Visualize microsatallite instability (MSI) analysis results

You can determine whether microsatallite instability (MSI) is present for amplicons in Ion Reporter™ Software with settings in analysis workflows that detect MSI. The MSI settings analyses detect MSI markers, which can identify a form of genomic instability in the replication of repetitive DNA.

The workflows include settings for MSI markers, which can identify a form of genomic instability in the replication of repetitive DNA.

Note: MSI parameters are available in the software only when you use these workflows. For more information, see MSI parameters.

  1. Do one of the following to open a visualization that includes MSI analysis results:

    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 want to visualize simultaneously, then click Visualize. Alternatively, click Actions > Visualize.

    To 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 Tumor Mutational Burden tab .

  2. Click the MSI tab.

    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-Low

    • MSS (MSI stable)

    • No Call (could not be evaluated)

    • QC Fail

    MSI parameter settings include thresholds that determine whether the status is MSI-High, MSI-Low, or MSS. A status of No Call or QC Fail is based on the MSI marker coverage.

    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 Coverage

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

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

  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.