Assay Designer FAQs

No. ArcherDX’s Anchored Multiplex PCR (AMP™) chemistry enables you to detect any fusion partner to your target of interest. You do, however, need to specify the exon of interest for each target as well as the direction of the fusion partner from the target exon (3’ or 5’). Note that mid-exon breakpoint primer design is not supported by Assay Designer at this time. If you want to detect mid-exon breakpoint fusions, contact technical support at

Assay Designer assumes that all breakpoints are at the specified end of the exon (3’ or 5’). If you want to detect mid-exon breakpoint fusions, contact technical support at

After the design has been approved and submitted for order, you can expect to receive your equimolar primer pools in 6-8 weeks.

There is no specific maximum number of targets for Assay Designer. However, we will flag panel designs that we do not believe in silco design is sufficient to meet your expectations or ours. In this instance we will be in contact with you to discuss specifics and how you would best like to proceed with procuring a custom panel.

To provide you with the best chance of creating a successful primer design for your assay, a member of our team will carefully review each primer in your design and remove any primers expected to perform poorly. In some cases, we might recommend that the custom panel be redesigned by our in-house R&D team to ensure that they meet both your and our expectations.

There is no current minimum. However, the standard 8 controls included in our catalog panels will be included in any design.

No. Primers are designed in silico and ordered directly through Assay Designer. They are not tested in any way prior to shipping. They will arrive in an equimolar pool. For best results, it is recommended that you test the primer pool on DNA before use for fusion detection. Testing the primers on DNA will allow you to confirm that all primers are fully functional without the added complication of expression levels associated with target amplification of RNA. If you are interested in having ArcherDX, Inc. functionally test your primers and balance your primer pools, contact technical support at

No. The primer search setting in Assay Designer are fixed so that primers are optimal and likely to be fully functional with our assay. If you need assistance recovering important targets, contact technical support for assistance at

Assay Designer might fail to design a primer to a target region for one or more of the following reasons:

  1. Target region has high similarity to other regions in the genome, which would result in off-targeting
  2. GC content in target region is too high or too low
  3. There are known mutations present in the primer site

A custom fusion panel can be made at Exons from genes can be selected and added to the custom fusion panel. It is also possible to upload a .csv file with the appropriate information. Once the design has been submitted, a representative from ArcherDX, Inc. will contact you to make sure the design is correct. The Quiver® Fusion database ( can also be used to find known fusions that can then be added to the custom design.

Archer Assay Designer is our free online tool used to create your own custom assays. It can be found here:

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