Customize Oncomine™ Tumor Mutation Load - w3.0 - DNA - Single Sample analysis workflow

The Oncomine™ Tumor Mutation Load - w3.0 - DNA - Single Sample analysis workflow calls variants at ≥5% allelic frequency at positions with sufficient read coverage ≥60 for tumor mutational burden calculation. Poor sample fixation can artificially increase the determined tumor mutational burden due to deamination. Deamination is reported as the Deamination Score under the Sample QC tab. Samples with low tumor content can have true biological somatic C:G>T:A mutations that are counted towards deamination. Such counts can affect whether the estimated SNP proportion is consistent with the deamination (mainly FFPE) number.

You can modify the Oncomine™ Tumor Mutation Load - w3.0 - DNA - Single Sample analysis workflow to reduce the affect of deamination in low-quality FFPEs and achieve a higher minimum allele frequency for a tumor mutational burden calculation.

IMPORTANT! Use the default parameter settings unless you are an advanced user.

  1. In the Workflows tab, click Overview.
  2. In the Overview screen, you can use the Oncology-ImmunOncology Research Category filter and DNA Research Application filters to limit the list of analysis workflows.
  3. 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, then click  (Actions) > Copy.

    The Edit workflow bar opens to the Research Application step with the Research Application and Sample Groups preselected. When you copy analysis workflow templates, 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. In the Parameters step, click the Annotation tab, then select the Tumor Mutational Burden tab, scroll to the TMB Variant Minimum Allele Frequency parameter and set the allele frequency value to a higher value.

    For example, set From = value to 0.05 for ≥5% allele frequency, and to 0.1 for ≥10% allele frequency.

    IMPORTANT! Do not change other parameters, which can negatively affect analysis results.

  6. Click Next.
  7. In the Confirm step, enter an analysis workflow name and optional description, then click Save Workflow.

The modified analysis workflow is now available for use in the Workflows tab, Overview screen.