},{"value":2586,"label":"Mutation monitoring"},{"value":2585,"label":"Next-generation sequencing"},{"value":2542,"label":"precision oncology"}]},"featured_image_src_large":["https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/04\/mulitplexing-image.png",760,426,false],"author_info":{"display_name":"Behind The Bench Staff","author_link":"https:\/\/admin.acceleratingscience.com\/author\/behind-the-bench-staff\/"},"comment_info":0,"category_info":[{"term_id":54,"name":"Cancer Research","slug":"cancer-research","term_group":0,"term_taxonomy_id":54,"taxonomy":"category","description":"","parent":0,"count":142,"filter":"raw","meta":[],"cat_ID":54,"category_count":142,"category_description":"","cat_name":"Cancer Research","category_nicename":"cancer-research","category_parent":0}],"tag_info":[{"term_id":1844,"name":"cancer research","slug":"cancer-research","term_group":0,"term_taxonomy_id":1844,"taxonomy":"post_tag","description":"","parent":0,"count":21,"filter":"raw","meta":[]},{"term_id":273,"name":"cell-free DNA","slug":"cell-free-dna","term_group":0,"term_taxonomy_id":273,"taxonomy":"post_tag","description":"","parent":0,"count":3,"filter":"raw","meta":[]},{"term_id":57,"name":"digital PCR","slug":"digital-pcr","term_group":0,"term_taxonomy_id":57,"taxonomy":"post_tag","description":"","parent":0,"count":50,"filter":"raw","meta":[]},{"term_id":119,"name":"liquid biopsy","slug":"liquid-biopsy","term_group":0,"term_taxonomy_id":119,"taxonomy":"post_tag","description":"","parent":0,"count":13,"filter":"raw","meta":[]},{"term_id":2584,"name":"Minimal residual disease","slug":"minimal-residual-disease","term_group":0,"term_taxonomy_id":2584,"taxonomy":"post_tag","description":"","parent":0,"count":2,"filter":"raw","meta":[]},{"term_id":2586,"name":"Mutation monitoring","slug":"mutation-monitoring","term_group":0,"term_taxonomy_id":2586,"taxonomy":"post_tag","description":"","parent":0,"count":2,"filter":"raw","meta":[]},{"term_id":2585,"name":"Next-generation sequencing","slug":"next-generation-sequencing-2","term_group":0,"term_taxonomy_id":2585,"taxonomy":"post_tag","description":"","parent":0,"count":3,"filter":"raw","meta":[]},{"term_id":2542,"name":"precision oncology","slug":"precision-oncology","term_group":0,"term_taxonomy_id":2542,"taxonomy":"post_tag","description":"","parent":0,"count":4,"filter":"raw","meta":[]}],"jetpack-related-posts":[{"id":19966,"url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/multiplex-assay-optimization-qpcr\/","url_meta":{"origin":19606,"position":0},"title":"Building Better Multiplex Panels: Identifying Assay Interactions Early","author":"Ashleigh Barlow","date":"September 8, 2026","format":false,"excerpt":"Multiplex qPCR has transformed molecular research by enabling scientists to detect multiple targets in a single reaction. The benefits are clear: reduced sample consumption, lower costs, faster workflows, and more data from every experiment. However, designing successful multiplex assays isn't always straightforward. Traditionally, identifying problematic assay combinations required extensive wet-lab\u2026","rel":"","context":"In &quot;Lab Tips and Tricks&quot;","block_context":{"text":"Lab Tips and Tricks","link":"https:\/\/admin.acceleratingscience.com\/behindthebench\/lab-tips-and-tricks\/"},"img":{"alt_text":"For Research Use Only. Not for use in diagnostic procedures. \u00a9 2026 Thermo Fisher Scientific Inc. All rights reserved. All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified.","src":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/Header-banner-scaled.jpg?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/Header-banner-scaled.jpg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/Header-banner-scaled.jpg?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/Header-banner-scaled.jpg?resize=700%2C400&ssl=1 2x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/Header-banner-scaled.jpg?resize=1050%2C600&ssl=1 3x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/Header-banner-scaled.jpg?resize=1400%2C800&ssl=1 4x"},"classes":[]},{"id":19685,"url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/multiplex-qpcr-primer-optimization\/","url_meta":{"origin":19606,"position":1},"title":"Multiplex qPCR primer optimization: How to balance amplification across targets","author":"Ashleigh Barlow","date":"May 1, 2026","format":false,"excerpt":"What happens when one target amplifies more efficiently than another in a multiplex qPCR reaction? In many experiments, targets are not present at equal abundance. Some amplify earlier, generate stronger signals, and begin to dominate the reaction. Others may appear delayed, or not at all. These effects are not always\u2026","rel":"","context":"In &quot;Lab Tips and Tricks&quot;","block_context":{"text":"Lab Tips and Tricks","link":"https:\/\/admin.acceleratingscience.com\/behindthebench\/lab-tips-and-tricks\/"},"img":{"alt_text":"DNA strands with multicolored signals representing simultaneous detection of multiple targets in multiplex qPCR.","src":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/05\/Blog_qPCR_Reagent_multiplex_qPCR_primerlimitations-1-Multiplex-qPCR_hero.jpeg?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/05\/Blog_qPCR_Reagent_multiplex_qPCR_primerlimitations-1-Multiplex-qPCR_hero.jpeg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/05\/Blog_qPCR_Reagent_multiplex_qPCR_primerlimitations-1-Multiplex-qPCR_hero.jpeg?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/05\/Blog_qPCR_Reagent_multiplex_qPCR_primerlimitations-1-Multiplex-qPCR_hero.jpeg?resize=700%2C400&ssl=1 2x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/05\/Blog_qPCR_Reagent_multiplex_qPCR_primerlimitations-1-Multiplex-qPCR_hero.jpeg?resize=1050%2C600&ssl=1 3x"},"classes":[]},{"id":19271,"url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/multiplex-qpcr-basics-guide\/","url_meta":{"origin":19606,"position":2},"title":"Multiplex vs. Singleplex qPCR: What do I need to know?","author":"Ashleigh Barlow","date":"December 3, 2025","format":false,"excerpt":"Real-time PCR (qPCR) has transformed how scientists detect and quantify nucleic acid targets, offering analytical sensitivity, speed, and scalability. Many real-time PCR reactions measure a single target per well \u2014 a setup called singleplex qPCR. However, the effectiveness of real-time PCR can be increased by an approach called multiplex qPCR.\u2026","rel":"","context":"In &quot;General&quot;","block_context":{"text":"General","link":"https:\/\/admin.acceleratingscience.com\/behindthebench\/general\/"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2025\/12\/Web-header-900-x-600-custom-web-page-size-feature-pods.png?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2025\/12\/Web-header-900-x-600-custom-web-page-size-feature-pods.png?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2025\/12\/Web-header-900-x-600-custom-web-page-size-feature-pods.png?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2025\/12\/Web-header-900-x-600-custom-web-page-size-feature-pods.png?resize=700%2C400&ssl=1 2x"},"classes":[]},{"id":19911,"url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/multiplex-mirna-profiling-precision-oncology\/","url_meta":{"origin":19606,"position":3},"title":"A scalable multiplex miRNA profiling workflow for precision oncology research","author":"Ashleigh Barlow","date":"August 18, 2026","format":false,"excerpt":"The promise of precision oncology rests on our ability to reliably monitor tumor biology in real time. Circulating microRNAs (miRNAs) offer that opportunity, serving as potentially stable, non-invasive biomarkers linked to disease progression and therapeutic response; however, their adoption in routine practice remains constrained by technical hurdles. (1,2) Because cancer\u2026","rel":"","context":"In &quot;Cancer Research&quot;","block_context":{"text":"Cancer Research","link":"https:\/\/admin.acceleratingscience.com\/behindthebench\/cancer-research\/"},"img":{"alt_text":"Scientist pipetting a laboratory sample during molecular biomarker research.","src":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/lisa-blog-picture.jpg?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/lisa-blog-picture.jpg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/lisa-blog-picture.jpg?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/lisa-blog-picture.jpg?resize=700%2C400&ssl=1 2x"},"classes":[]},{"id":19922,"url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/qpcr-master-mix-comparison\/","url_meta":{"origin":19606,"position":4},"title":"Think your supermix is good enough? Prove it.","author":"Ashleigh Barlow","date":"August 21, 2026","format":false,"excerpt":"The chemistry of your qPCR supermix can influence analytical sensitivity, specificity, precision, and overall assay performance. Even when you keep the same instrument, assays, and samples, different master mixes can perform differently. That's why we challenge you to put your supermix to the test. Compare it side by side with\u2026","rel":"","context":"In &quot;General&quot;","block_context":{"text":"General","link":"https:\/\/admin.acceleratingscience.com\/behindthebench\/general\/"},"img":{"alt_text":"Applied Biosystems probe-based and SYBR Green qPCR master mixes for real-time PCR workflows.","src":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/Untitled-August-18-2026-at-08.39.51-5.jpeg?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/Untitled-August-18-2026-at-08.39.51-5.jpeg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/Untitled-August-18-2026-at-08.39.51-5.jpeg?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/Untitled-August-18-2026-at-08.39.51-5.jpeg?resize=700%2C400&ssl=1 2x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/Untitled-August-18-2026-at-08.39.51-5.jpeg?resize=1050%2C600&ssl=1 3x"},"classes":[]},{"id":19640,"url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/direct-from-lysate-snp-genotyping-in-research-applications\/","url_meta":{"origin":19606,"position":5},"title":"Direct-from-Lysate SNP Genotyping in Research Applications","author":"Ashleigh Barlow","date":"April 6, 2026","format":false,"excerpt":"Direct-from-lysate workflow enabled by DNA Extract All Reagents compared to traditional DNA purification for SNP genotyping applications. Can You Perform SNP Genotyping Without DNA Purification? The short answer: In many research workflows, direct-from-lysate SNP genotyping can be performed without traditional DNA purification\u2014when appropriate chemistries and verification procedures are used. Direct-from-lysate\u2026","rel":"","context":"In &quot;General&quot;","block_context":{"text":"General","link":"https:\/\/admin.acceleratingscience.com\/behindthebench\/general\/"},"img":{"alt_text":"Comparison of traditional DNA purification workflow and direct-from-lysate workflow using DNA Extract All Reagents for SNP genotyping prior to qPCR.","src":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/04\/blog-image-1.png?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/04\/blog-image-1.png?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/04\/blog-image-1.png?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/04\/blog-image-1.png?resize=700%2C400&ssl=1 2x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/04\/blog-image-1.png?resize=1050%2C600&ssl=1 3x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/04\/blog-image-1.png?resize=1400%2C800&ssl=1 4x"},"classes":[]}],"jetpack_sharing_enabled":true,"jetpack_featured_media_url":"https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/04\/mulitplexing-image.png","_links":{"self":[{"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/posts\/19606","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/users\/120"}],"replies":[{"embeddable":true,"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/comments?post=19606"}],"version-history":[{"count":0,"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/posts\/19606\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/media\/19610"}],"wp:attachment":[{"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/media?parent=19606"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/categories?post=19606"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/tags?post=19606"},{"taxonomy":"division","embeddable":true,"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/division?post=19606"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}