Handling variants of uncertain significance (VUS) in clinical trials

When a person undergoes genetic testing, they often expect to find definitive answers about their genes. However, around 20% of genetic tests identify variants of uncertain significance (VUS). These enigmatic genetic mutations often leave researchers and patients with more questions than answers. Unlike harmful mutations that may cause cancers or benign ones that aren't linked to illness, researchers lack sufficient information about VUS to determine their association with any conditions. Here, we'll outline what VUS actually are, their significance in clinical trials, and some effective strategies to manage them.

Defining variants of uncertain significance

Human bodies contain trillions of cells, which regularly replicate their DNA as part of their natural renewal process. This creates opportunities for genetic errors to occur, resulting in variants or mutations. While most genetic variations are harmless polymorphisms, some mutations are linked to illnesses like cancers. VUS, on the other hand, neither clearly indicate harmful or unharmful traits. At the moment, these variations are classified on a spectrum, from "benign" to "likely pathogenic," depending on the gene. The prevalence of VUS can vary, with well-studied genes like those involved in Cystic Fibrosis development having fewer VUS. Others, especially those linked to rare diseases, may have more.

Encountering a VUS during genomic testing is not uncommon. For example, roughly 35% of individuals undergoing next-generation sequencing (NGS) for hereditary breast cancer-related genes encounter one or more of them. It's important to understand that VUS results can be confusing for patients and frustrating for researchers and healthcare providers, as they lack immediate actionable implications. Although most VUS will eventually be reclassified as likely pathogenic or benign, this process can be time-consuming, taking years to reach a definitive conclusion. Until then, clinical recommendations are based on personal and family medical histories. Researchers can also use databases like CLINVar, along with scientific literature, to gather information on VUS they find to ensure that information on different variations is constantly being updated.

Implications for clinical trials

In clinical trials, variants of uncertain significance have the potential to complicate patient stratification, treatment decisions, and overall trial outcomes, all of which depend on precise genetic data interpretation. When researchers are sequencing all or part of the genome in order to make assumptions about a certain condition, it can be difficult to learn from VUS. The lack of significant data can lead to their omission from medical reports, which excludes important genetic information from the study and leaves patients with uncertainties. Neglecting VUS can jeopardise the integrity of research efforts, with potential repercussions for patient care.

Strategies for addressing VUS

In clinical trials, the following strategies can be implemented to manage variants of uncertain significance:

• Collaboration with genetic experts: Engaging genetic counsellors and specialists can help participants gain a deeper understanding of the nature and potential implications of VUS and guide researchers in making informed decisions.
• Long-term monitoring: Recognising that VUS can evolve over time, longitudinal patient monitoring can be a crucial tool for researchers to accumulate data on the behaviour and clinical significance of these mutations.
• Functional studies: Functional studies can also help researchers to learn about the impact of VUS on genetic processes. Researchers can conduct these studies to gain a deeper understanding of the clinical relevance of VUS.

More than anything, diversity of genomic data is essential in addressing VUS effectively. At the moment, there is far more genetic information available for individuals of European ancestry, leading to a higher prevalence of VUS in other population groups. Expanding research studies to include more participants from non-European backgrounds is key to learning more about different VUS and helping researchers understand their relevance (or lack thereof) to various diseases. At the same time, it's vital that researchers take the time to look into VUS that come up, particularly if a number of their participants possess the same one. Sharing the information they learn is also critical; they can collate their findings with ClinVar or research the VUS on the ClinVar Miner website, which has information on over 670,000 variants.

Role of genetic counselling

Genetic counselling can be really effective for helping researchers and participants who undergo genetic testing understand the phenotypic implications of their genotype. VUS is one of the many things that they can provide support on. They communicate the significance and limitations of these uncertain variants with clarity and expertise, and by combining insights from family history and available variant information, genetic counsellors can also provide patients with a better understanding of the potential clinical significance of their VUS.

While most patients find solace in a VUS finding, some grapple with the ambiguity it brings. Genetic counsellors can offer guidance to individuals who may be particularly anxious, proposing options like more targeted genetic testing to mitigate the chances of encountering a VUS. Despite the inherent uncertainty, genetic counsellors reassure patients that the majority of variants of uncertain significance are harmless. Through supportive counselling, genetic counsellors can help empower patients and researchers to make informed decisions throughout the genetic testing and analysis processes.

Regulatory considerations

The American College of Medical Genetics and Genomics (ACMG) has created guidance for interpreting sequence variants, particularly for clinical genetic testing. With the rapid evolution of sequencing technology, the ACMG assembled a workgroup of clinical laboratory directors and clinicians to revise standards and guidelines for interpreting sequence variants. These recommendations provide a structured framework for classifying variants based on various types of evidence – this framework makes up the spectrum mentioned earlier: 

The ACMG also emphasises the importance of performing clinical molecular genetic testing in CLIA-approved laboratories and having results interpreted by qualified experts.

A recent legal case involving the misclassification of a genetic variant linked to epilepsy underscored the need for guidelines like these and those created by the UK Association of Clinical Genetic Science. While these guidelines can help prevent issues like this, they are not legally mandatory – but of course, it is always best to adhere to guidelines and be as transparent as possible with participants about the potential challenges that surround genetic testing, including VUS. Continuous monitoring and re-evaluation of VUS is also vital, as new information can emerge that alters variant classifications. Finally, laboratories must be willing to share their data with clinical databases like ClinVar to collectively accumulate evidence for informed decision-making in the future.

Conclusion

Variants of uncertain significance can pose a challenge in genetic research, especially within clinical trials. While VUS may cause uncertainty for both researchers and participants, taking a proactive approach through genetic counselling and rigorous ongoing analysis is essential to ensure that we learn as much as possible about these variations and help patients get the answers they need.