Order a custom Oncomine™ tumor specific panel

You can add or remove genes to core or predesigned Oncomine™ tumor specific panels. You can also customize previously created and locked custom panels, or create new panels from custom gene lists. The core and predesigned Oncomine™ tumor specific panels are locked and ready to order. To customize a locked panel, you must first unlock the design. In an unlocked state, you can add or remove genes from the panel and edit the design name and details. After you have finalized the customized panel, you must lock the design in order to download panel-specific files, view amplicon distribution, and order the panel.

Note: The Oncomine™ tumor specific RNA panel can not be customized and is not available with the Oncomine™ Lymphoma panel or with custom panels created from scratch using a gene list.

To customize a previously created and locked custom design, click My Designs > Oncomine Tumor Specific, then in the Design column, click the name of the design of interest. In the panel design screen, click More Actions > Copy Design, then proceed to step 3a.

  1. In the Home screen, use one of the following approaches to start a custom Oncomine™ design.

    Option

    Description

    Customize a core or predesigned panel

    In the Oncomine™ tumor specific panels pane, click Browse tumor types, then proceed to step 2.

    Check gene availability, then start a new design from a custom gene list

    1. Click Check gene availability.

    2. In the Check gene availability window, in the Enter your gene list field, enter the genes of interest, then click Submit.

      The Search Results table displays whether the genes are available, unavailable, or available for spike in designs only.

    3. After finalizing the list of genes, click Start Oncomine™ Design.

    4. In the Start Oncomine™ Design screen, enter the design name and optional details.

    5. If needed, edit the list of genes in the Add Your Gene List field. Alternatively, upload a CSV file that contains the list of genes by clicking Choose file.

      To view an example file, click Input Specifications, then click Download this example.

    6. Click Next, then proceed to step 5.

    The design is added to the list of designs in My Designs > Oncomine™ Tumor Specific.

    Add a custom gene list

    1. Click Or Add gene list.

    2. In the Start Oncomine™ Design screen, enter the design name and optional details.

    3. In the Add Your Gene List field, enter the list of genes. Alternatively, upload a CSV file that contains the list of genes by clicking Choose file.

      To view an example file, click Input Specifications, then click Download this example.

    4. Click Next, then proceed to step 5.

    The design is added to the list of designs in My Designs > Oncomine™ Tumor Specific.

    Note: The Oncomine™ tumor specific RNA panel is not available for order with panels created from a custom gene list.

  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. In the panel design screen, click Customize, then in the Customize window, enter a panel name and details.
    1. (Required) In the Name field, enter a unique name for the custom panel.

      The panel name can be up to 20 characters in length and must be unique.

    2. In the Details field, enter more information for the custom panel if needed.
  4. Click Save.

    The selected panel is unlocked and enabled for customization. Unlocked designs display next to the panel name in the panel design screen.

  5. Add or remove genes of interest.

    Option

    Description

    Add core genes or associated research genes

    (For customizing core or predesigned panels only) In the Core Genes section or in the Associated Research Genes section, use one of the following approaches to add one or more genes to the new customized panel.

    • Select a checkbox for each gene that you want to include in the panel (see callout 3 in Figure 1).

    • Click Include All to select the displayed genes to be included in the panel.

    Genes that are included in a panel are marked in green (see callout 1 in Figure 1).

    Add in-stock genes

    1. Click Add In Stock Genes (see callout 6 in Figure 1).

      The Add In Stock Genes window opens.

    2. Manually add individual genes to the panel or input a list of genes of interest by file.

      • In the Add Genes tab, enter a gene symbol for each gene that you want to add (for example, enter AKT1). If you add more than one gene, separate each gene symbol by a comma, a space, or a new line (by pressing Return after each gene symbol).

      • In the Upload File tab, click Choose File, navigate to a CSV file that contains a list of gene symbols for genes that you want to add to the custom panel, then click Open.

        To view an example file, click Download this example.

    In-stock genes are added to the Added Genes section (see callout 5 in Figure 1).

    Remove genes

    In the Core Genes, Associated Research Genes, or Added Genes section, use one of the following approaches to remove one or more genes from the custom panel.

    • Deselect a checkbox for each gene that you want to exclude from the custom panel (see callout 3 in Figure 1).

    • Click to remove a gene from a panel (see callout 4 in Figure 1).

      This action also removes a gene from the panel design screen. If you remove a gene by mistake, you can add the gene back to the custom panel using the Add In Stock Genes functionality.

    • Click Exclude All to exclude all core genes or associated research genes from the custom panel.

    Genes that are excluded from a panel appear greyed out (see callout 2 in Figure 1).

    Note: The Oncomine™ tumor specific RNA panel can not be changed.

    Figure 1. Custom panel design screen

    1. A gene that is included in the panel.

    2. A gene that is excluded from the panel.

    3. Select a checkbox to include a gene in the panel or deselect a checkbox to exclude a gene from the panel.

    4. Click to remove a gene from a panel and the panel design screen.

    5. Added Genes section displays in-stock genes that have been added to the panel.

    6. Click Add In Stock Genes to add one or more in-stock genes to the panel.

    7. Click Finalize Design to finalize and lock the design.

  6. Click Finalize Design (see callout 7 in Figure 1).
    1. In the Finalize Design dialog box, click DNA only or DNA and Fusions.
    2. Click Finalize Design.

    It can take up to 30 minutes to finalize the design. When complete, the Finalize Design button is replaced by Preview Order.

  7. Click Download Files. In the Download Files dialog box, select either DNA only or DNA and Fusions depending on the selected panels, then click Download.

    Note: You can only download files for finalized ( locked) designs.

    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.

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

    Option

    Description

    Edit Design Name & Details

    (Unlocked custom designs only) Open the Edit Custom Design window and edit design name and details.

    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 7.

    Copy Design

    (Custom designs only) Copy a design.

    The design is added to the My Designs list in the Oncomine™ Tumor Specific tab.

    Sharing

    (Locked custom designs only) Share a design. For more information, see Manage shared designs.

    Restore

    (Unlocked custom designs only) Restore a custom panel back to the core design.

    Delete

    (Custom designs only) Permanently delete a design.

  9. When you are ready to order the panel, click Preview Order.
  10. In the Order options: GeneStudio dialog box, click Next.
  11. In the Library preparation format/reactions dialog box, select Manual or Ion Chef™ format, then select the number of reactions. Click Next.
  12. 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 11.

    For RNA library preparation, the NGS Reverse Transcription Kit is added to the cart by the software. You can 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 or click to set the value to 0 to remove the kit from 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.

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.

For custom designs, you must download the <panel ID>_ Oncomine_ Designed.bed file. The BED file is needed to create a custom Torrent Suite™ Software planned run template and Ion Reporter™ Software analysis workflow. Planned run templates and analysis workflows are required for templating, sequencing, and data analysis of each customized tumor specific panel.

Related Topics
Parent topic: Oncomine™ tumor specific panels