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(Abst. 3.344), 2015

Using next generation genetic sequencing in children with treatment resistant epilepsy
Authors: Eric Segal, Helio Pedro, Evan Fertig, Jomard Sabri, Sloka Iyengar, Karen Valdez-Gonzalez, Sarah Parisotto, Felicia Gliksman
Content: Rationale: Diagnostic evaluation for medication refractory pediatric epilepsy includes clinical history, physical, EEG, imaging studies, and genetic testing. Genetic testing includes chromosomal microarray(CMA). If CMA is uninformative, next generation sequencing(NGS) can be utilized. Since NGS testing for pediatric refractory epilepsy is relatively new, we evaluated the diagnostic yield of NGS in non-acquired treatment resistant pediatric epilepsy with negative CMA.Methods: A retrospective chart review of treatment-resistant epilepsy patients between 0-18 years old was conducted. Treatment resistant was defined as poor response to at least two different anti-epileptic medications. Etiologies were categorized etiologies using the 2010 ILAE Epilepsy Etiology Classification criteria. Charts were reviewed for brain imaging studies, metabolic evaluation(plasma amino acids, urine organic acids, further studies based on clinical phenotype), CMA, single gene molecular analysis and NGS panels. The CMA were performed by various vendors depending on patient insurance or hospital contracts (Quest Diagnostics, San Juan Capistrano, CA; Labcorp, Research Triangle Park, NC; Mayo Medical Laboratories, Rochester, MN; Bioreference Laboratories, Elmwood Park, NJ). NGS was performed at either GeneDx (Gaithersburg, MD) or at Courtagen Life Sciences (Woburn, MA).Results: Thirty-nine patients (20 were male) with medication-refractory epilepsy underwent both next-generation sequencing and CMA testing. Mean age of onset of epilepsy was 2.94 ±4.91 years. Of the 35 subjects with documented developmental histories, 62.9%(n=22) exhibited development delay. Family histories were documented in 28 subjects, and 25%(n= 9) had a family history of epilepsy. Dysmorphic features were found in 6.25%(n=2) and 34.6%(n=9) had abnormal MRI findings. The most commonly identified epilepsy syndromes were generalized genetic epilepsies (10%, n=4), Dravet Syndrome (10%; n=4) and spasms (2%, n=2). All other syndromes were represented at the same 2.56% prevalence (n=1), such as Lennox-Gastaut Syndrome(LGS). Sixty-four percent(n=25) of subjects had an unknown etiology, 23%(n=9) had a presumed genetic etiology, and 12.8%(n=5) structural/metabolic. NGS identified abnormal sequence variants in 56.4% subjects(n=22), of which 22.7%(n=5) were judged to be clinically significant. Abnormal CMA was found in 28.2%(n=11) of subjects, none of which were found to be clinically significant to explain patient’s epilepsy. One patient was diagnosed with atypical Rett Syndrome(MECP2) mutation, and one patient had a mutation in a gene responsible for clustering of the NMDA receptor(DLG3).Conclusions: To our knowledge, this is the first study to explore the yield of NGS in children with treatment resistant epilepsy with uninformative CMA. The additional yield of NGS with uninformative CMA was 12.8%. Positive findings were primarily seen in those with Dravet Syndrome, all with SCN1A mutations. Given the small sample size, a larger prospective study would be helpful to determine the clinical yield of NGS. This study provides an impetus for more investigations.