Create a copy number baseline workflow preset

You can create a copy number 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 custom copy number baseline to an analysis workflow that you can use as a baseline control for analyses.

You must use a minimum of 48 samples, and at least 6 of the samples must be normal, to create a copy number baseline workflow preset.

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

  1. In the Workflows tab, click Presets, then click Create Preset > Copy Number Baseline.
  2. In the Copy Number step of the Create Copy Number Baseline workflow bar, select the baseline type that corresponds to the type of libraries that you use.

    Baseline Type

    Description

    AmpliSeq HD

    Create copy number baselines for Ion AmpliSeq™ HD libraries. For more information, see VCIB baseline workflow presets.

    AmpliSeq

    Create copy number baselines for Ion AmpliSeq™ and Oncomine™ libraries (not Exome). For more information, see VCIB baseline workflow presets.

    AmpliSeq-Exome

    Create copy number baselines for Ion AmpliSeq™ Exome libraries.

    TagSeq

    Create copy number baselines for Ion TagSeq libraries. For more information, see VCIB baseline workflow presets.

    TargetSeq-Exome

    Create copy number baselines for Ion TargetSeq™ Exome or other targeted libraries.

    Low-coverage Whole-Genome

    Create copy number baselines for whole genome libraries with low coverage (for example, Aneuploidy).

  3. Select a reference genome.
    • GRCH38

    • hg19

  4. Select the Target Regions file that corresponds to the panel. If the target regions file is not available in the panel, you can upload the file.
  5. Use the following options to import AmpliSeq libraries and panel files:

    Option

    Import DNA panel files

    Custom Panel

    1. Under Target Regions, 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 panel files.

    3. Enter your user name and password and then click List My AmpliSeq Panels.

    4. Select the panel files that you want to import from the dropdown list, then click Import.

    Fixed Panel

    1. Under Target Regions, click AmpliSeq Import.

    2. In the Import for AmpliSeq dialog box, select the Fixed Panel tab for On-Demand or Ready-to-Use panel files.

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

    4. Click Import.

  6. Click Next.
  7. If you selected AmpliSeq HD, AmpliSeq, or TagSeq baseline types, you can use an existing baseline and augument the baseline with additional samples.
    1. In the Altorithm step, select Select an existing CNV baseline option to use an existing baseline that you can add more samples to.
  8. In the Samples step, select the samples to be used in the baseline creation, based on the guidelines that are included in the software. If you do not see your samples in the table, see Sample definition for information on how to upload or define a sample.
  9. Click Next, then advance to the Confirm step.
  10. In the Confirm step, enter a name, or accept the default name, and enter an optional description for the baseline.
  11. Click Create Baseline.

The baseline creation job is started and the baseline with its status now appears on the screen. When the job completes, it is selectable in the Copy Number step for analysis workflow creation. For more information, see Apply a baseline workflow preset to an analysis workflow.