Over 400 Custom NGS Panels have been expertly designed and shipped to over 200 NGS labs globally for research and testing applications ranging from tumor profiling, cancer liquid biopsy, non-invasive prenatal testing, pharmacogenomics, neurology, cardiology to forensics, food safety and agrigenomics.

NEW! We are accepting cancer fusion custom panel design requests now! Our OmniFusion™ technology will enable you to detect both known and unknown fusion genes. Scroll to the end of this page to submit your design consultation requests.


Get your custom NGS amplicon panel in 4 weeks

Easily build a CleanPlex Custom NGS Amplicon Panel to accelerate your research and assay development. Multiplex up to 20,000+ amplicons in each reaction and take advantage of CleanPlex Technology’s high sensitivity, rapid single-tube workflow, and cost-effective sequencing.

Use ParagonDesigner, our free, web-based tool, to submit your target regions of interest and instantly receive a design coverage report to review. Our custom amplicon panel design experts will be available through the process to provide you a quote, help you with any questions, and make further optimization to meet your needs. Once you approve the design, your custom NGS amplicon panel will be ready for shipment in 4 weeks.

» Start designing now and obtain a quote 


Build better and smarter NGS assays

CleanPlex® Custom NGS Amplicon Panels are powered by Paragon Genomics’ CleanPlex NGS Amplicon Sequencing Technology – an ultra-high multiplex PCR-based target enrichment technology for next-generation sequencing (NGS). It features a highly advanced proprietary primer design algorithm and an innovative, patented background cleaning chemistry. Together, they allow CleanPlex Custom NGS Amplicon Panels to break the limits of existing target enrichment technologies (Read this blog article about how). 

» View applications and customer testimonials


Enjoy the highest level of personalization

Our expert scientists are ready to design and optimize CleanPlex Custom NGS Amplicon Panels to meet your desired specifications. CleanPlex Custom NGS Amplicon Panels are designed using Paragon Genomics’ proprietary ParagonDesigner™ algorithm and iteratively optimized in-silico to ensure success of your NGS-based assays. Amplicon size can tailored for your sample types according to your specified input DNA fragment size to generate the highest level of performance.

» View custom NGS amplicon panel specifications


Build your panel faster on top of Paragon curated gene content

To speed up your custom NGS assay development, our team has consulted with leading experts and curated relevant gene content for specific applications such as cardiac diseases and neurodegenerative diseases. These pre-designed NGS amplicon panels have already been evaluated in silico and can be made to order fast. You have the option to add new content or modify the existing content of these panels. 

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Why Choose CleanPlex Custom NGS Amplicon Panels?

Design Custom NGS Assays Online with ParagonDesigner

Get your answers sooner! Using the ParagonDesigner online portal to create a new CleanPlex Custom NGS Panel is quick and easy. Just follow 3 simple steps and our intuitive user interface will guide you through the process. Our design experts will be available to answer your questions, implement additional customization, and provide you a quote.

Remember to register before you begin. We just need a few basic information so we can create an account for you to view and track your designs. We promise signing up will be a breeze!

» Start Designing Now

More Than 3,400 Clinically-Relevant Genes with Pre-Designed Solutions

ParagonDesigner features a database of more than 3,400 human genes that have been pre-designed using our advanced primer design algorithm to allow custom NGS gene panels to be created instantly. The database includes genes associated with both rare and common cancers, as well as all guideline-recommended genes in solid tumors, hereditary cancers and genetic disorders including those with companion diagnostic indications.

» Explore the Entire List

When we decided to choose a sequencing platform, we had several choices and I am delighted that we chose Paragon Genomics. Paragon Genomics has enabled us to move our sequencing in-house with an affordable and easy-to-use product. They assisted us every step along the way from choosing the amplicons, to guiding us through library preparation to assisting with analysis. I strongly recommend their CleanPlex® amplicon-based targeted sequencing approach and could not be happier with their product.

Elliot Stieglitz, MD, Assistant Professor, University of California San Francisco

Need Functional Validation?

Our expert scientists are here to support you from design to validation for your assay development project. Paragon Genomics provides extensive wet-lab validation and optimization to ensure optimal performance of your NGS assay on your specified sample type and quick transition of the assay into your lab.

What’s Included in My CleanPlex Custom NGS Amplicon Panel?

Each CleanPlex Custom NGS Amplicon Panel contains all reagents necessary to construct target-enriched, sequencing-ready NGS amplicon libraries from input DNA. Your CleanPlex Custom NGS Amplicon Panel will include a CleanPlex Targeted Library Kit, your custom multiplex PCR primer mix, CleanMag® Magnetic Beads for bead purification, and Illumina® or Ion Torrent index primers for multiplexing and sequencing on the platform of your choice.

Request a Free Custom Amplicon Panel Design Consultation

Enter your email below to schedule a free consultation with our PhD-level expert scientists to learn how our best-in-class custom NGS panel design services can help you advance your genomic testing or research.