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.
  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. The tumor mutational burden is displayed at the top of the results screen in mutations per Mb. QC Metrics are displayed in the Analysis Visualization screen. For more information, see QC metrics.

    See the Ion Reporter™ Software help for more options.

  5. In the Analysis Results table, sort or filter the data using the Oncomine™-specific annotations.
    1. The default Filter Chain is Oncomine Variants (5.12), 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, 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: The Variant Details TSV file 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.