TMB Tumor Mutation Burden

Question

[abibioinformatics]

HI,

Can someone help me with the formulae or a tool to identify the Tumor Mutation Burden from a Whole Exome Sequence?

Thanks,

Abilesh

[Shicheng Guo]

The TMB is defined as the total number of nonsynonymous mutations per coding area of a tumor genome. Initially, it was determined using whole exome sequencing, but due to the high costs and long turnaround time of this method, targeted panel sequencing is currently being explored to measure TMB.

samtools flagstat can be used for total base calculation.

[igor]

It looks like that definition came from this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6249625/

As already mentioned in other answers here, it's frequently any mutations (not just nonsynonymous), so the definition is not very exact.

Answer 1

[Nicolas Rosewick]

You can start by this paper : https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-017-0424-2

In the method part :

TMB was defined as the number of somatic, coding, base substitution, and indel mutations per megabase of genome examined.

[dariober]

I think the "number of mutations per magabase" could be a misleading estimate of TMB. The deeper you sequence the more mutations per magabase you find since you detect more and more variants with low allele frequency. Maybe one should weight a variant by its frequency in order to compute TMB. (NB, I just glanced through the paper.)

[Jeremy Leipzig]

I think they sequence to ridiculously high median depth (500X) so they might have started to saturate by then?

That having been said it's a crude metric for 2018 to say the least. I'm surprised it even has a name.

Answer 2

[roy.granit]

Note that the human exome size is ~30Mb. So you can take the number of somatic mutations in a given tumor sample an divide that by 30 to obtain the Mut/Mb value (normally > 4-6 is considered 'hyper mutation')

Or maybe you can try this tool

[markus.riester]

Instead of using 30 as denominator, I would use tools like GATK CallableLoci to get the exact number of bases.

[poisonAlien]

I believe standard WXS capture sizes are around 50 mb. (eg; Agilent sure select)

[ivivek_ngs]

I would go with either the GATK CallableLoci or the capture size , that should be the one in use rather than something arbitrary.

[lincaijin1994]

Hi. How to get the capture size of WXS. I have some bed files but I dont know which of the below was used to get the capture size.

[design ID]_Regions.bed - This BED file contains a single track of the target regions of interest that SureDesign used to select the probes. You can use this track to see the exact regions that the program was attempting to cover when selecting the probes.

[design ID]_Covered.bed - This BED file contains a single track of the genomic regions that are covered by one or more probes in the design. The fourth column of the file contains annotation information. You can use this file for assessing coverage metrics.

Answer 3

[igor]

Just to add a little more confusion to this topic, there is another method implemented in Varlociraptor:

Varlociraptor enables an uncertainty aware computation of the tumor mutational burden (TMB). TMB is usually defined as the number of somatic, non-synonymous coding mutations per megabase of the measured coding genome. ... the TMB is calculated as expected value over the posterior probabilities for each variant to be somatic. Hence, the TMB estimate properly considers the uncertainty in the data. Moreover, as we show a TMB estimate for each minimum allele frequency, it becomes possible to reason over the clonal structure of the tumor, instead of considering only a single overall number. We expect this to increase the predictive power of the TMB.