View the tumor mutational burden statistics

The tumor mutational burden value is calculated automatically when the Oncomine™ Tumor Mutation Load - w3.0 - DNA - Single Sample is launched. You can download the tumor mutational burden statistics to view more details of the analysis, such as the TMB algorithm version that is used, and information about how the tumor mutational burden is calculated.

  1. Download, then extract a results file to your hard drive.

    For more information, see Download analysis files.

  2. In the RESULTS folder, open the statistic.txt file in a compatible text editor. The tumor mutational burden and the data that are used to calculate its value are listed.

    In this example, the tumor mutational burden value is calculated from the values for Total Exonic Bases with Sufficient Depth of Base Coverage, Germline Calibration Intercept, TMB Standardization Slope, Mutation Load (Mutations/Mb), and Nonsynonymous.

    IR Sample Name='JH_TMB_colon1_4_N.bam.JH_TEST_BAM'IR
    Analysis Name='JH_TMB_colon1_4_N.bam.JH_TEST_BAM_1564544352260'Released with Ion Reporter 'ir512'.
    TMB Algorithm Version='V3.0'Minimum Read Depth of Base Coverage required=60.0
    Maximum Deamination Score allowed=100.0
    Minimum Variant Allele Frequency required=0.05
    Deamination=16 (QC: PASS; observed (16) < threshold (100.0))
    Total Bases (sequenced bases in the panel / in the design bed file) with Sufficient Depth of Base Coverage=1652887
    Average Coverage=1300.0
    Total Exonic Bases with Sufficient Depth of Base Coverage=1198355
    Denominator used for TMB Calculation (as specified in the workflow parameters)=1198355
    Total Somatic Filtered Variants Count (numerator for TMB calculation)=19('missense=18,frameshiftDeletion=0, frameshiftInsertion=0,
    nonframeshiftDeletion=0, nonframeshiftInsertion=0, nonsense=1')
    Germline Calibration='Not Applied'Germline Calibration Slope=1.4637
    Germline Calibration Intercept=0.0TMB Standardization='Not Applied'
    TMB Standardization Slope=1.0
    TMB Standardization Intercept=0.0
    Mutation Load (Mutations/Mb)=15.86
    TMB classification (based on specified parameters)='Intermediate
    'Variant count (Germline + somatic)=1098
    Variant count: 19COSMIC Annotated Somatic Variants=2
    Variant count=19
    Nonsynonymous=19
    Synonymous=0

Tumor Mutational Burden calculation

Ion Reporter™ Software 5.12 uses TMB Algorithm v3.0:

precalibration TMB = (SM x 1066)
                                   Total Exonic Bases with Sufficient Coverage

where

  • TMB is Tumor Mutational Burden

  • SM is Somatic Mutations

Note: In Ion Reporter™ Software 5.12, you can control how somatic mutations are calculated. You can also select between Exonic bases or all of the genomic bases that are covered by the panel. Similarly, the ‘Sufficient Coverage’ threshold can be modified. By default, the TMB calculation are done using Total Exonic Bases with ≥60bp coverage.

The following settings apply:

  • applyTMBStandardization: Customizable parameter (default value: off)

  • standardization intercept: TMB Standardization Factor: Intercept (default value: 0)

  • standardization slope: TMB Standardization Factor: Slope (default value: 1)

It is apparent from the values that even if the standardization is enabled with the current default values, the TMB score value will not be adjusted until the user provides values for the intercept and the slope.

Note: Standardization is independent of the germline calibration.