Discussion

In this article, we looked at the usage of genetic panels by an epileptologist in an adult epilepsy clinic over a 6-year period. In the last decades, genetic testing has become more and more affordable and clinically accessible to clinicians. Many options for genetic testing exist and vary in terms of sensitivity, specificity, turnaround time, and cost. ^{Reference Katsanis and Katsanis6} A 2019 meta-analytic cost-effectiveness study of genetic testing strategies in individuals with epilepsy of unknown etiology showed that, after adjusting for potential publication bias, genetic panels were the most cost-effective test, followed by whole exome sequencing. This same publication reported a pooled genetic panel positivity yield of 23%, though most of the patients included in the nine articles used to generate this estimate were children. ^{Reference Sanchez Fernandez, Loddenkemper, Gainza-Lein, Sheidley and Poduri15} A larger 2020 meta-analysis generated a pooled genetic testing positivity yield of 24% in epilepsy, though this yield represented a mix of both genetic panels and exome sequencing, and most included works still reported on pediatric patients. ^{Reference Stefanski, Calle-Lopez, Leu, Perez-Palma, Pestana-Knight and Lal16} In fact, most of the research on genetic testing in epilepsy has so far focused on pediatric samples; the yield of genetic panels in the adult setting has long remained understudied. Studies that do report adult yields often select their patients with strict criteria. For instance, two studies published in the last years reported a genetic panel positivity yield of 22% and of 23% in adults with epilepsy (most of whom also had comorbid ID), respectively. ^{Reference Borlot, de Almeida, Combe, Andrade, Filloux and Myers17,Reference Johannesen, Nikanorova and Marjanovic18} Nevertheless, McKnight et al. very recently published a landmark study evaluating 2,008 adults with epilepsy, with at least 21.8% of whom having comorbid ID, and reported a genetic panel diagnostic yield of 10.9%. ^{Reference McKnight, Bristow and Truty19} To date, this study is the largest to investigate genetic panels results in adults with epilepsy without strict inclusion criteria (such as presence of comorbid ID or of a family history of epilepsy), and its cohort is therefore the most representative of the average adult epilepsy clinic. In comparison, our genetic panel positivity yield was 11%, and our diagnostic yield was 4.3%, a diagnostic yield lower than the 10.9% reported by McKnight et al. This discrepancy can probably be explained through differences in the cohorts and the panels used. Notably, our cohort was smaller and had a lesser proportion of individuals with comorbid ID (10% versus at least 21.8%). In addition, almost none of the genetic panels ordered in this study evaluated more than 150 genes, whereas 56.5% of the panels in McKnight et al.’s study evaluated more than 150 genes. As for the gap between our panel positivity yield and our diagnostic yield, this was due to the fact that patients who had only one autosomal recessive PV or LPV were considered to have a positive panel result but not a confirmed genetic diagnosis.

Obtaining a genetic diagnosis can have a considerable impact on the individual with epilepsy by informing prognosis, limiting additional investigations, aiding in the identification of potential comorbidities, guiding pregnancy counseling, bringing a sense of closure to the families involved, and even informing treatment options. ^{Reference Jain, Andrade and Donner12,Reference Ottman, Hirose and Jain20} In our study, though only seven genetic diagnoses were emitted, five were clinically actionable, meaning that they had tangible consequences on the patient’s treatment. In SCARB2 AMRF, affected individuals should benefit from close renal function surveillance, and carbamazepine, oxcarbazepine, and lamotrigine should be avoided. ^{Reference Amrom, Andermann, Andermann, Adam, Ardinger, Pagon and tal21} In DEPDC5 epilepsy, focal cortical dysplasia should be searched for potential epilepsy surgery while a potential role for mTORC1 inhibitors is under investigation. ^{Reference Baulac, Weckhuysen, Adam, Ardinger and Pagon22,Reference Myers and Scheffer23} Clobazam and bromide have been suggested to be the most effective medications in the often refractory PCDH19 epilepsy. ^{Reference Samanta24} In SCN1A epilepsy, sodium channel blockers should be avoided, epilepsy surgery should probably not be pursued unless the phenotype is mild, and a potential use of cannabidiol, stiripentol, fenfluramine, and clemizole in the treatment of this condition is under investigation. ^{Reference Musto, Gardella and Moller25–Reference Strzelczyk and Schubert-Bast28} In MELAS syndrome, multidisciplinary care is crucial, and valproic acid as well as many other ASMs should be avoided due to concerns of mitochondrial toxicity. ^{Reference El-Hattab, Adesina, Jones and Scaglia29} Whereas in McKnight et al.’s study 55.5% of genetic diagnoses were clinically actionable, in our study, 71% of diagnoses were clinically actionable. This discrepancy is probably due to differences in sample sizes, as McKnight et al.’s study reported 218 genetic diagnoses, whereas we only reported seven. ^{Reference McKnight, Bristow and Truty19}

On a separate note, despite that many genetic diagnoses may indeed lead to changes in management, the real utility of genetic panels in the adult epilepsy setting is unsure, as confirmed diagnoses remain uncommon. Most panels, both in McKnight et al.’s study and in our study, yielded uncertain or negative results and consequently were not considered to have had any tangible, treatment-modifying impact. Still, the actual utility of genetic panels in the adult epilepsy setting is more nuanced, as even negative panels may theoretically have some impact on individuals by, for instance, conveying a sense of closure. Uncertain panel results, which were the most frequent results, could also hypothetically affect management on a case-by-case basis, though according to the ACMG guidelines, a VUS should not be used in clinical decision-making. ^{Reference Richards, Aziz and Bale30} Nevertheless, because they are predominantly found in sequencing-based genetic tests (49% in our study), VUS pose a significant clinical challenge. VUS that are identified from a targeted genetic panel (rather than from exploratory WES) can often be a good fit with a patient’s clinical presentation; in these cases, further in vitro and/or in vivo functional testing could help confirm, exclude, or at least guide clinicians toward a diagnosis. Functional characterization is usually performed in research laboratories using different in vitro models like biochemical assays and patient-derived cells or using in vivo animal models. Although the latter can be considered as the gold standard of functional characterization, in vivo models remain expensive and time-consuming. The development of a platform for the functional characterization of VUS has been shown to be very successful in the field of oncology (particularly for breast cancers associated with mutations in BRCA genes), leading to a significant improvement in the clinical management of cancer patients. ^{Reference Woods, Baskin and Golubeva31–Reference Federici and Soddu33} Interestingly, a recent work using nematodes described an in vivo platform for screening the pathogenicity of VUS in the STXBP1 gene, which is associated with epileptic syndromes. ^{Reference McCormick, Brock and Wood34} This illustrates how simple in vivo assays could quickly and accurately determine if a VUS is pathogenic or benign. Based on our data, it is worth noting that if only 10% of the VUS identified in our cohort could be functionally validated (a rather conservative estimate), this would have the potential of increasing by 70% the overall positivity yield of our genetic testing. Thus, the clinical advantages of genetic testing can be multiplied via the concomitant development of approaches that aim at functionally validating VUS. Further analysis of the utility of VUS was however considered beyond the scope of this study.

Currently, there are no up-to-date international guidelines on genetic testing in adults with epilepsy. A report on genetic testing in epilepsy from the ILAE Genetics Commission was last published in 2010. Due to how rapidly genetic research is taking place, instead of offering specific recommendations, the ILAE Genetics Commission offered a general framework for evaluating the utility of genetic testing in various situations. It was nonetheless established at that time that although many genes had been identified for epilepsy syndromes, few were very clinically useful to test for. Much has changed since 2010, notably in terms of the rising accessibility of genetic testing and the discovery of a plethora of new genes associated with epilepsy. ^{Reference Katsanis and Katsanis6,Reference Wang, Lin and Liu35} A set of guidelines on genetic testing in epilepsy was released in 2019 by a Genetic Testing Advisory Committee in Ontario, Canada. This publication represents to our knowledge the most recent guidelines on the topic in North America. Suggested indications for genetic testing in epilepsy were as follows: a) clinically consistent with a distinct epilepsy syndrome, b) poor prognosis or high likelihood of lethal outcome, c) refractory epilepsy with no apparent acquired cause, d) suggestive of inborn errors of metabolism, e) associated with malformations of cortical development, f) associated with paroxysmal neurological features (e.g., hemiplegic migraine), g) associated with syndromic features such as ID or dysmorphic features, and h) positive family history of epilepsy. ^{Reference Jain, Andrade and Donner12} According to these guidelines, a comprehensive gene panel can be ordered when a distinct epilepsy syndrome/group is not suspected (otherwise, a focused gene panel may be preferable). Furthermore, genetic testing should not proceed without the ability to ensure pre- and post-test genetic counseling. ^{Reference Jain, Andrade and Donner12} In our practice, we were probably more liberal in ordering panels than what was recommended by the Ontarian guidelines, since we proposed a panel to all adults with epilepsy of unknown etiology. Nevertheless, most of these individuals had refractory epilepsy, and several individuals had focal cortical dysplasia, comorbid ID, or a positive family history of epilepsy. About a quarter of our panels were ordered in the context of a presurgical evaluation, a scenario that was not discussed in the Ontarian guidelines. Surprisingly little is known about the value of genetic testing in the preoperative workup for epilepsy surgery. However, a 2018 systematic review of surgical outcomes in patients with genetic epilepsies showed that surgery was almost never effective in epilepsies caused by channelopathies and disorders of synaptic transmission (with perhaps the exception of SCN1B epilepsy) but was often effective in epilepsies caused by mTOR pathway mutations. ^{Reference Stevelink, Sanders and Tuinman36} The preoperative evaluation for epilepsy surgery is complex, and though genetic testing may eventually be shown to be a useful modality for determining surgical candidacy, it remains unknown how genetic findings should be interpreted in light of other preoperative findings. In our cohort, two genetic diagnoses were confirmed in individuals who are, as of this study’s redaction, still undergoing their presurgical evaluation. For the individual with DEPDC5 epilepsy, this genetic diagnosis could be used as an argument in favor of surgery, as epilepsies caused by mTOR pathway mutations seem to respond well to surgical interventions. ^{Reference Stevelink, Sanders and Tuinman36} For the individual with PCDH19 epilepsy, though a few successful surgeries have been reported for this condition, the evidence for or against surgery remains scarce. ^{Reference Samanta24} Otherwise, none of the patients featured in our cohort were determined to be inadequate surgical candidates on basis of genetic results alone, though our panel yield and sample size were clear limiting factors in this analysis. As for the ability to ensure timely pre- and post-test genetic counseling to patients, integrating a genetic counselor to the epilepsy clinic would probably be the optimal solution. More data is necessary to investigate the utility of genetic testing in the preoperative workup for epilepsy surgery and the practical impact of integrating a genetic counselor in the epilepsy clinic.

Proposing recommendations for genetic testing in epilepsy is difficult considering the speed at which the realm of genetics is advancing. In the upcoming years, it is predicted that the cost of genetic testing will continue to fall; eventually, whole exome sequencing and whole genome sequencing may become more cost-effective than genetic panels. More and more companies are commercializing genetic testing, many of which are already building business models around offering whole exome sequencing and whole genome sequencing directly to the patient. ^{Reference Wolff and Wolff37} New epilepsy genes are continually being discovered, and there is no evidence that this trend will soon end. The landscape of genetic testing is consequently in constant flux, and whatever recommendations exist today may be modified in the future. Nevertheless, perhaps precisely because genetic testing is advancing at such a rapid pace, there is a dire need for regularly updated recommendations to guide clinicians, including those in adult epilepsy clinics. To do so, more data need to be gathered on genetic testing in adults with epilepsy, and we hope our study may encourage future research on this understudied topic.

This study featured several limitations. Firstly, we had little control over which epilepsy panel was ordered; the choice was made by our institution’s genetic medicine service based on provincial reimbursement criteria, cost efficiency, the suspected genetic condition, estimated processing delays, etc. Providers also changed over time, and, as such, our study featured different types of genetic panels that evaluated varying sets of genes (although many genes were common amongst panels – see Supplementary Table S1). Secondly, panels were only ordered in individuals who consented. Thirdly, an unknown but probably growing number of patients who we inherited from pediatric neurologists over the years had already undergone genetic panels. Since a repeat panel would not have been necessary for those with a positive genetic finding, this could have had a negative impact on the diagnostic yield we report here. This may also explain why positive panel interpretations were associated to an older age at seizure onset, since patients who were younger at seizure onset and who had previously undergone a genetic panel with positive results were probably less represented in our cohort. Fourthly, tissue analyses to evaluate for somatic mutations were not carried out in this study, which could once more decrease our yields. Finally, none of the VUS were revaluated to see if they could be reclassified into PV or BV.