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. We recommend that you use the sample files provided for download from thermofisher.com/connect, however you can use any sample BAM file if preferred.

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. If you have already uploaded the Target Regions <panel ID>_Oncomine_Designed.bed file for the panel, select it from the dropdown list. Alternatively, click (Upload), then select the <panel ID>_Oncomine_Designed.bed file of the panel that you downloaded from Ion AmpliSeq™ Designer.
  5. 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.
  6. 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.

    1 Only the CNV VCIB algorithm is available for AmpliSeq HD and TagSeq analysis workflows.
    2 This option is not available for all AmpliSeq HD and TagSeq analysis workflows.
    3 This option is not available for some versions of the Oncomine™ Focus Assay target region files.
  7. Click Next.
  8. In the Algorithm Type workflow bar step, for some analysis workflows, you can select the detection algorithm that you want to apply to the analysis workflow. Note that the Algorithm Type workflow bar step is only available for AmpliSeq HD and TagSeq analysis workflows, and for AmpliSeq libraries when you also select an Oncomine™ target region file.

    • For AmpliSeq HD and TagSeq analysis workflows:

    Option[1]

    Description

    Create a new baseline.

    Deselect the Start with an existing CNV baseline checkbox.

    Use an existing baseline and augment the baseline with additional samples.[2]

    For more information, see Augment an existing VCIB baseline workflow preset.

    Select Start with an existing CNV baseline.

    The target region file selected in the Baseline Type step is shown in the dropdown list.

    1 Only the CNV VCIB algorithm is available for AmpliSeq HD and TagSeq analysis workflows.
    2 This option is not available for all AmpliSeq HD and TagSeq analysis workflows.
    3 This option is not available for some versions of the Oncomine™ Focus Assay target region files.

    • For AmpliSeq libraries when you also select an Oncomine™ target region file:

    Option

    Description

    Apply the CNV VCIB algorithm and use an existing baseline and augment the baseline with additional samples.[3]

    For more information, see Augment an existing VCIB baseline workflow preset.

    1. Select the CNV VCIB algorithm.

    2. Select the Start with an existing CNV baseline checkbox.

    Apply the CNV VCIB algorithm and create a new baseline.

    1. Select the CNV VCIB algorithm.

    2. Deselect the Start with an existing CNV baseline checkbox.

    Apply the CNV Informatics Baseline algorithm and create a new baseline.

    Select the CNV Informatics Baseline algorithm.
    1 Only the CNV VCIB algorithm is available for AmpliSeq HD and TagSeq analysis workflows.
    2 This option is not available for all AmpliSeq HD and TagSeq analysis workflows.
    3 This option is not available for some versions of the Oncomine™ Focus Assay target region files.
  9. 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.
  10. Click Next to advance to the Confirm step.
  11. In the Confirm step, enter a name, or accept the default name, and enter an optional description for the baseline.
  12. 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 copy number baseline workflow preset to an analysis workflow.

Related Topics
Parent topic: Copy Number Variant detection
1 Only the CNV VCIB algorithm is available for AmpliSeq HD and TagSeq analysis workflows.
2 This option is not available for all AmpliSeq HD and TagSeq analysis workflows.
3 This option is not available for some versions of the Oncomine™ Focus Assay target region files.