Order a core or predesigned Oncomine™ tumor specific panel

Select and order one of the wet-lab tested Oncomine™ tumor specific panels that are available in Ion AmpliSeq™ Designer to use as-is. Two types of designs are available: core panels and predesigned panels.

The core panel genes have been wet lab tested together. All core panels have dedicated analysis workflows available in Ion Reporter™ Software.

Predesigned panels can contain genes from both core panels and inventory. Each gene has been wet lab tested in the context of all inventory genes similar to custom panels. Predesigned panels do not have dedicated Ion Reporter™ Software. Analysis is supported with a BED file provided, similar to a custom panel.

  1. In the Home screen, in the Oncomine™ tumor specific panels pane, click Browse tumor types.
  2. In the Oncomine™ tumor specific panels for cancer research screen, click the pane of a Core Panel or a Predesigned Panel to select the panel of interest, then click Next.

    The panel design screen opens, where you can view panel details, download panel-specific files, and customize the panel. For more information, see Panel design screen.

  3. (Finalized / locked designs only) Download panel-specific files.
    1. Click Download Files, then in the Download Files dialog box, select either DNA only or DNA and Fusions, depending on the panels chosen.
    2. Click Download.

    A ZIP file that contains gene lists, amplicon pool information, amplicon size histogram, targeted hotspots, and gene coverage data is downloaded to the computer. For more information about file contents, see Oncomine tumor specific panel files.

  4. (Optional) Click More Actions, then select one of the following options from the dropdown list.

    Option

    Description

    Export Targets

    Export the CSV file (<panel ID>_Oncomine_selected_targets.csv) that contains the list of targets included in the design to the computer.

    Amplicon Distribution

    View the amplicon size histogram for the design.

    To export the PNG file (<panel ID>_Oncomine_amplicon_size_histogram.png) that contains the amplicon size histogram for the design to the computer, click Download in the Amplicon Distribution window.

    Note: The <panel ID>_Oncomine_amplicon_size_histogram.png is also downloaded as part of the ZIP file described in step 3.
  5. When you are ready to order the panel, click Preview Order.
  6. In the Order options: panel type dialog box, select DNA only or DNA and Fusions, then click Next.
  7. In the Order options: GeneStudio dialog box, click Next.
  8. In the Library preparation format/reactions: GeneStudio dialog box, select Manual or Ion Chef™ format, then select the number of reactions. Click Next.
  9. In the Order preview screen for the design, review order details, then, if needed, make changes or add consumables to the order.

    • The appropriate library preparation kit is added to the cart by the software . This selection cannot be modified. The kit that is added is based on the Library preparation format/reactions that you select in step 8.

    • For RNA library preparation, the NGS Reverse Transcription Kit is added to the cart by the software. You can change the quantity or remove the NGS Reverse Transcription Kit from the cart.

    1. If needed, in the row for the NGS Reverse Transcription Kit, in the Qty field, enter 0 to remove the kit from the cart or click or to edit the quantity of the kits in the cart.
    2. Click List recommended consumables, then add other items to the cart.

      A list of available kits is shown. The kits that are listed depend on the previous selections and can include groups of lists in Library preparation, Template preparation and sequencing, Barcodes, and Chips sections.

    3. In the row of each kit that you want to add to the order, enter the quantity in the Qty field or click to set the value to the desired quantity.

      The list price for the item or items is updated.

    4. Make corrections if needed.

      • Enter a new value in the Qty field or click or to change the quantity of a kit.

      • In the Qty field, enter 0 or click to set the value to 0 to remove an item from the list.

      • Click Clear all quantities to remove all items.

      • Click Cancel to return to the design screen.

    5. When finished, click Add all to cart.

      The design that is added to the cart is based on the sequencing platform, template preparation, and ordering format selections that you have made.

    You are redirected to the Cart on thermofisher.com, where you can add or remove items from the order if needed, view product price estimates, and start the checkout process.

    Note: Removal of the pre-selected library kit from the cart can result in an invalid order. The order can not be processed in this case. Any Assessment Controls Kit, templating kits, and chips can be removed without affecting the ordering process.

The core Oncomine™ tumor specific panels are ready to use with the provided Torrent Suite™ Software planned run templates and Ion Reporter™ Software analysis workflows.

If needed, delete or empty the cart, then repeat the steps in this procedure with different selections to make changes to the sequencing platform, template preparation, and ordering format selections.

Related Topics
Parent topic: Oncomine™ tumor specific panels