View tumor mutational burden analysis results

You can view the results and calculated tumor mutational burden (TMB mutations/Mb) when you open analysis results that used a workflow with tumor mutational burden enabled.

Note: Microsoft™ Excel™, or other spreadsheet tool, is required for viewing VCF, CSV, and TSV files.

  1. Click the Analyses tab.
  2. In the Overview screen, use the Workflow filter to limit the list of analyses to limit the list of analyses that use an Oncomine™ Tumor Mutation Load workflow.
  3. Click a row in the Analyses table to view the Details of the analysis.

    In the Details pane you can view Workflow Details, and access the Actions list.

  4. Click the link for the name of the Analysis to open the Analysis Results screen.

    The Analysis Results screen opens to the Oncomine tab that displays displaying variants that are annotated with Oncomine™ annotated variants that are relevant to cancer with Oncomine™ Gene Class and Oncomine™ Variant Class information.

    Information for tumor mutational burden that is displayed at the top of the Analysis Results screen is as follows.

    Item

    Description

    Tumor Mutational Burden (Mutations/Mb)result

    The value of the result for the tumor mutational burden calculation.

    For more information, see Example: Tumor Mutational Burden calculation.

    TMB classification

    A score of High, Intermediate, or Low.

    Thresholds to determine the TMB classification are set with the TMB-Low Threshold and TMB-High Threshold parameters. For more information, see Annotation parameters.

    A classification status of Undefined indicates that either the TMB classification thresholds settings were not included in the analysis workflow or were set incorrectly.

    Note:

    Threshold values are not provided in the factory-shipped analysis workflow. The analysis workflow always reports Undefined as the TMB classification status unless a user sets the thresholds in the parameter settings.
  5. In the Analysis Results table, sort or filter the data using the Oncomine™-specific annotations.
    1. The default Filter Chain is Oncomine Variants, which runs the Oncomine™ Variant Annotator plugin, a plugin that integrates data from more than 24,000 exomes across solid tumor and hematological cancer types and annotates variants relevant to cancer research with Oncomine™ Gene Class and Oncomine™ Variant Class information. For a variant to be filtered in on the results, the variant that is called must meet all the criteria for the filter chain. For more information, see Predefined filter chains .
      • Select No Filter to view all the variant calls attempted by the variant caller.

      • If you save a filter chain other than Oncomine Variants (5.12), changes can occur to the variant calls that are saved in the VCF file and can affect results for downstream processes, such as the results in Oncomine™ Reporter Software.

    2. In the Oncomine tab, click the column headings to sort the list of variants by Oncomine Variant Class or Oncomine Gene Class.
  6. To download a results file.
    1. Click Download , then select All Variants, Filtered Variants, Selected Variants or Current Results TSV.

      For more information on the downloads, see Variants file downloads.

    2. In the Home tab, click Notifications, then click next to the file name. Alternatively, select one or more rows, then click Download.

The software generates a ZIP file with 4 folders: RESULTS, QC, Variants, and Workflow_Settings.

Folder

Contents of folder

RESULTS

Note: A TSV file that contains variant details can be downloaded separately. For more information, see Visualize tumor mutational burden analysis results.

If the Tumor Mutational Burden parameter is enabled, or an analysis workflow for the Tumor Mutation Load Assay is used, a Results folder is generated that contains:

  • filter_variants.tsv and somatic_variants.tsv—TSV files that contain post-filter and somatic variants.

  • <tmb report>.pdf—PDF report that contains tumor mutational load results.

  • statistic.txt—contains tumor mutational load statistics.

  • PNG files that contain images of:

    • allele frequency distribution of germline and somatic variants

    • allele frequency distribution of only somatic variants

    • bar plot of signature type and context of somatic mutations

    • pie chart of substitution type of somatic mutations

    • pie chart of signature pattern of somatic mutations

QC

Contains a PDF of the QC report, and a folder containing coverage statistics files.

Variants

  • Contains intermediate and Oncomine™ annotated VCF files, which are used by Oncomine™ Reporter Software. For more information, see the Oncomine™ Reporter 3.0 User Guide.

  • TSV files that contain Oncomine™-filtered and all somatic variants.

Workflow_Settings

Contains folders with:

  • A text file that describes settings used for the analysis. Open the file with a text editor.

  • Configuration files used by the Ion Reporter™ Software in the workflow settings.