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Create amplicon panels optimized for content of interest with our free, user-friendly, online tool

AmpliSeq for Illumina Custom Panels

If your genes of interest are not available as ready-to-use panels, consider designing a custom AmpliSeq for Illumina panel. Include just the genes and targets you’re interested in.

Use DesignStudio, a free, web-based assay design tool, to submit your target regions of interest and receive personalized panel content that fits the needs of your study.

Custom Assay Design
Custom Panel Design Demo Graphic
Custom Panel Design in DesignStudio

View a brief walkthrough of the amplicon panel design process.

Whether you start from an AmpliSeq for Illumina Ready-to Use or Community Panel, or by directly adding targets in DesignStudio, we offer multiple customizable design solutions for you.

With the simple user interface, robust algorithms, and dynamic feedback provided by DesignStudio, custom panels can be designed quickly and easily, allowing you to start finding answers sooner.

To start a new custom AmpliSeq for Illumina panel, simply log onto your personalized account. Select a preloaded reference genome and then start adding in your genomic regions of interest.

If you like the content from ready-to-use or community panels, you can directly upload Product Manifest Files into DesignStudio as a starting point for further customization.

Custom DNA panels can be designed for standard DNA or formalin-fixed paraffin-embedded (FFPE) tissue. Up to 3,072 amplicons can be designed per pool, with an overall maximum of 12,288 amplicons for the entire panel.

Custom RNA panels can be designed to measure gene expression for 12 to 1200 targets in a single assay. Targets can be chosen from over 20,000 RefSeq genes.

Support for uploading custom reference genomes for gene designs will be available through DesignStudio later in 2019.

Available Design Options

Sequencing by synthesis (SBS) technology delivers the fewest false positives, fewest false negatives, and fewest miscalls among leading sequencing platforms. Combine with AmpliSeq for Illumina amplicon chemistry for simple and fast library construction. Expedite your research with a 2.5-day workflow from DNA to variants, or a 2-day workflow from RNA to gene expression profiles.

Wondering how the various AmpliSeq for Illumina sequencing panels differ? Have questions about which components you’ll need, panel customization and post-sequencing analysis options, or where to go for technical support?

Visit Our FAQ Page

Illumina Concierge design support can help improve coverage and enable add-on or nonhuman species designs. You can also assess the AmpliSeq for Illumina targeted resequencing solution with your own samples on an Illumina sequencing system before investing. 

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Next Steps


Ready to start designing panels?

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