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  • Writer's pictureJohn Lantos

The false-negative phenotype

We generally don't think of phenotypes as being "positive" or "negative." With genomics, that is changing. We can now imagine the concept of a "false-negative phenotype." Let me explain.

Genetic sequencing (GS) is now commonly used to diagnose rare conditions in patients with unusual clinical findings. There is debate about whether it should be used more widely with some experts proposing that every newborn should have their genome sequenced. Others disagree.

The primary arguments against sequencing focus on two things: cost and the ambiguity of many results. The two are related. The cost of sequencing technology is coming down so that cost is not as stiff a barrier as it once was. But the cost of interpretation of results is not coming down. In fact, if testing is used in the general population, interpretation may become more difficult rather than less. That is because we do not know the population prevalence of most genomic variants so it is difficult to know the sensitivity and specificity of tests. In other words, we don’t know whether or not a positive finding in an asymptomatic patient is a false positive. Here’s an example showing how that might be detrimental:

A previously healthy 10-year-old who collapsed while playing soccer. She was successfully resuscitated and found to have hypertrophic cardiomyopathy (HCM). Genetic testing revealed a gene variant that had been previously reported in several unrelated patients with HCM. (MYBPC3 NM_000256.3:c.1484G>A, p.Arg495Gln). This variant was thought to predict HCM.

The girl’s parents and siblings were advised to have clinical evaluations and genetic testing. Her 16-year-old brother, a high school basketball player, was found to carry the same genetic variant. A comprehensive cardiology evaluation revealed no sign of HCM or other cardiac pathology. The cardiologists then had a dilemma. What follow-up care is appropriate for the brother? Does he need regular screening for HCM? If so, how often and for how long? Is there a time when he will no longer need screening? There are no evidence-based answers to these questions.

We know that patients who have a clinical diagnosis of HCM are at high risk for multiple problems throughout their lifetimes and need careful clinical monitoring. But we don’t whether the same is true for people who have a pathogenic variant but have none of the diagnostic findings of the disease.

The case illustrates some of the complexities of interpreting genome-sequencing results. Professional societies recommend a careful and complex process to interpret variants. Richards et al write, “Our understanding of the clinical significance of any given sequence variant falls along a gradient, ranging from those in which the variant is almost certainly pathogenic for a disorder to those that are almost certainly benign.”

In order to classify genetic variants, interpreters must consider population data on the frequency of the allele in question, computational and predictive data (“in silico models”) that suggest a deleterious effect from the variant, functional studies, family history, and the patient’s own history and physical exam. It is a laborious process that can be considered as much an art as a science. The art requires value judgments about the risks of “calling” a variant as pathogenic. There are risks to both false positives and false negatives.

ften, the classification of a genetic variant as pathogenic or benign changes over time as a result of new information. For example, a variant in the TCAP3 gene (TCAP NM_003673.3: c.37_39delGAG, p.Glu13del ) had been reported to be associated with HCM. However, further research found that this variant was also common in asymptomatic control populations and it was reclassified from “likely pathogenic” to “likely benign.”

With our current imperfect state of knowledge, it may be hard to know whether a finding of a pathogenic variant in an asymptomatic patient ought to be considered a false-positive test or whether, instead, such a test result should be considered a warning flag indicating a higher than average probability that the person will develop disease in the future. Some have referred to people in this situation as “patients-in-waiting” who “experience prolonged liminality between a state of normal health and pathology.”

I’d like to suggest, in a manner only partially tongue-in-cheek, that such a situation could also be characterized as a “false-negative phenotype.” With either label, the implications are that the patient will be treated as if they were at risk of developing disease in the future. This may lead to increased anxiety, extra diagnostic testing, and, in some cases, even treatment for disease that may or may not ever occur.

Some of these interpretive ambiguities might disappear as we learn more about genomic variation. That will only happen, however, if the resources are available to do the long-term follow-up studies that quantify differences in expressivity, penetrance, and epigenetic modification. Given the ubiquity of genomic variation, however, it is unlikely that such long-term follow-up studies will be done for even a small fraction of known (or yet to be discovered) genomic variants.

Thus, it seems likely that, for most genomic variations, interpretive uncertainties will increase over time. We will see more and more cases in which a seemingly pathologic genomic variant occurs in an asymptomatic person. In such situations, we will have to decide whether to call the test a false positive or the phenotype a false negative. The decision will have implications for our assessment of the risks, costs, and benefits of genomic testing. If the test results are seen as false positives, then genomic sequencing will seem far less useful than if they are seen and reported as accurate molecular diagnoses with false negative phenotypes.

The proper response to a false negative test is to re-assure patients and families that they are not at risk. The proper response to a false negative phenotype is to tell people that they are at risk, and, depending on the situation, recommend some forms of enhanced surveillance. Such enhanced surveillance will be expensive, worrisome, and potentially dangerous. The phenomenon of the false-negative phenotype illustrates some of the perils of genomic sequencing.

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