Comprehensive Tumor Profiling

The tumor mutational burden, also known as TMB, is the amount of gene mutations occurring in a patient’s tumor but not occurring in the patient’s healthy tissue. Thus, these mutations are coding, somatic mutations. The tumor mutational burden is defined as mutations per megabase (mut/Mb). It should not be confused with the variant allele frequency that only indicates the frequency of an allele. In contrast, the tumor mutational burden is the total amount of mutations per megabase in a sample. Depending on the tumor entity, the tumor mutational burden varies: Some tumors do not show high mutation rates, such as Ewing sarcoma or acute myeloid leukemia. Other cancer types, such as melanomas or lung squamous cell carcinomas, hold a high tumor mutational burden. Thus, the tumor can be classified as low, intermediate, or highly mutated using the tumor mutational burden. The tumor mutational burden is a promising predictive immunotherapeutic biomarker, for example, in immune checkpoint inhibitor therapy. Such an immunotherapy is especially effective in patients with a high tumor mutational burden. A higher number of tumor-specific mutations leads to a higher number of altered proteins, so-called neoantigens. These neoantigens are different from the healthy proteins, resulting in an increased difference of the tumor tissue compared to the healthy tissue.

Both tumor and healthy cells present parts of their protein content on their cell surface. These presented protein parts are also called peptides. Immune cells regularly check the peptides on the surfaces of the proteins. If the peptides are recognized as foreign, the immune system is activated. The tumor peptides, the neoantigens, are foreign to the immune system. Thus, a higher tumor mutational burden correlates with more mutations and more neoantigens that are recognized as foreign by the immune system. With a higher tumor mutational burden, the immune system is activated more easily.

Another immunotherapeutic biomarker is microsatellite instability, also known as MSI. The microsatellite instability indicates the number of mutations in satellite regions. These satellite regions are special DNA repeat sequences. The satellite regions of the DNA are the main component of the functional centromeres, forming the main structure of the heterochromatin. A disturbed DNA mismatch repair mechanisms (MMR) can lead to genetic hypermutability in the satellite regions, resulting in microsatellite instability. The microsatellite instability is classified as stable for a low MSI score or unstable for a high MSI score.

Cells with homologous recombination deficiency (HRD) are characterized by a dysfunctional homologous recombination (HR) pathway, which can play a crucial role in carcinogenesis and tumor progression. A tumor cell’s HRD status can have pivotal implications for treatment options, as HRD-positive tumors are sensitive to PARP inhibitors. Thus, assessing a tumor’s HR status can be crucial in the treatment decision.