New Study Shows How Different Testing Methods Can Change Tumor Mutation Burden (TMB) Results

Tumor mutation burden, or TMB, is an important measure used to predict whether cancer patients will respond well to immunotherapy treatments. TMB measures how many genetic mutations are present in a tumor. If the TMB is high, the immune system might be better able to recognize and attack the cancer. Because of this, TMB is often used as a guide when choosing immune checkpoint inhibitor therapies for patients with solid tumors.

Traditionally, TMB has been measured using whole exome sequencing, which reads all the coding regions of the genome. However, this method is expensive and requires large amounts of DNA, making it hard to use in everyday clinical settings. To solve this, doctors now often use targeted next-generation sequencing, or NGS panels, which focus only on specific parts of the genome. These panels are cheaper, faster, and require less material. But there is still a big question: do different NGS methods produce different TMB results?

Comparing Two Ways to Measure TMB

A new study explored this by comparing two popular ways to perform NGS-based TMB testing. One method, called Tumor-Only (TO), analyzes just the tumor tissue. The other, called Tumor-Control (TC), analyzes both tumor tissue and normal white blood cells from the same patient to better filter out inherited mutations. Researchers tested these two approaches on 24 solid tumor samples collected from newly diagnosed cancer patients. They wanted to see whether different methods would give the same or different TMB results, and how this might affect treatment decisions.

High Accuracy, But Some Differences in Results

The study showed that both TO and TC methods were highly accurate and specific when tested on standard reference materials. Both methods captured a shared set of 298 genes that covered important parts of the cancer genome. However, when they tested real patient samples, the two methods did not always agree. While the overall consistency between the two methods was high, about 92 percent, there were still important differences in individual cases. For example, two patients had TMB results that crossed the critical treatment threshold of 10 mutations per megabase, depending on which method was used. This means that using one method versus the other could lead to different decisions about whether a patient qualifies for immunotherapy.

TC Method Often Shows Higher TMB Values

The study found that the TC method often produced higher TMB values than the TO method. In particular, in cancers like non-small cell lung cancer, using TC identified more mutations, possibly because it better filtered out inherited, non-cancerous mutations. In contrast, breast cancer cases, which can involve inherited mutations, sometimes showed lower TMB values with the TC method compared to TO. This difference is crucial because it can influence whether a patient is considered to have "high" or "low" TMB, and therefore whether they might benefit from immunotherapy.

Why These Differences Matter for Patients

Researchers pointed out that many factors can influence TMB results, including the quality of the sample, the design of the gene panel, the sequencing depth, and the data analysis pipelines. They suggested that when a TMB result is close to the 10 mutation-per-megabase cutoff, it is safer to combine TMB testing with other methods like PD-L1 testing, rather than relying on TMB alone.

This study also recommends that for rare cancers such as bladder cancer, head and neck cancer, or kidney cancer, where standard mutation profiles are less well-known, using a Tumor-Control approach might be more reliable. It helps reduce errors caused by confusing inherited mutations with cancer mutations.

Limitations and Future Research

The study had some limitations. The number of samples was small, and the findings are considered preliminary. Larger studies will be needed to fully understand how different testing methods impact clinical decisions. 

To learn more, see this!: Different NGS identification methods of somatic mutation sites in solid tumors impact TMB results | BMC Cancer | Full Text