The Tumor Mutational Burden (TMB) or tumor mutation load is considered an effective and clinically verifiable biomarker in multiple cancer types. Unfortunately, because there are many different ways employed by different clinics and labs to measure TMB, and there is no clear standard, VarSome Clinical currently does not offer a calculation of TMB in somatic samples as it would be impossible to provide a TMB metric that could satisfy all of our customers. However, VarSome Clinical offers the necessary tools to get the approximate number of germline and somatic variants and so calculate the TMB using your own definition.
First, you need to know the total number of variants found in your sample. This metric can be found, for example, in the Analyses menu, under the column Variants.
If you are starting your somatic analysis from FASTQ, it is important to bear in mind that VarSome Clinical reports all variants found in the sample no matter their quality. Therefore, as a first step to calculate the TMB, we highly recommend you to get the total number of variants found with a Call status of PASS, meaning that you will be counting only those variants passing the quality filters. To do this, please go to "Filters" > "Create" > "Call status", and create a filter to keep only the variants that have passed the quality filters.
Once the filter is applied to your sample, you will get the total number of variants found with a PASS call status:
Then, you can filter by allelic balance as an approach to differentiate between germline and somatic variants in your sample. This can be assessed through the "Call Status" filter too. This filter contains the allelic balance field where you can include a specific range of allelic balance to retain and count the number of potential germline variants in your somatic sample.
To do this, please, create a new Call Status filter, selecting the variants with a PASS call status and the allelic balance range for germline variants.
Note: the allelic balance range shown in the screenshot above might not be appropriate in your case. Please provide your own allelic balance range.
Finally, once you have obtained the number of germline variants, you can use this number and the total number of variants previously obtained to calculate the number of somatic variants found in your sample. These metrics can be used to calculate the TMB using your own definition.