Visualize MSI analysis results

  1. There are 2 ways to visualize MSI analysis results in Ion Reporter™ Software:

    Option

    Description

    Visualize MSI results from one or more analyses simultaneously from the Analyses table.

    In the Analyses table, select a row for an analysis or select the checkbox next to one or more analyses that you want to visualize simultaneously, then click Visualize. Alternatively, click ActionsVisualize.

    Visualize analysis results individually from the Analysis Results screen.

    In the Analyses table, click an analysis hyperlink in the Analysis column to open the Analysis Results, then click Visualize.

    The Analysis Visualization screen opens to the TMB tab.

  2. Click the MSI tab.

    A table with MSI Status, MSI Score, MSI Coverage, and MSI QC is shown.

    Item

    Description

    MSI Status

    A sample is assigned an MSI status that is based on the MSI Score. The MSI status can be one of the following:

    • MSI-High—MSI score is greater than the threshold value set in the MSI-High Threshold parameter.

    • MSS—MSI score is less than the threshold value set in the MSS Threshold parameter.

    • No Call—MSI score is equal to or greater than the value entered in the MSS Threshold parameter AND less than or equal to the value entered in the MSI- ThresholdHigh parameter.

    • QCFail—Indicates determination of MSI status was not reliable due to the MSI baseline.

    MSI Score

    A sample-level MSI score that is calculated with individual MSI marker scores. The overall score is used to determine the MSI status of the sample.

    MSI QC

    Alert messages for quality control of the MSI analysis results. Messages include the following.

    • Number of Forward markers with expected coverage is low.

    • Number of Reverse markers with expected coverage is low.

    • Tumor Fraction: Cannot calculate MSI with TF. No TF information was provided.

    • No warning

    MSI Coverage

    A combined sample-level coverage that is calculated with the individual MSI marker-level coverage.

    Control Sample

    Specifies the name of the control sample used as MSI on-chip control for the analysis. Control Sample is available only for analysis results from sequencing runs that use Oncomine™ Comprehensive Assay Plus analysis workflows on the Ion 560™ Chip. For results from other sequencing runs on the Ion 550™ Chip, the value "NA" is displayed.
  3. Click Download Results to download a report of the MSI results. The report is downloaded to the folder that is used for downloads, depending on the browser settings.