MSI parameters

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 for Oncomine™ Comprehensive Assay Plus, DNA Ion Reporter™ Software analysis workflows, 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 the default setting of this parameter for other analysis workflows unless you understand how the change can affect your analysis.

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. This parameter is listed for informational purposes only and cannot be changed.

Allows the selection of a control for use in MSI calculation. Select RMC, or an MSI On-Chip control sample, from the same chip that is uploaded at the same time as the sample that is analyzed. MSI Control Type is available only for analysis results from sequencing runs that use Oncomine™ Comprehensive Assay Plus analysis workflows on the Ion 560™ Chip.

The RMC control captures sample and library preparation variations. The on-Chip Control, which is generally a designated normal sample on the chip, is used to help determine sequencing based variations. The MSI signal generated by the on-chip control is used to evaluate the MSI signal generated for all DNA samples that are sequenced on the same chip to generate an MSI score. With use of the MSI on-chip control samples, the addition of RMC controls is still required during the library preparation.

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.

Select an MSI baseline file for use in MSI analysis. This file contains baseline information that accounts for variations in sample preparation or run conditions to support robust MSI detection.

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

The MSI score above which a sample is considered MSI-High. This score is reported in analysis results. ^[1][2]

The MSI score below which a sample reports MSS in analysis results. ^{[1] [2]}

When enabled (value = 1), the MSI algorithm uses the tumor cellularity percentage in its calculation. We recommend that you do NOT change this parameter.