MSI parameters

You can adjust the following MSI parameters to optimize your analysis results when you create or edit analysis workflows in Ion Reporter™ Software. MSI parameters are available only for some Oncomine™ analysis workflows.

Parameter name

Description

Main tab

Enable MSI Detection

When set to true, this parameter enables detection of MSI markers for the workflow. These markers can identify a form of genomic instability in the replication of repetitive DNA. MSI often occurs in tumor cells. It leads to the appearance of multiple alleles at microsatellite loci, which can be easily identified.

This parameter is set to True by default, and is intended for use only in select Oncomine™ analysis workflows. If you do not want to include MSI results in an Oncomine™ analysis, you can set to the parameter to False. Do not change this setting in other analysis workflows.

MSI Algorithm Version

The version of the algorithm that is used to generate MSI results. The algorithm version can provide information about how the data was analyzed and can be useful if earlier versions of the software were used, or in the case of troubleshooting.

MSI Marker Regions

The MSI Marker regions file contains information about the genomic position of the MSI markers, the version of the MSI algorithm and additional information that is used by the MSI detection algorithm. It is blank by default until the release of analysis workflows that are designed for use with MSI detection.

The MSI marker regions file is set as the default for some Oncomine™ analysis workflows. The MSI marker regions file contains information about the genomic position of the MSI markers, and additional information that is used by the MSI detection algorithm. Data in the file includes chromosome name, chromosome start and end positions, and the name of the MSI markers.

MSI Baseline File

Select an MSI baseline file—this file contains baseline information that is used if the spike-in that is used does not meet the RMC performance threshold that is set for the sequencing run.

MSI Marker Threshold

The MSI Marker Score (Forward or Reverse) above which the marker will be considered in the Total Marker Score (Forward or Reverse)

Minimal MSI Marker Coverage

The minimum number of filter reads per direction that is required for an MSI Marker Score (Forward or Reverse) to be calculated

MSI-High Threshold

The MSI score above which a sample is considered MSI-High. This score is reported in analysis results. [1]

MSS Threshold

The MSI score below which a sample will report MSS in analysis results. [2]

1 If the MSI Score falls between the MSI-High Threshold and the MSS Threshold, a No Call is reported in the analysis results.
2 If the MSI Score falls between the MSI-High Threshold and the MSS Threshold, a No Call is reported in the analysis results.