Abstracts

Rationale: Finding the best genetic testing strategy for patients with epilepsy is complicated by the increasing array of testing options. In a retrospective study, we have compared the performance of two genetic test strategies, NextGen panels and Whole Exome Sequencing (WES), for patients with epilepsy and neurodevelopmental disorders (NDD) performed in a molecular diagnostic laboratory.Methods: One cohort of patients was tested using targeted gene panels that included next generation sequencing and microarray-based exon-level deletion/duplication testing (n=5776). The targeted panels encompassed up to 70 genes known to cause different genetic forms of epilepsy and related disorders with onset in infancy (53 genes, n=1620) or childhood (50 genes, n=837), progressive myoclonic epilepsy (17 genes, n=89), Rett/Angelman syndrome (11 genes, n=98) or a comprehensive panel (70 genes, n=2919). Another cohort of 529 patients with epilepsy and NDD was evaluated by WES either as proband only (WES-Proband, n=79), or proband-parent trio test (WES-Trio, n=450) in which the proband and parents are sequenced and analyzed simultaneously. A positive result was defined as one or two pathogenic or likely pathogenic variants in a single gene, depending on the mode of inheritance of the disorder.Results: The highest diagnostic yield for patients with epilepsy and NDD was achieved by the WES-Trio approach with a positive rate of 38% (171/450). WES-Proband testing yielded a strikingly lower positive rate of only 23% (18/79), which was comparable to that obtained for targeted multi-gene panel testing. For instance, 21% (340/1620) of probands tested with the infantile onset panel had a positive finding, while collectively the diagnostic yield for the various epilepsy panels was 16% (899/5776). Using WES-Trio, the majority of patients were found to have de novo mutations associated with AD or XL disorders (83% and 69%, respectively). This finding demonstrates the value of concurrent parental testing and explains the much higher yield of WES-Trio. Moreover, the number of genes associated with epilepsy-related disorders is rapidly expanding and often the mutation spectrum of these newly-emerging genes is unknown. The clinical significance of novel missense variants in one of these genes can be a challenge to characterize but a de novo observation can aid in proper variant classification. This concept was evident in just five new epilepsy-related genes, ALG13, GABRB2, KCNB1, NR2F1, and WDR45, where novel de novo missenses accounted for 9% (15/171) of the positive WES-Trio results in our cohort.Conclusions: Our data demonstrate that WES-Trio is a high-yield diagnostic test for patients with epilepsy and NDD due to the high rate of de novo variants in this cohort. When parents are not available for genetic testing, and thus the inheritance of novel variants is unknown, WES achieves only a marginally better yield than a targeted epilepsy panel. These data may assist clinicians in determining the most effective testing strategy for their patients with epilepsy and NDD.