View the tumor mutational burden statistics

The tumor mutational burden value is calculated automatically when you launch an analysis workflow for the Oncomine™ Comprehensive Assay Plus DNA or an Oncomine™ Tumor Mutation Load Assay. 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, and Total Somatic Filtered Variants Count (numerator for TMB calculation). TMB Standardization is off by default, that is, 0.0TMB Standardization='Not Applied'. Observed TMB score was set to 25, which is below the calibration threshold, so that the germline calibration was also not applied. That is Germline Calibration='Not Applied'.

    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='V4.0'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=0.0
    TMB 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