Start a new Ion AmpliSeq™ RNA Gene Fusion design

You can create RNA Gene Fusion panels to detect expression of known gene fusions of interest in your samples.

IMPORTANT! Each gene fusion design must contain at least 12 targets per panel that are expected to be expressed in your test samples. Once created, your design is pre-populated with 12 gene expression assays to get you started. You can accept the pre-populated targets or substitute with genes of interest to meet your custom panel needs.

  1. In the home screen, in the Ion AmpliSeq™ Custom panels pane, click Create Custom panel.
  2. In the Start a new Ion AmpliSeq™ design screen, in the Name and details step, enter a design name and optional details.
  3. In the Application Type step, click RNA Gene Fusion designs (multi‑pool).

    Selecting the application type filters the genomes to display only the selections that are compatible.

  4. In the Select genome to use step, click Human (RefSeq/Ensembl).

    IMPORTANT! RNA Gene Fusion designs are only compatible with Human (RefSeq/Ensemble) genomes.

  5. Click Next: Add Targets.

    A draft design screen opens (see Figure 1).

  6. Add targets using the options available in the target addition pane (see callout 1 in Figure 1).

    For guidelines on how to add targets, see Ion AmpliSeq Custom panels: RNA Gene Fusion design input specifications.

    Option

    Description

    Add Fusion

    Add each target manually using a HGNC-approved gene symbols that follow the HUGO nomenclature.

    1. In the Add Fusion tab, in the Symbol Pair field, select the desired fusion using one of the following options.

      • Enter a complete donor-acceptor gene symbol pair in the [DONOR]-[ACCEPTOR] format, then select the desired donor-acceptor pair from the dropdown list.

        For example, enter ALK-PTPN3.

      • Start typing a donor or acceptor gene symbol, then select the desired donor-acceptor pair from the dropdown list.

      • Start typing a donor or acceptor gene symbol, then select <gene symbol>: All Fusions from the dropdown list.

      The target addition pane populates with a list of all available fusions for a gene or a gene pair. If you selected the <gene symbol>: All Fusions option, then all the available fusions for a gene are listed.

    2. Select the checkbox in the row of each fusion that you want to add to your design, then click Add fusion(s) (see callout 2 in Figure 1).

      If a target was added successfully, the Target saved successfully message appears. If a duplicated target is detected, 1 duplicate fusion ignored message is displayed, and the duplicated target is not added.

    3. Repeat steps 1–2 for each additional fusion target.

    Upload File

    Upload multiple targets at one time using a CSV file.

    1. In the Upload File tab, click Choose File, select the file of interest, then click Open.

    2. Click Upload.

    Figure 1. Draft design screen

    1. A target addition pane with multiple methods for adding targets to a design.

    2. Select one or more fusions of interest, then click Add fusion(s) to add the selections to your design.

    3. Targets table lists all added targets in a design. The Fusion tab lists the fusions that are included in your design. The Genes tab lists the gene expression assays that are included in your design.

    4. Select the checkbox in the row of each target that you want to delete.

    5. Click to submit a design.

    6. Click to delete the selected targets (see callout 4).

    7. Click to delete all targets.

    8. Select from the dropdown list to display a different design.

    9. Click to edit design name and details.

    10. Click to copy targets to a new custom design.

    The software uploads the targets, checks them, and verifies regions. The targets are added to the targets table under the Fusions tab (see callout 3 in Figure 1).

  7. In the targets table, click the Genes tab, then edit the pre-populated list of genes or add new gene expression assays (see callout 3 in Figure 1).

    IMPORTANT! At least 12 target are required.

    For guidelines on how to add targets, see Ion AmpliSeq Custom panels: RNA Gene Expression design input specifications.

    Option

    Description

    Add Gene/​Transcript

    Add each target manually using a HGNC-approved gene symbols or a valid RefSeq transcript accession number.

    1. In the Add Gene/Transcript tab, in the provided field, enter a gene symbol or a RefSeq transcript accession number. Alternatively, start typing the gene symbol or accession number, then select the gene or accession number from the dropdown list.

    2. Click Add target after each entry.

      If a target was added successfully, the Target saved successfully message appears. If a target accession number or symbol is invalid, the Target could not be saved error message appears. If needed, you can correct or update targets in the Name column the targets table (see step 8).

    Upload File

    Upload multiple targets at one time using a CSV or Gene List (TXT) file.

    1. In the Upload File tab, click Choose File, select the file of interest, then click Open.

    2. Click Upload.

  8. Review and modify the design as needed.

    Action

    Description

    (Gene expression assays only) Correct erroneous targets

    Gene expression assay targets that contain errors are highlighted in red in the targets table in the Gene tab. In the row of each erroneous target, modify the gene symbol or transcript accession number in the Name column.

    Delete targets

    In the targets table, select the checkbox in the row of one or more targets, then click Delete. To delete all targets, click Delete all (see callouts 4, 6, and 7 in Figure 1).

    Edit design name and details

    Click Edit, then in the Edit your design screen, modify design name and details as needed. Click Save. See callout 9 in Figure 1.

    Copy targets to a new design

    Click Copy Targets, then in the Copy Design dialog, select the panel type and enter the name and details for the new design. Click Save. See callout 10 in Figure 1.

    The new design is added to the list of your custom designs. To view or edit the new design, click My Designs > AmpliSeq Custom in the navigation bar. Alternatively, open a new design by selecting a design from the Switch design dropdown list (see callout 8 in Figure 1). For designs that have been submitted, or locked, the design opens to the Results ready screen.
  9. To submit your panel, click Submit targets, then click OK to confirm your submission (see callout 5 in Figure 1).

    Up to 5 designs can be submitted at one time.

    After submission, a submitted design screen opens, displaying the design confirmation message.

After you submit your design, the targets are locked () and can no longer be edited. When the assay design results are ready, you receive an e‑mail notification instructing you to review the results in Ion AmpliSeq™ Designer. Click the View results link provided in the email to be directed to the results page. Alternatively, sign in to Ion AmpliSeq™ Designer (AmpliSeq.com), then in the navigation bar click My Designs > AmpliSeq Custom > Results Ready to access the results for your design (see My Designs).

To review design details and place an order, proceed to Order an Ion AmpliSeq custom panel.

Related Topics
Parent topic: Ion AmpliSeq™ Custom panels
Child Topics
Ion AmpliSeq™ Custom panels: RNA Gene Fusion design input specifications