Skip to content

Mutation Burden

Data

Measure of the relative counts of various types of mutations compared to those from a given cohort of samples. The "role" determines with comparator these values are calculated in reference to

{
    "mutationBurden": [
        {
            "snv": 4,
            "snvTruncating": 0,
            "indels": 0,
            "indelsFrameshift": 0,
            "sv": 92,
            "svExpressed": 40,
            "snvPercentile": 4,
            "indelPercentile": 10,
            "svPercentile": 60,
            "role": "primary"
        }
    ],
}
Field Type Example Description
role (required) string
indelPercentile number 1 Percentile of the count of indels in the current sample relative to a reference distribution
indels integer Absolute number of indels in the current sample
indelsFrameshift integer Absolute number of indels which result in a frameshift in the current sample
snv integer Absolute number of single nucleotide variants in the current sample
snvPercentile number Percentile of the count of single nucleotide variants in the current sample relative to a reference distribution
snvTruncating integer Absolute number of single nucleotide variants which are truncating in the current sample
sv integer Absolute number of structural variants in the current sample
svExpressed integer Absolute number of expressed (support in RNA) structural variants in the current sample
svPercentile number Percentile of the count of structural variants in the current sample relative to a reference distribution

Comparators and Roles

The role used by the mutation burden data is linked to the mutation burden images in the report that is created by the comparators input.

The images use the following key: mutationBurden\.(barplot|density|legend)_(sv|snv|indel)\.(primary|secondary|tertiary|quaternary)

which maps to the comparators

  • mutation burden (primary)
  • mutation burden (secondary)
  • mutation burden (tertiary)
  • mutation burden (quaternary)

Therefore for a complete mutation burden entry one might see the following

{
    "mutationBurden": [
        {
            "snv": 4,
            "snvTruncating": 0,
            "indels": 0,
            "indelsFrameshift": 0,
            "sv": 92,
            "svExpressed": 40,
            "snvPercentile": 4,
            "indelPercentile": 10,
            "svPercentile": 60,
            "role": "primary"
        }
    ],
    "comparators": [
        {
            "analysisRole": "mutation burden (primary)",
            "name": "TCGA COAD"
        }
    ],
    "images": [
        {
            "key": "mutationBurden.barplot_snv.primary",
            "path": "/path/to/image/file.png"
        },
        {
            "key": "mutationBurden.legend_snv.primary",
            "path": "/path/to/other/image/file.png"
        },
        {
            "key": "mutationBurden.density_snv.primary",
            "path": "/path/to/other-other/image/file.png"
        }
    ]
}

Note that the above only loaded images for the SNVs but similar images would be expected for SVs and indels.

Images

A number of images can optionally be included and will be displayed in the mutation burden section of the report. These are summary images which represent the count of a variant type in the current report relative to the counts of samples in the reference distribution (based on the comparators listed above). These images are generated by the user prior to creating the report.

full pattern: mutationBurden\.(barplot|density|legend)_(sv|snv|indel)\.(primary|secondary|tertiary|quaternary)

SNVs

key: mutationBurden\.density_snv\.(primary|secondary|tertiary|quaternary)

snv density plot

key: mutationBurden\.barplot_snv\.(primary|secondary|tertiary|quaternary)

snv bar plot

key: mutationBurden\.density_indel\.(primary|secondary|tertiary|quaternary)

Indels

indel density plot

key: mutationBurden\.barplot_indel\.(primary|secondary|tertiary|quaternary)

indel bar plot

Structural Variants

key: mutationBurden\.density_sv\.(primary|secondary|tertiary|quaternary)

sv density plot

SV-specific Comparator Overloading

There are special overload comparators for stuctural variants since they often have a different comparator data set from the SNV and Indels. Specifying an SV specific comparator will overload the more general comparator for the SV types

  • mutation burden SV (primary)
  • mutation burden SV (secondary)
  • mutation burden SV (tertiary)
  • mutation burden SV (quaternary)

This means that when the report client lists the comparator that corresponds to the images and data it will use the SV-specific value where it exists instead of the more general comparator name.

Back to top