Red Flags to Consider Additional Cancer Biomarker Testing

Summary: This resource provides a quick reference for the factors that may warrant further cancer biomarker testing.

By Clinical Education at JAX | January 2024

Cancer biomarker testing assesses variants in genes and proteins that influence cancer growth and/or response to targeted treatments. Results from this testing can provide useful information for treatment decision-making, but it can be challenging to determine if the testing was sufficient to assess the most important biomarkers. 

Indications to consider additional cancer biomarker testing to assess appropriateness of targeted treatments

Testing (all or part) failed due to insufficient sample. Reordering the original test with a different sample from the original biopsy is generally the best next step, if it is available.  

Tumor mutational burden (TMB) was not able to be assessed. TMB is calculated based on the number of mutations detected in the tumor cells. When TMB is part of a testing panel but not able to be performed or inconclusive, this may also indicate that there was insufficient tumor sample. Limited tests such as hotspot panels and some liquid biopsy panels cannot calculate TMB. 

Liquid biopsy testing is negative for actionable variants. There are a number of reasons liquid biopsy testing may not detect actionable variables that are present, including when the tumor is not shedding DNA into the blood. In this case, consider ordering solid tumor testing, if possible. Solid tumor testing may identify more variants because it directly assesses a sample from the tumor, assesses more biomarkers, and uses higher concentrations of tumor DNA for testing, providing higher sensitivity for some types of biomarkers.

Identifying a germline variant may influence treatment options. Tumor testing is not optimized to identify germline variants. While tumor testing can detect single nucleotide variants (SNVs), small insertions and deletions, and small copy number alterations, this type of testing generally cannot detect large deletions or duplications. Tumor testing may miss up to 10% of germline variants. 

Certain testing is recommended for specific variants or therapies. RNA analysis can detect fusions and other structural variants that might not be detected with DNA testing. Homologous recombination repair (HRD) assays and loss of heterozygosity (LOH) scores can inform likelihood of response to PARP inhibition therapy for some cancer types. 

Biomarkers identified do not align with tumor type. Many tumors have a typical biomarker profile, also called its genomic signature. If you do not see the typical biomarker profile, you may need to determine whether the tissue specimen had a sufficient tumor percentage, whether all the relevant variants were assessed, and, in some cases, whether the cancer type was misdiagnosed.

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