Create a CNV Informatics Baseline workflow preset

You can create a CNV Informatics Baseline workflow preset in Ion Reporter™ Software to determine copy number changes in the sample of interest, without the use of a matched control. You can later add the CNV Informatics Baseline to an analysis workflow that you can use as a baseline control for analyses.

Use the following guidelines when you select samples to use in the baseline.

  • Select a cohort of diverse sample types. This includes germline samples and cell-lines.

  • Select samples with no known CNV aberrations. If this information is not available, a large cohort size can compensate any CNV aberrations.

If you import a custom copy number baseline, the target regions file that was used to create the copy number baseline must be available in the software. Then the imported copy baseline is shown in the list of available copy number baselines.

  1. In the Workflows tab, click Presets, then click Create PresetCopy Number Baseline.
    The Create Copy Number Baseline screen opens.
  2. In the Baseline Type step, make the following selections.
    1. Select AmpliSeq, TargetSeq-Exome, or AmpliSeq-Exome for the baseline type.
    2. Select a reference genome.
      GRCH38
      hg19
    3. Select the Target Regions file that corresponds to the panel.

      • If you have already uploaded a germline Target Regions <panelID>_Designed.bed file for the custom Ion AmpliSeq™ panel, select it from the dropdown list.

      • If the target regions file is not available in the dropdown list, click (Upload), then select the <panelID>_Designed.bed file of the panel that you imported from Ion AmpliSeq™ Designer to upload the file from your computer.

      • If the Target Regions is not imported from Ion AmpliSeq™ Designer Use the following option to import AmpliSeq libraries and panel files.

      1. Click AmpliSeq Import.

      2. In the Import for AmpliSeq dialog box, select the Custom Panel tab for Ion AmpliSeq™ or Ion AmpliSeq™ HD Made-to-Order, or Ion AmpliSeq™ On Demand panel files, or select the Fixed Panel tab for Community or Ready-to-Use panel files.

      3. Enter an account user name.

      4. In the Password field, enter the access code. For more information, see Generate an access code for AmpliSeq.com.

      5. Click List My AmpliSeq Panels.

      6. From the list, select the fusion panel file that you want to import.

      7. Click Import.

  3. Click Next.
  4. In the CNV Detection Type workflow bar step, verify that Germline (CNV Informatics Baseline) is selected, to apply the CNV detection algorithm to the analysis workflow.
    Based on the selections in the previous step, the Germline (CNV Informatics Baseline) is automatically selected.
  5. In the Samples step, select the required number of samples for the baseline. For accurate baselines, ensure that the samples selected for the baseline have been run with the same panel as the baseline.

    If you do not select the minimum number of samples that are required for the baseline, you cannot proceed.

  6. Click Next to advance to the Confirm step.
  7. In the Confirm step, enter a name for the baseline, or use the default name, and enter an optional description for the baseline.
  8. Click Create Baseline.

    The baseline creation job is started and its status is shown in the Presets screen.

When the baseline creation is complete, it is locked and shown in the Presets screen with a State of Successful and is available for use in the software. The new baseline can be added to an analysis workflow. For more information, see Create a new analysis workflowCopy and edit an existing analysis workflow, and Apply a copy number baseline workflow preset to an analysis workflow.

If the State of a copy number baseline is Failed, place the pointer over the row of the copy number baseline and click View Log to open the log in a separate browser tab, or click Download Log to download the log. This record can help you troubleshoot the failure.