QC metrics for tumor mutational burden

QC metrics for tumor mutational burden are listed at the top of Analysis Visualization in the TMB tab when you visualize analysis results with Ion Reporter™ Software.

QC metric

Definition

Average Coverage

The following formula is used to calculate average coverage:

If the average coverage is below 150, the analysis completes successfully but Tumor Mutational Burden is reported as -1.

Note: This setting cannot be changed in Ion Reporter™ Software.

Number of bases used in calculating TMB

The number of bases used as a denominator for the tumor mutational burden calculation. Only bases with sufficient base coverage are used in the calculation, as defined in the workflow parameters. In the parameters, you can also select only the exonic regions covered by the panel to be used instead of all genomic regions. See the View the tumor mutational burden statistics for more information.

Number of variant calls

The number of somatic variants that are identified in the sample. This value is reported in the statistic.txt file as Total Somatic Filtered Variants Count (numerator for TMB calculation) and Variant Count.

For more information, see View the tumor mutational burden statistics.

Deamination score

Deamination score was previously reported as the estimated SNP proportion consistent with deamination (mainly FFPE). The deamination score can be used to determine the quality of the FFPE sample. For more information on how to minimize the impact of high deamination on a tumor mutational burden score, see View the tumor mutational burden statistics.

A deamination QC status of PASS/FAIL is also reported. The threshold for this QC can be adjusted in the analysis workflow parameter settings. For more information, see View the tumor mutational burden statistics.