RNA Gene Fusion Designs

Publication Number MAN0010907 - Ion AmpliSeq Designer 7.4: Getting Started (5.9 MB PDF download)

Start an RNA Gene Fusions design

To make RNA Gene Fusions panels with a combination of Gene Fusion and Gene Expression Assays (GEX), follow the steps below.

Important: For successful panels, you must have at least 12 GEX assays per panel. We provide 12 default GEX assays for each panel that you may accept or replace with targets of your choice. For panels requiring two pools, the GEX assays will be split between the two pools.

If you are already on Ampliseq.com working in another application, click the “home” icon in the navigation bar to return to the main page:

  1. Enter a Design Name and, optionally, details. The Start a new design page now expands to add additional elements for creating a new panel.
  2. Select RNA Gene Fusion designs (multi-pool) button, in application type.

    Note: Human (RefSeq/Ensembl) is the only genome permitted with this panel type.

  3. Click Next: Add Targets button. At the top of this screen, you can Add Fusions by Symbol Pair or upload them from a file. Click “Input Specifications” link for details. At the bottom of the screen you see two tabs, one to add gene fusion targets and the other to add gene expression targets. These tabs represent the two stages mentioned in the introduction for this section. By default the Fusion tab is selected.
  4. On the Fusions tab, add your targets.
    1. Start typing the gene symbol that you would like to add the targets for, and the available fusions partners are displayed.
    2. Select the desired gene pair. The available fusions for that gene pair are displayed.
    3. Add the fusions by checking each checkbox on the left of each target, and then click the Add fusion(s) button.
  5. Repeat step 4 a-c to add additional targets.

    Ion AmpliSeq Designer uploads the targets and checks them. Once complete, a status message appears at the top of the screen: either “Target saved successfully” in green text, or “# duplicate fusions ignored” in red text.

Gene Expression Assays

Now add your gene expression assays. Every pool is required to have 12 gene expression assays, and we have pre-selected them to get you started. If you want to pick your own gene expression assays, delete the proposed ones and add your own gene expression targets by gene symbol or RefSeq transcript accession.

  1. Click on the Genes tab.
  2. At the top of the screen, enter valid gene symbols (preferably an HGNC-approved symbol) or valid RNA RefSeq accession numbers as in the example below and click Add target.

    Alternatively, you can upload your own gene expression assays. Please click Input Specification link in the software user interface for more details and a CSV template for creating your own list of genes or RefSeq Accession numbers.

    Note: If you would like to restore the pre-populated gene expression assays, click the Restore pre-populated genes button and they will be restored.

  3. Repeat step 2 to add additional genes or RNA RefSeq accession numbers.
  4. To submit your design once you have selected your gene fusion targets and gene expression assays, click Submit targets button. New in AmpliSeq v5.0, two designs can be submitted at a time.
  5. Confirm your submission.

    Note: You can submit a second submission if required.

    Acknowledgement of the submission appears at the top of the screen and is also sent to you via email.

  6. When your fusion results are ready, you will receive an email instructing you to review the results in Ion AmpliSeq Designer.

    Note: You may need to check your Spam folder and move the email to your Inbox and therefore enable its links.

  7. Click the link provided in the email, or go to website and navigate to the Review Completed Designs & Order tab.
  8. Click on the Design.
  9. Review results on the Fusions tab and make changes if necessary by clicking the Copy Targets button and submitting a new design with your changes.
    1. Switch design: Click the drop-down menu to change the design in view.
    2. Edit: Allows you to edit the Design Name and Details only.
    3. Copy Targets: Allows you to copy your design if you want to make modifications to it.
    4. Start a new design: Starts a new design. Once you have reviewed your designs, you can go ahead and place the order.
    5. Add to cart: When this button is green you may click it to add the highlighted design to your cart.
    6. Download results: Design data results are available for download once your assay design is complete. A compressed folder will download containing a number of results files.
    7. Export targets: Downloads your targets as a CSV file.
    8. Copy Amplicons: Not applicable for RNA designs.
    9. View Cart: Once you add your designs to your cart you may view the cart and request a quote.
  10. Review gene assay results on the Genes tab.
  11. Click on the “Gene” link to view its compatible transcripts.