Enable tumor mutational burden calculation in existing analysis workflows

Tumor mutational burden (TMB) is a calculation of somatic mutations per megabase (Mb). You can enable the calculation in any DNA – Single Sample, or DNA and Fusions – Single Sample analysis workflow. When enabled, tumor mutational burden and other data values are included in analysis results from that analysis workflow. To enable the tumor mutational burden calculation, copy and edit any predefined analysis workflow, or edit an existing custom analysis workflow that is not locked.

An analysis workflow that is enabled for tumor mutational burden calculates mutations per megabase (Mb) and adds graphics and other information about the mutations to Ion Reporter™ Software analysis results and visualizations. Analysis workflows for use with the Oncomine™ Tumor Mutation Load Assay, such as Oncomine™ Tumor Mutation Load - w3.1 - DNA - Single Sample analysis workflow, are enabled for tumor mutational burden by default.

Note: Tumor mutational burden calculation is available in Ion Reporter™ Software 5.10 or later.

  1. In the Workflows tab, click Overview.
  2. In the list of analysis workflows, select the row for the DNA – Single Sample, or DNA and Fusions – Single Sample analysis workflow that you want to copy. The Details pane shows information about the selected workflow.
  3. Click  (Actions) > Copy .

    The Edit workflow bar opens to the Research Application step with the Research Application and Sample Groups preselected. When you copy an analysis workflow template, you cannot change these settings.

  4. Click Next multiple times to proceed to the Parameters step. Alternatively, click each step in the workflow bar to go to the parameter step.
  5. To enable the tumor mutational burden calculation, ensure that the Tumor Mutational Burden Filter Chain parameter is set.
    1. In the Parameters step, under annotation, select the Tumor Mutational Burden tab.
    2. Find the Tumor Mutational Burden Filter Chain parameter, then change the value to TMB (Non-germline Mutations).
    You can review the algorithm version that is used to calculate tumor mutational burden in the Tumor Mutational Burden Calculation Version parameter.

    For parameter descriptions see Annotation parameters.

  6. Change other tumor mutational burden parameters, if needed.

    For more information, see Annotation parameters.

    IMPORTANT! The parameter settings of an Oncomine™ Tumor Mutation Load are optimized. If you are using these parameters for another type of analysis workflow, change the parameters if needed. Contact your Field Bioinformatics Specialist (FSB) for assistance.

  7. Click Next, then enter a Workflow Name and an optional Description for the analysis workflow.
  8. Click Save Workflow.

    The custom analysis workflow is saved and is added to the Workflows table.

To ensure that the analysis workflow was saved, click the Workflows tab, then click Overview, and search for the analysis workflow name. To analyze samples with your new tumor mutational burden calculation enabled analysis workflow, see Manually launch an analysis.