Sample results

The Oncomine™ Tumor Mutation Load Assay results are represented graphically in the TMB tab when you visualize analysis results with Ion Reporter™ Software.

Germline and Somatic Variants

A histogram showing frequency distribution of allele ratio for total called germline and somatic variants. Listed below the figure is the combined total of called germline and somatic variants. The value is reported in the statistic.txt file as Total Variant Count. For more information, seeView the tumor mutational burden statistics.

Only Somatic Variants

A histogram showing frequency distribution of allele ratio for only somatic mutations as determined by the selected TMB filter chain. Listed below the figure are:

  • The number of Total Somatic Variants (Value is reported in the statistic.txt file as Total Somatic Variant Count.

  • A break down of the number of mutations determined to be nonsynonymous (detrimental) and synonymous (non-detrimental) as annotated by Ion Reporter™ Software. Values are reported in the statistic.txt file.

  • The number of detected somatic variants found in the COSMIC database. The value is reported in the statistic.txt file as COSMIC Annotated Somatic Variants.

For more information, seeView the tumor mutational burden statistics.

Substitution Type and Context of Somatic Mutations

C>A

C>G

C>T

T>A

T>C

T>G

Somatic mutations can be divided into 6 base substitution classes (that is, C>A, C>G, C>T, T>A, T>C, T>G) based on their substitution type. After incorporating information on the bases immediately 5′ and 3′ to each mutated base, 96 possible mutation types are in this classification. These 96 mutation types are represented on the x‑axis, and variant frequency for mutation type on the y‑axis. Bars for each substitution class are grouped and displayed with different color.

Substitution Type of Somatic Mutations

A pie chart dividing somatic mutations into 6 base substitution classes

(that is, C>A, C>G, C>T, T>A, T>C, T>G) based on their substitution type.

C>T

C>G

C>A

T>G

T>C

T>A

Signature Pattern of Somatic Mutations

A pie chart dividing somatic mutations in groups consistent with specific mechanisms.

C>T at [AG]CG

C>T at [CT]CG

C>T at NCC,CC[ACT],TC[ACT]

C>T at other sites

C>A

T>A and T>C

Rest

In the pie chart, a small fraction of multiple signature types can be observed in the sample. However, significant dominance of a single signature pattern often correlates to the respective tumor type. For example, 56.7% of the variants detected (sum of blue, green, and yellow) are an observed UV damage signature in this sample.

Note: Underlined bases represent the reference base being substituted (for example, CpG in the first bullet is same as to [ACGT]CG).